text:
Samsung CLP 775ND Driver Download
Samsung CLP 775ND Driver Download-Samsung CLP 775ND is a machine with shading printer has energy to save for a boisterous work bunch. The Samsung printer CLP 775ND is all situated for utilization high volume. Traditional capacities comprising of programmed duplexing, include a 500 sheet essential info plate and offers 100 sheet multipurpose plate, effectively open through a 350 sheet yield and a front board plate.
This phenomenal contemporary printer gadget for working environment gadgets and truly easy to work and use, notwithstanding for first time clients. Has 4 line 16 character, foundation LCD control board and compass route framework to supply thoroughly free help and direction issues at work. Also, you will absolutely esteem the serene operation of this printer is ideal for a boisterous work environment.
The Samsung CLP 775ND Driver Download can interface by USB or ethernet. Setup is basic on both Macs and pcs. The printer's driver and control board are without hardly lifting a finger added to, the recent including a four-line monochrome LCD and an uncomplicated assortment of route and alternative catches.
Pace is an abundance and an extraordinary motivation to utilize the Samsung CLP-775ND. Outfitted and included with a 600 MHz 2 center processor and 384 MB of memory (expandable to 896 MB), it printed archive pages at a quick rate of 18.1 ppm (pages every moment) on the portable workstation or PC, this offers a decent 3 to 4 ppm much quicker than the normal rate distributed by different printers in its class.
|Samsung CLP 775ND
Samsung CLP 775ND Driver Download
System Requirements And Compability:
- Windows 8, 8.1
- Windows 7
- Windows Vista
- Windows XP
- Mac OS
- Linkx
Procedures For Installing The Device:
Please open device drivers that you have downloaded:
- In the device driver you make sure the device you are trying to install is not already registered from previous attempts to install. If the device is discovered by highlight it and remove it from the Device Manager to prevent conflicts during installation.
- After Device Manager looks Ok/Yes reboot computer.
- As new hardware installation wizard computers should appear if Windows detects the new hardware to use this wizard You must be able to demonstrate the Windows folder that contains your driver CD, floppy disk, or folder that contains the file that you downloaded.
Give you the printer driver and scanner for Samsung CLP 775ND. Please click the download link to download the driver you want. In addition, you can check the compatibility of the driver that will be in harmony with your OS.
Samsung CLP 775ND Driver Download
For Windows 32 bit
OS Description
Windows 8.1, Windows 8
Windows 7, Windows XP, Windows Vista
Directions And Note:
- Begin your organizer of connection Acquire Website
- Simply click twice 2x on the driver record Acquire
- Click Next, next furthermore joins the following sign


text:
"You're only 19 or so," Lam's judge said to him at the hearing. "I'm sure it's difficult to conceive or imagine that many years in custody. But I think that leads some people to go to trial and after they get a sentence with life, then think, 'what did I do? I'm here for the rest of my life, most likely.' There's not a huge difference, I don't see, between 20 years and 25 years, when it means you get out. You can have a life. And quite frankly, for a fleeting moment, I thought, 'Oh you want a trial? You want to spend the rest of your life in prison?'''
'He COULD Have Done It, But I Don't Think He Did'
By Debora Gordon Lam offered me contact information for his attorney, David Kelvin, who agreed to speak with me in last October. I felt limited in my knowledge of the criminal justice system, even though I'd taught American government. I'd had no first-hand experience with the law beyond the very occasional moving violation, and a …Read more…
Snail Mail Part III: Is Forgiveness for the Victim or the Forgiven?
"On the topic of forgiveness. I have always felt we all deserve a second chance.Would I be able to forgive the person who rape and killed my daughter? I can't say for sure because I would know. But I've forgiven the people or person who shot me. If you think about it, I put myself in that situation and that was part of the gang banging life style. So why should I keep that hatred for them when I am moving on in life."
Snail Mail Part II: A Mellow or a Violent Guy?
"Being locked (up) is not a good thing but for some like me, we need a scary situation to set us straight. If only there were a machine who can tell if a person has truly learn and have change for the better. I would be release real soon. Being in here has stop a lot of my plans and goals but I look at is this is time to build a better me for the future. It is what it is."
The Lam Vo You(r'e) Looking For
Dear Ms. Gordon, Unfortunately, I am the Lam Vo your (sic) looking for.
Fall 2007: Lam Writes About His Crime
The essay described an evening in May or June of that year, in which he was riding around Oakland in a car with some other teenage boys he claimed not to know very well. At some point during long the way, they gave Lam a gun, and the boys together attempted to rob a corner store.
'Get a Straight Job' & Stop Gang Banging!
I responded to the email Lam sent from Juvenile Hall within an hour of receiving it. That was more than 5 years ago, so I am trying to look back and remember what I was feeling and thinking about him back then. I was very moved that he was reaching out to me, the clichéd …Read more…
'Lam Jail, Lam Jail'
Towards the end of the very last week, his mother came to see me unexpectedly. No one on our staff knew Vietnamese, and she spoke virtually no English. All she could really say was "Lam jail, Lam jail."

subset: commoncrawl


text:
- close
- Who we are
- What we do
- Media
- Get involved
- Contact us
Media freedom is a pillar of our democracy, but it is increasingly under threat in our continent. The infamous example of Italy, in which media power and political power have coincided for twenty years, has become a successful model for others to follow. Viktor Orban in Hungary has made media manipulation and control a cornerstone of his semi-authoritarian politics. In advanced democracies such as France and the UK, media freedom is in danger, through the murky appointment of the President of France Télévisions to the Murdoch control of an increasing share of British media. In newer democracies, such as Bulgaria and Romania, freedom of expression is under threat by an increasing concentration of media power in the hands of a few politically-connected moguls.


text:
30 November 2011
127th Annual Upper Class Twit of the Year
Contestant No. 1 - Vivian Smith-Smythe-Smith, He's in the Grenadier Guards but can count up to four.
Contestant No. 2 - Simon-Zinc-Trumpet-Harris, He's an Old Etonian and married to a very attractive table lamp.
Contestant No. 3 - Nigel Incubator Jones, His best friend is a tree and in his spare time he's a stock broker.
Contestant No. 4 - Gervaise Brook-Hamster, He's in the wine trade and his father uses him as a waste paper basket.
Contestant No. 5 - Oliver St John-Mollusc, Another Old Etonian, his father was a cabinet minister and his mother won the Derby.
18 comments:
- Vintage Whistles - Vintage Menwear said...
They just dont make them like this anymore... brilliant! : )
- 30 November, 2011 07:17
- tintin said...
Vintage- check out the Wiki entry for Old Etonian for some amazing double-barrel names. You guys carry any Trilbys?
- 30 November, 2011 07:51
Actually, they do (kind of) make them like that still. Check out the Hipster Olympics on Youtube youtube.com/watch?v=kAO4EVMlpwM
- 30 November, 2011 11:40
- tintin said...
Oyster Guy - I saw that video, like so long ago..
- 30 November, 2011 11:52
Of course, Sargent! Just looking out for the less hip Specialists, Sargent.
- 30 November, 2011 12:12
- tintin said...
Oyster Guy- You must've been an officer. Sergeant T.
PS I wore Filson in the womb.
- 30 November, 2011 12:26
- Main Line Sportsman said...
The names of the Twits was probably the funniest thing in the sketch....Thanks for the mention...I hope you read my deer camp piece...
- 30 November, 2011 13:39
- Yankee-Whisky-Papa said...
A friend of mine did one of these (one in London, I think?). Here is a part of his email to me:
"I showed some pictures to my father and he said that the last time he saw arm-bands being worn over tweed jackets was when people were also hurrying out of the cities on bicycle, but it was during the early 1940's".
Trump card.
MLS is right.. the names are the best. My vote is for "Gervaise Brook-Hamster".
- 30 November, 2011 14:10
- tintin said...
Main Line- Zinc-Trumpet-Harris sounds like a new line of toiletries from London.
I seen the deer camp. It's a keeper. Every one, go on over to Main Line's blog and see what it's like to be in a deer camp. But why didn't you tell some of the dirty stories?
- 30 November, 2011 14:14
I still can't spell...I blame wrestling with four languages : British English,Canadian French, American English, and Canadian English.
- 30 November, 2011 14:18
- tintin said...
YWP- Nicely done, Dad.
This is my problem w/ everything RL touches. A great apparel aesthetic is turned into douche-bag-central by overkill.
It's like covering an 18th century wing chair in alligator. Whoops, they've already done that.
If things continue to go the way they're going...I don't doubt for a nano-second there will be a R.L. Douche Bag Store on Wooster Street in 2021.
Oyster Guy - I know the problem. I speak British, Canadian, American and Carolinian. "Fixin' to sort out my day, eh?"
- 30 November, 2011 14:28
As for RL, I had a thought the other day about how they could increase sales and improve the bottom line. RL should offer the same items WITHOUT the logo and labels AND charge $5 MORE. Whadayathink?
- 30 November, 2011 15:19
- tintin said...
Oyster Guy- I'd pay $10 if they removed it while I waited.
- 30 November, 2011 15:24
- 30 November, 2011 17:30
- tintin said...
Jeff P - It's not Cafe Flesh but it'll do.
- 30 November, 2011 17:54
Oyster Guy - BMW de-badged cars (factory order only) cost a little more than the badged ones. I think.
- 30 November, 2011 23:25
- Scale Worm said...
I ran myself over on my way to work today, I do not see the humour, at all, in this...
- 01 December, 2011 00:07
- gentleman mac said...
Several years ago, I scored a 100% cashmere RL Polo polo-style sweater at TJ Max for $20. The kicker: no logo.
- 01 December, 2011 07:50


text:
No words can do justice to seeing the Macy's Thanksgiving Day Parade live and in person, so check out my Flickr photos. The crowds were awesome and the balloons, celebrities and floats exquisite. I watched from the end of my street, right where the parade began. Then it was off to eat Indian food and hang out with my amazing friend Lisa, her smart & handsome husband and charming bro-in-law. Couldn't ask for better conversation, camaraderie and food for my first NYC Thanksgiving. Am I feeling an abundance of gratitude? You betcha!
Friday, November 23, 2007
NYC Thanksgiving Part III: Macy's Parade 2007!!!
Posted by Mary Hilton at 1:02 PM 1 comments Links to this post
Labels: Unique New York
NYC Thanksgiving Part II: Macy's Balloon Inflation
Not but a block from my apartment, the balloons for the Macy's Thanksgiving Day Parade are blown up to their full glory. The crowds are unbelievable, with visitors from all over the world stopping by the night before Thanksgiving to gaze upon the gigantic, wondrous cartoon characters and holiday symbols. It is a remarkable event that I wish everyone could see, so check out my Flickr photos on the festivities. My evening was topped off to perfection with a dinner at Isabella's with 19 of my extraordinary neighbors, as hosted by Joe B., the charming and generous 'mayor of the block' and president of Landmark 76. What a fantastic and magical night it was!
Posted by Mary Hilton at 10:58 AM 2 comments Links to this post
Labels: Unique New York
Tuesday, November 20, 2007
New York City Thanksgiving - Part I
Thanksgiving in New York City is celebratory beyond compare. So to start the holiday off right, today I had the honor of helping my friend Susie and other incredible volunteers assemble completely stocked turkey dinners for families in need. Held at NYC's Chelsea Piers and starting at a challenging 4 o'clock in the morning (yes, they served a boatload of coffee!), the effort was on behalf of of the non-profit FeedingNYC. The charity was founded in 2001 by LivePerson CEO Robert LoCascio, who has seen the meal count rise from 40 dinners to the whopping 1,500 assembled today. Volunteering was a blast, but you can also donate moo-lah if you don't live here - yet! Oh, and shout out to fellow volunteer and blogger of NYC Stories!
Posted by Mary Hilton at 10:16 PM 1 comments Links to this post
Labels: Feel Good, Unique New York
Thursday, November 15, 2007
Private Screening of Close Up: Photographers at Work
Photography is a most intimate visual form of storytelling, and at its best its narrator remains humbly anonymous while simultaneously captivating the viewer. So it was a rare honor to glimpse the genius behind the image at the private screening Thursday of Close Up: Photographers at Work. This extraordinary new documentary by director Rebecca Dreyfus is stunning in its balance, illuminating both art and craft equally through a series of probing, revelatory interviews with those that have lived their lives behind the lens.
Produced for Ovation TV by Maysles Films, the hour-long special will debut at 8pm on Nov. 18, kicking off a week of photo-focused programming on the acclaimed multi-platform arts and culture channel. Artistic greats Gregory Crewdson, Timothy Greenfield-Sanders, Albert Maysles, Andrew Moore and Sylvia Plachy reveal how the sometimes arduous process of picture taking can translate our ideals into a form of fervid visual communication both immediate and sublime.
Bonus: Attended by many of the interviewees, including portrait genius Greenfield-Sanders and the soulful talent Plachy, the screening was a celebration of art meets artful TV. Legendary documentarian Maysles and his daughters Rebekah and Sarah, famed gallery owner Steven Kasher, artist/musician and frequent Greenfield-Sanders subject Lou Reed and Ovation TV programming head Kris Slava also contributed to the night's considerable cultural wow-factor. Check out Ovation's photo-focused programming beginning Sunday, including specials on Cindy Sherman and David LaChappelle, as well as series The Genius of Photography. Also note Ovation TV's of-the-moment contest collaboration with Fotolog, the world's largest photoblogging community.
Posted by Mary Hilton at 10:58 PM 0 comments Links to this post
Sunday, November 11, 2007
Hamlet Gets The Shock Treatment
In The Wooster Group's trippy, tripped up production of Hamlet, currently playing at The Public, Shakespeare's greatest play is deconstructed into bits of visceral video lunacy. The result is compelling, confusing and as haunting as a freshly murdered monarch. Ultimately delivering a boldly visual, headbanging feast of experimental theater, the sheer bravery of this production is an informed achievement that occasionally veers into brilliance. While it may not completely satisfy, this disconcerting and challenging work acts as a thorn in the side of the NYC theater-goers psyche.
Juxtaposed against a backdrop of Richard Burton's 1964 filmed portrayal of the tragic prince, with characters digitally erased and technical glitches enhanced, the agile cast mirrors the screen in an odd start-and-stop choreography that is at once beautiful and as grating as nails on a chalkboard. But then, that is the point. Through the lens of legendary director Elizabeth LeCompte, in this world that Hamlet inhabits - where the revenge-obsessed dead claw the earth and mothers bed their bloodstained brothers-in-law - it is perfectly normal to have the tape of reality rewound, sliced and sped up to warp speed. Unfortunately, it also means that the humanness of Hamlet's pain, like his terror at mistakenly killing his beloved Ophelia's father and her resulting madness, is at times muddied and hidden beneath layers of directorial constraint.
Yet in the hands of this cast, particularly the beyond-brilliant Scott Shepherd as the prince and the double duty Gertrude/Ophelia turn by Kate Valk, the majority of Shakespeare's poetry is delivered with a grace that paradoxically grabs the throat. Ultimately, in the hands of the Wooster masters, this ghost in the machine production illuminates Shakespeare's musings on this mortal coil with a daring that shouldn't be missed. Extended through Dec. 2 at the Public Theater at 425 Lafayette St., just below Astor Place.
Posted by Mary Hilton at 7:12 PM 1 comments Links to this post
Labels: Theater
Monday, November 5, 2007
'Turn of the Screw' an Unsettling, Creepy Terror
Posted by Mary Hilton at 3:13 PM 1 comments Links to this post
Labels: Theater
Sunday, November 4, 2007
New York City Marathon: Paula Radcliffe Wins!
The excitement generated by the ING New York City Marathon, the premier event of the New York Road Runners, is beyond compare. Since I wasn't running the race today I got up early for a 50-minute run in Central Park, and ran across the finish line near Tavern on the Green pretending I was at mile 26.2.
Posted by Mary Hilton at 11:11 PM 1 comments Links to this post
Labels: Fit n Fun, Unique New York
Friday, November 2, 2007
Societal Decay Disarms in The Chaos Theories
In physics, chaos theory explains the underlying order and elegance in apparently random data, illuminating that the slightest act can ripple out wildly to global impact. In the recent production of Alexander Dinelaris' charged tragi-comedy The Chaos Theories, this idea is not only relevant in weather patterns and cosmic black holes, but also in the way the human spirit grapples with the desire for deep rooted connection in an age of post-9/11 fear.
In the hands of playwright-in-hyperdrive Dinelaris, who directed with Stewart M. Schulman, this play treats and teases with layer upon lush layer of vivid and relentless dialogue, masterfully handled by a team of eight actors playing 21 diverse characters. Each archetypal New Yorker is caught in their own personal chaos: A driven, trash-talking stockbroker pummels her client to humorous effect. An dotty, heartfelt homeless woman lives in remember-when land. A father berates his daughters beau, a senator's wife verbally castrates a smarmy lobbyist, a charming waiter serves acidic sarcasm on a platter. But if everyone would just put their cellphones and career drives aside for a split second, they'd discover they are all connected in the most human of ways - through loneliness, love, fear and loss.
To sometimes hysterical, often shocking effect, Dinelaris shows that underneath today's techno chatter there is a humanity striving to be released. In a world where the random is revered, the message of The Chaos Theories comes through crystal clear. Playing until Nov. 17 at the McGinn/Cazale Theater, 2162 Broadway (near W. 76th St.)
Bonus: There was an inspiring audience talkback with playwright Alexander Dinelaris after the performance, where he enthusiastically and refreshingly supported fellow writers and artists. Dinelaris' play Still Life is slated for Broadway in early 2008, and he is working on writing the screenplay for Alejandro González Iñárritu's (Babel, 21 Grams) next film.
Double Bonus: The courage of Dinelaris to have a play with a large cast, and the talented actors who fulfilled his vision. Check out Richard Bekins, Max Darwin, Alison Fraser, Todd Gearhart, Ted Koch, Amanda Mantovani, Darcie Siciliano and Maryann Towne in anything they do!
Posted by Mary Hilton at 10:32 AM 0 comments Links to this post
Labels: Theater
Thursday, November 1, 2007
Halloween NYC Style
There is no place better than New York City-the theatrical capital of the universe-to truly rock out Halloween. Just walking down the street, you see tons of ghoulish characters decked out in costumes better than those seen on B'way. Check out some of the best hauntings and gore-geous goings on, and mark your calendar for next year:
- ZombieCon: Dress up like Zombies and then go shopping!
- Tompkins Square Park Halloween Dog Parade: So cute! Look for the iPhone doggie!
- Greenwich Village Halloween Parade: Legendary, creepily creative, brazen & bold!
- The Blood Brothers Present: Pulp: Viciously fun, blood splattering theatrics!
- Blood Manor Haunted House: Has a reputation of seriously creeping you out!
- The Night of Nosferatu: The Rabbit Hole Ensemble adapts the legend of the eerie bloodsucker!
- Halloween Extravaganza and Procession of Ghouls at St John the Divine: Weird and spirited!
- Spine-Tingling & True: Ghost Stories of the Merchant's House Museum: Beware the real ghosts that prowl this landmark!
Posted by Mary Hilton at 3:34 PM 0 comments Links to this post
Labels: Unique New York


text:
- Research article
- Open Access
The large soybean (Glycine max) WRKY TF family expanded by segmental duplication events and subsequent divergent selection among subgroups
© Yin et al.; licensee BioMed Central Ltd. 2013
- Received: 25 June 2013
- Accepted: 1 October 2013
- Published: 3 October 2013
WRKY genes encode one of the most abundant groups of transcription factors in higher plants, and its members regulate important biological process such as growth, development, and responses to biotic and abiotic stresses. Although the soybean genome sequence has been published, functional studies on soybean genes still lag behind those of other species.
We identified a total of 133 WRKY members in the soybean genome. According to structural features of their encoded proteins and to the phylogenetic tree, the soybean WRKY family could be classified into three groups (groups I, II, and III). A majority of WRKY genes (76.7%; 102 of 133) were segmentally duplicated and 13.5% (18 of 133) of the genes were tandemly duplicated. This pattern was not apparent in Arabidopsis or rice. The transcriptome atlas revealed notable differential expression in either transcript abundance or in expression patterns under normal growth conditions, which indicated wide functional divergence in this family. Furthermore, some critical amino acids were detected using DIVERGE v2.0 in specific comparisons, suggesting that these sites have contributed to functional divergence among groups or subgroups. In addition, site model and branch-site model analyses of positive Darwinian selection (PDS) showed that different selection regimes could have affected the evolution of these groups. Sites with high probabilities of having been under PDS were found in groups I, II c, II e, and III. Together, these results contribute to a detailed understanding of the molecular evolution of the WRKY gene family in soybean.
In this work, all the WRKY genes, which were generated mainly through segmental duplication, were identified in the soybean genome. Moreover, differential expression and functional divergence of the duplicated WRKY genes were two major features of this family throughout their evolutionary history. Positive selection analysis revealed that the different groups have different evolutionary rates. Together, these results contribute to a detailed understanding of the molecular evolution of the WRKY gene family in soybean.
- Segmental Duplication
- WRKY Gene
- WRKY Domain
- WRKY Protein
- WRKY Family
The WRKY family is one of the largest transcription factor families in higher plants, but is absent in animals, extending throughout the entire green lineage. Recently, several WRKY genes were identified from non-plant eukaryotes, including Dictyostelium discoideum, a slime mold closely related to the animal and fungi lineages, and the green alga Chlamydomonas reinhardtii, an early branch of plants. This suggests that WRKY genes may have had an early origin in lower eukaryotes, which have since greatly expanded in plant species [1]. Since the first WRKY protein, SPF1, was cloned from sweet potato [2], more and more WRKY genes have been experimentally identified in various plant species [3–19]. Each WRKY protein in this family contains at least one WRKY domain of approximately 60 amino acids with the conserved amino acid sequence WRKYGQK at its N-terminus and a novel zinc finger motif, C2H2 (C–X4–5–C–X22–23–H–X–H) or C2HC (C–X7–C–X23–H–X–C), at the C-terminal region [20]. The WRKYGQK amino acid sequence forms a β-strand that facilitates binding to the promoters of target genes. Usually, the binding site is the W box, which is an element commonly found in the promoters of many stress-related plant genes [21]. WRKY proteins can be categorized into three groups based on their number of WRKY domains and the pattern of their zinc finger motif [22]. The first group contains two WRKY domains (N-terminal and C-terminal), including a C2H2 motif, whereas the other two groups have only one domain. Group III has a distinct zinc finger motif, C2HC rather than the C2H2 found in other groups. Group II proteins can be further subdivided into groups II a, II b, II c, II d, and II e based on the amino acid motifs contained outside the WRKY domain.
As transcription factors, plant WRKY proteins have been shown to be involved in responses to biotic and abiotic stresses, and in developmental processes [23]. It has been well documented that WRKY proteins play an important role in plant defense against biotic stresses, such as bacterial, fungal, and viral pathogens [24–27]. They are also key components in developmental processes, including embryogenesis [28], senescence [29], dormancy [30], trichome development [31], seed development [32], and some signal transduction processes mediated by plant hormones such as gibberellic acid [33], abscisic acid (ABA) [34], or salicylic acid [35]. Meanwhile, increasing evidence has revealed that WRKY proteins are involved in responses to various abiotic stresses [36]. In Arabidopsis, results of a microarray study demonstrated that the expressions of some WRKY transcripts are regulated in response to abiotic stresses, including salinity, drought, and cold [37–39]. In rice, under various abiotic and phytohormone treatments, the expression of WRKY genes showed significant differences [40]. In Poncirus trifoliate, a WRKY gene, PtrWRKY2, showed differential responses to cold and drought stresses [41], while in soybean, at least nine WRKY genes were found to be differentially expressed under abiotic stress [42]. Collectively, this evidence indicates that WRKY genes play important roles in various physiological processes in plants.
Soybean is one of the most important economic crops in the world. Genome and transcriptome sequencing of the palaeopolyploid soybean have been completed [43, 44]. In the present study, we searched this genome sequence to identify WRKY proteins, and compared the structure of the encoded proteins with those of their putative homologous WRKY genes in Arabidopsis. In order to investigate tandem duplication events, soybean chromosome sequence information was applied to map WRKY transcripts to their corresponding genetic loci on chromosomes. A phylogenetic tree was constructed to evaluate evolutionary relationships among WRKY genes in the two plant species. In addition, we analyzed the transcriptome atlas of WRKY genes in different tissues under normal conditions, and found notable differential expression between groups, which indicated broad functional divergence in this family. Positive selection analysis revealed that evolutionary rates differed among the different groups. Moreover, evolutionary patterns of the WRKY gene family were examined in Arabidopsis, rice, and soybean. The results indicated that WRKY genes in soybean were duplicated mainly through segmental duplication, which differed from homologous genes in Arabidopsis and rice. These results provide useful information for future studies of molecular evolution of the WRKY gene family in soybean.
Identification and distribution of the WRKY gene family in soybean
Multiple sequence alignment and structure analysis
The phylogenetic classification was found to be consistent with the motif composition among group or subgroup. Differences between groups or subgroups were observed in not only the type of motifs in one WRKY protein, but also in the motif number in one WRKY protein. As displayed schematically in Additional file 2 and Additional file 3, nine types of motifs were detected, including three types of WRKY motifs. The majority of the proteins of subgroups I (73.9%; 17 of 23), II c (93.8%; 30 of 32) and II d (93.3%; 14 of 15), together with those of group III (87.5%; 14 of 16), share a unique WRKY motif, which is shown in red color in Additional file 3. Subgroups II a and II b have the same motif components, suggesting a close phylogenetic relationship. The motif number in each WRKY protein ranged from two to six, and this difference is apparent in groups or subgroups of the WRKY family. For example, all members of group III and the majority of subgroups II e and II d members have two motifs, including a WRKY motif. Interestingly, the relative motif positions in different groups or subgroups also vary significantly. Therefore, motif composition can shed light on phylogenetic relationships of the WRKY family.
Comparison of full-length cDNA sequences with corresponding genomic DNA sequences suggested that the exon number of soybean WRKY genes ranged from two to eight. The results of intron/exon structure identification (Additional file 4) showed that most of the WRKY domain-containing protein genes in different groups or subgroups have very conservative exon numbers. Members of group II d have three exons, and 14 of the 16 genes in group III have three exons. Notably, except for their differences in exon numbers, the relative exon positions in different groups or subgroups also vary significantly. The exon/intron analysis showed clear differences in both exon positions and exon numbers across the different groups or subgroups.
Together, these results indicated that soybean WRKY domains could be classified into three large groups: group I, group II, including group II a-e, and group III. Basic information of all soybean WRKY family members, including conserved heptapeptide, zinc-finger type, domain number, group, coding sequence (CDS) length, and gene length, is provided in Additional file 1.
Transcriptome atlas and promoter analysis
The above results indicated that the 133 WRKY genes in soybean display differential expression, either in their transcript abundance or in their expression patterns under normal growth conditions in different groups or subgroups.
Detection of positive selection and functional divergence analysis (FDA)
Site models and branch-site models in PAML [61] were used to detect positive selection in the WRKY gene family of soybean. Substitution rate ratios of non-synonymous (dN or Ka) versus synonymous (dS or Ks) mutations (dN/dS or ω) were calculated. A Ka/Ks ratio of 1 indicates genes that are subject to neutral selection, <1 indicates genes subject to negative selection, and >1 indicates genes subject to positive selection [62]. Additional file 6 lists parameter estimates and log-likelihood values for each site model. Two pairs of models (M0/M3 and M7/M8) were selected and compared. The site-homogeneous model, M0 (one-ratio), assumes one ω for all sites, whereas M3 (discrete) assumes a general discrete distribution. Two other models used were M7 (beta), which assumes a beta distribution of ω that is limited to the range (0, 1), and M8 (beta & ω), which adds an extra site class with ω estimated [63]. In addition, to test for variable omega ratios among lineages, we conducted the likelihood ratio test (LRT) to compare the two extreme models. The log likelihood values under the one-ratio model and the discrete model were determined to be −8608.409 and −8272.457, respectively. Twice the log likelihood difference value, 2ΔlnL = 335.95, was found to be strongly statistically significant (p < 0.01), thus revealing a heterogeneous selective pressure among lineages. Moreover, the log likelihood value under the beta model and the beta & ω were −8253.022 and −10197.202, respectively. Twice the log likelihood difference, 2ΔlnL = 1944.18, was also strongly statistically significant (p < 0.01). The comparison of M3 versus M0 revealed that none of the codon sites appeared to be under the influence of positive selection (ω > 1). By contrast, comparing the M7 model to the M8 model indicated that ~0.001% of codons fell within an estimated ω value of 2.638, suggesting positive selection. We also used Bayes empirical Bayes (BEB) estimation methods in model M8 [64] to identify sites under positive selection. We found only one positive selection site at the 0.05 significance level, and three sites at the 0.01 significance level. Together, these results indicate that no strong positive selection sites could be detected under the site model in the soybean WRKY gene family.
Parameters estimation and likelihood ratio tests for the branch-site models
Branch-site model
Foreground branches
Estimates of parameter
Positive selection sites (BEB) 4
Site class10
Site class 1
Site class 2a
Site class 2b
Group 1
P2a = 0.16768
P2b = 0.01315
ω0(b)2 = 0.05978
ω1(b) = 1.00000
ω2a(b) = 0.05978
ω2b(b) = 1.00000
ω0(f)3 = 0.05978
ω1(f) = 1.00000
ω2a(f) = 232.95169
ω2b(f) = 232.95169
Group 2a
P2a = 0.92727
P2b = 0.07273
ω0(b) = 0.06077
ω1(b) = 1.00000
ω2a(b) = 0.06077
ω2b(b) = 1.00000
ω0(f) = 0.06077
ω1(f) = 1.00000
ω2a(f) = 999.00000
ω2b(f) = 999.00000
Group 2b
P2a = 0.92726
P2b = 0.07273
ω0(b) = 0.06039
ω1(b) = 1.00000
ω2a(b) = 0.06039
ω2b(b) = 1.00000
ω0(f) = 0.06039
ω1(f) = 1.00000
ω2a(f) = 1.00000
ω2b(f) = 1.00000
Group 2c
P2a = 0.12223
P2b = 0.00958
ω0(b) = 0.06042
ω1(b) = 1.00000
ω2a(b) = 0.06042
ω2b(b) = 1.00000
ω0(f) = 0.06042
ω1(f) = 1.00000
ω2a(f) = 167.23585
ω2b(f) = 167.23585
Group 2d
P2a = 0.92727
P2b = 0.07273
ω0(b) = 0.06118
ω1(b) = 1.00000
ω2a(b) = 0.06118
ω2b(b) = 1.00000
ω0(f) = 0.06118
ω1(f) = 1.00000
ω2a(f) = 981.94932
ω2b(f) = 981.94932
Group 2e
P2a = 0.16008
P2b = 0.01253
ω0(b) = 0.06061
ω1(b) = 1.00000
ω2a(b) = 0.06061
ω2b(b) = 1.00000
ω0(f) = 0.06061
ω1(f) = 1.00000
ω2a(f) = 999.00000
ω2b(f) = 999.00000
Group 3
P2a = 0.29262
P2b = 0.02295
ω0(b) = 0.06176
ω1(b) = 1.00000
ω2a(b) = 0.06176
ω2b(b) = 1.00000
ω0(f) = 0.06176
ω1(f) = 1.00000
ω2a(f) = 999.00000
ω2b(f) = 999.00000
Type I functional divergence (shifted evolutionary rate) and Type II functional divergence (altered amino acid physicochemical property) between gene clusters of the WRKY gene family were estimated by posterior analysis using the program DIVERGE v2.0 [66, 67]. Because these methods are not sensitive to saturation of synonymous sites, they have been extensively applied in research of various gene families [68–70]. The estimation was based on the WRKY protein neighbor-joining tree, in which seven major clades were clearly present. Pairwise comparisons of paralogous WRKY genes from group I, group II a-e, and group III were carried out, and the rate of amino acid evolution at each sequence position was estimated. Our results (Additional file 7) indicated that with nine exceptions (group pairs II d/II e, II d/III, II d/II a, II d/I, II e/III, III/II a, and II b/I), the coefficients of Type-I functional divergence (θML) between WRKY groups were moderately statistically significant (p < 0.05), with θML values ranging from 0.201 to 0.395, or strongly statistically significant (p < 0.01) with θ ML values ranging from 0.311 to 0.618. These results indicated significant site-specific altered selective constraints on some members of the WRKY family, leading to subgroup-specific functional evolution after diversification. Additionally, Type-I functional divergence was not evident in the comparison of group II d with the other four groups, which suggests that group II d may be the most conservative clade. Type-II functional divergence was evident in all groups or subgroups (Additional file 8), with θ-II values ranging from 0.033 to 0.288 (p < 0.05), indicating a radical shift of amino acid properties. These results suggest that the relative importance of Type-I and Type-II functional divergence might be associated with specific functional classes of the WRKY gene family in soybean.
Furthermore, some critical amino acid residues responsible for functional divergence were predicted with suitable cut-off values derived from the Qk of each comparison. In order to reduce false positives, Qk > 0.8 was used as the cutoff to identify Type-I and Type-II functional divergence-related residues in all comparisons between the seven WRKY groups or subgroups. Results showed distinct differences in the number and distribution of predicted sites for functional divergence within each pairwise comparison. However, some critical amino acid sites still showed evidence of both Type-I and Type-II functional divergence in corresponding pairs. For example, five critical residues were predicted for the subgroup II e/II c (248E, 258P, 264Y, 275R, 295 V) and II e/II b (248E, 258P, 275R, 276G, 298E) pairwise comparisons, whereas three critical amino acids sites were predicted for the subgroup II e/I (248E, 264Y, 275R) and III/II b (264Y, 295 V, 298E) pairwise comparisons, respectively. Similar cases were found in other subgroup pairwise comparisons. Shifted evolutionary rates and altered amino acid physicochemical properties co-occurred at the same amino acid sites, revealing that these sites have played important roles in functional divergence during the process of evolution.
Expansion pattern of the WRKY family in soybean
Estimates of the dates for the segmental duplication events of WRKY family in soybean
Segment pairs
Number of anchors
KS (mean ± s.d.)
Estimated time (mya)
Glyma01g05050 & Glyma18g16170
0.60 ± 0.20
Glyma01g06550 & Glyma02g12490
0.17 ± 0.06
Glyma01g06870 & Glyma02g12830
0.16 ± 0.08
Glyma01g31920 & Glyma03g05220
0.19 ± 0.06
Glyma01g31920 & Glyma18g44030
0.71 ± 0.22
Glyma01g39600 & Glyma11g05650
0.17 ± 0.07
Glyma01g43420 & Glyma05g36970
0.70 ± 0.19
Glyma01g43420 & Glyma08g02580
0.68 ± 0.17
Glyma02g01420 & Glyma03g37940
0.67 ± 0.11
Glyma02g01420 & Glyma10g01450
0.20 ± 0.11
Glyma02g01420 & Glyma19g40560
0.72 ± 0.17
Glyma02g15920 & Glyma03g31630
0.60 ± 0.16
Glyma02g15920 & Glyma10g03820
0.15 ± 0.11
Glyma02g36510 & Glyma17g08170
0.13 ± 0.05
Glyma02g45530 & Glyma14g03280
0.12 ± 0.05
Glyma02g46690 & Glyma08g43770
0.61 ± 0.19
Glyma02g46690 & Glyma14g01980
0.13 ± 0.07
Glyma02g47650 & Glyma14g01010
0.14 ± 0.08
Glyma03g00460 & Glyma09g41050
0.51 ± 0.12
Glyma03g31630 & Glyma10g03820
0.55 ± 0.10
Glyma03g33380 & Glyma19g36100
0.19 ± 0.17
Glyma03g37870 & Glyma19g40470
0.15 ± 0.07
Glyma03g37940 & Glyma10g01450
0.73 ± 0.16
Glyma03g37940 & Glyma19g40560
0.15 ± 0.07
Glyma03g38360 & Glyma19g40950
0.16 ± 0.09
Glyma03g41750 & Glyma07g06320
0.66 ± 0.23
Glyma03g41750 & Glyma16g02960
0.62 ± 0.26
Glyma03g41750 & Glyma19g44380
0.18 ± 0.13
Glyma04g08060 & Glyma06g08120
0.18 ± 0.12
Glyma04g39620 & Glyma06g15260
0.23 ± 0.19
Glyma04g39650 & Glyma05g31800
0.72 ± 0.19
Glyma04g39650 & Glyma06g15220
0.22 ± 0.19
Glyma04g39650 & Glyma08g15050
0.66 ± 0.19
Glyma04g40130 & Glyma06g14720
0.25 ± 0.25
Glyma05g01280 & Glyma06g20300
0.57 ± 0.21
Glyma05g25330 & Glyma08g08340
0.21 ± 0.19
Glyma05g25770 & Glyma08g08720
0.20 ± 0.15
Glyma05g29310 & Glyma08g12460
0.16 ± 0.07
Glyma05g31800 & Glyma06g15220
0.63 ± 0.22
Glyma05g31800 & Glyma08g15050
0.14 ± 0.08
Glyma05g36970 & Glyma08g02580
0.22 ± 0.15
Glyma05g37390 & Glyma08g02160
0.14 ± 0.08
Glyma06g15220 & Glyma08g15050
0.68 ± 0.23
Glyma06g15260 & Glyma08g15210
0.71 ± 0.21
Glyma06g46420 & Glyma12g10350
0.23 ± 0.19
Glyma06g46420 & Glyma13g38630
0.72 ± 0.11
Glyma07g02630 & Glyma08g23380
0.22 ± 0.18
Glyma07g02630 & Glyma13g44730
0.56 ± 0.18
Glyma07g02630 & Glyma15g00570
0.54 ± 0.15
Glyma07g06320 & Glyma16g02960
0.16 ± 0.07
Glyma07g06320 & Glyma19g44380
0.61 ± 0.17
Glyma07g36640 & Glyma15g14860
0.59 ± 0.21
Glyma07g36640 & Glyma17g03950
0.23 ± 0.23
Glyma07g36640 & Glyma09g03900
0.73 ± 0.18
Glyma07g39250 & Glyma09g00820
0.63 ± 0.15
Glyma07g39250 & Glyma15g11680
0.65 ± 0.18
Glyma07g39250 & Glyma17g01490
0.17 ± 0.11
Glyma08g23380 & Glyma13g44730
0.49 ± 0.18
Glyma08g23380 & Glyma15g00570
0.52 ± 0.17
Glyma08g26230 & Glyma18g49830
0.21 ± 0.08
Glyma08g43770 & Glyma14g01980
0.56 ± 0.13
Glyma09g00820 & Glyma15g11680
0.20 ± 0.14
Glyma09g00820 & Glyma17g01490
0.67 ± 0.21
Glyma09g03450 & Glyma15g14370
0.20 ± 0.15
Glyma09g03900 & Glyma15g14860
0.25 ± 0.21
Glyma09g03900 & Glyma17g03950
0.59 ± 0.17
Glyma09g06980 & Glyma13g00380
0.69 ± 0.18
Glyma09g06980 & Glyma15g18250
0.22 ± 0.21
Glyma09g06980 & Glyma17g06450
0.56 ± 0.11
Glyma09g39000 & Glyma18g47350
0.19 ± 0.10
Glyma09g39040 & Glyma18g47300
0.18 ± 0.10
Glyma09g41050 & Glyma18g44560
0.16 ± 0.06
Glyma10g01450 & Glyma19g40560
0.70 ± 0.17
Glyma10g37460 & Glyma20g30290
0.13 ± 0.05
Glyma11g05650 & Glyma17g18480
0.71 ± 0.23
Glyma12g10350 & Glyma13g38630
0.73 ± 0.10
Glyma12g33990 & Glyma13g36540
0.23 ± 0.20
Glyma13g00380 & Glyma17g06450
0.19 ± 0.13
Glyma13g17800 & Glyma17g04710
0.20 ± 0.17
Glyma13g44730 & Glyma15g00570
0.12 ± 0.06
Glyma14g11440 & Glyma17g34210
0.32 ± 0.19
Glyma14g11920 & Glyma17g33920
0.17 ± 0.05
Glyma15g11680 & Glyma17g01490
0.67 ± 0.20
Glyma15g14860 & Glyma17g03950
0.58 ± 0.24
Glyma15g18250 & Glyma17g06450
0.68 ± 0.16
Glyma16g02960 & Glyma19g44380
0.58 ± 0.17
We also used Ks, as the proxy for time, and the conserved flanking protein-coding genes to estimate the dates of the segmental duplication events. The mean Ks values and the estimated dates for all segmental duplication events corresponding to WRKY genes are listed in Table 2. The segmental duplicated events in soybean appear to have occurred recently, and focus on two periods, 10–20 mya and 40–60 mya, which is consistent with the ages of the genome duplication events [43]. Taken together, our analyses suggested that segmental duplication is the main mechanism for expansion of this WRKY gene family, accompanied by tandem duplications.
Identification, classification, and phylogenetic analysis of the soybean WRKY gene family
The genome sequence and transcriptome profiles of soybean provide a large amount of useful data to explore functional diversity from multiple perspectives. In this study, we identified 133 WRKY members in the soybean genome. A phylogenetic tree including 133 distinct protein sequences clearly demonstrated that these genes could be divided into three groups. This classification was further supported by the results of motifs and exon/intron analyses. The topology of our phylogenetic tree constructed from WRKY genes of two species (soybean and Arabidopsis) is largely consistent with that derived from Arabidopsis alone. All of the evidence obtained suggested that the classification was reasonable and reliable.
WRKY transcription factors have their evolutionary origin in ancient eukaryotes, whose genomes contain a single WRKY gene with two WRKY domains. The presence of a group I WRKY protein in these ancient organisms suggests that group I WRKY genes represent the ancestral form, with other groups arising later through losses and gains of WRKY domains [22]. In the present study, phylogenetic analysis based on the relationship of different groups, indicated that domain gain and loss has indeed been a driving force in the expansion of the WRKY gene family. For example, subgroups II a, II b, and II c were phylogenetically closer to the C-terminal WRKY domain of group I.
Glyma14g37960 and Glyma18g39970 were not assigned to any groups or subgroups. Glyma14g37960 has one WRKY domain; however, it is phylogenetically closer to group I N. Thus, Glyma14g37960 may have arisen from a two-domain WRKY protein that lost one of its WRKY domains during evolution, whereas in Glyma18g39970, a mutation in the sequence outside of the WRKY domain may have occurred before or after the domain loss.
Transcriptome atlas, positive selection, and FDA of soybean WRKY proteins
The transcriptome atlas revealed differential expression of the WRKY gene family under normal growth conditions. Furthermore, results of the promoter analysis were compatible with differential expression patterns. The elements were distributed across three main functional categories, including biotic and abiotic stresses and developmental processes. Surprisingly, Skn-1 motif elements, which are required for high levels of endosperm expression in cooperative interaction with other motifs (AACA, GCN4, ACGT) [77], were found to be abundant in all groups or subgroups. This result appears to contradict with the expression analysis, in which only one gene showed the highest transcript accumulation level in seed tissue. Since the function of cis-acting elements is to regulate gene expression, we speculated that the reason for this phenomenon might be due to the deficiency of Skn-1 motif element partners, AACA and ACGT elements, which were rarely detected in our study. On the other hand, according to the transcriptome atlas of the soybean WRKY gene family, the majority of GmWRKYs showed relatively reduced expression in seed development compared to other organs, which suggests that the expression of genes can be significantly affected when the Skn-1 motif lacks its partners. To further investigate the reason for this differential expression, we performed a positive selection analysis and a functional divergence analysis.
We used both site models and branch-site models to detect positive selection. The results of site models indicated that one category of ω did not fit the data well to describe the variability in selection pressures across amino acid sites. Therefore, the branch-site models, which allowed ω ratios to vary among sites and lineages simultaneously, appeared to be most suitable for describing evolutionary processes of the WRKY gene family. The branch-site analysis revealed that several sites were under positive selection. Along the group II e clade, the following sites were identified to be under positive selection: 248E, 249Y, 286A, 288D, 298E, and 299G. Similar results were found in the group I, III, and II c clades.
Number of WRKY genes in Arabidopsis, rice, and soybean
Functional innovations include subfunctionalization [81], neofunctionalization [82], and subneofunctionalization [83]. Gene duplication may result in altered functional constraints between the gene clusters of a gene family. The results of the functional divergence analysis suggested that WRKY genes should be significantly functionally divergent from each other, especially with respect to the four amino acid residues (248E, 275R, 288D and 298E) identified by both PAML 4 and DIVERGE 2.0 analyses, which were inferred to have played important roles during evolution. On the other hand, functional divergence might reflect the existence of long-term selective pressures.
The soybean WRKY gene family arose mainly through segmental duplication
The dramatic variation we observe in gene family size and distribution may have resulted owing to many processes, including tandem duplication with high rates of birth and death and gene duplication resulting from larger scale genome events such as polyploidy or duplications of chromosomal regions (here referred to as "segmental duplications").
The current investigation revealed the duplication pattern of the soybean WRKY gene family. One hundred two genes were found to evolve from segmental duplication, suggesting that segmental duplication likely played a pivotal role in WRKY gene expansion in the soybean genome. The genome sequencing results revealed two genome duplication events in soybean, aging ~13 mya and ~57 mya [43], which is consistent with results of the present study. We inferred that the expansion of the WRKY gene family occurred along with genome duplication events, and that these genes were retained during evolution. The structural similarity and variation between genes located on the same chromosome and the phylogenetic analysis might help to explain the order of duplication events of the soybean WRKY genes on the same chromosome. For example, Glyma02g01420, Glyma02g12830, and Glyma02g15920, which are located in different duplication blocks of the same chromosome, all have two introns flanked by three exons. However, phylogenetic analysis showed that Glyma02g01420 was more similar to Glyma10g01450, and Glyma02g15920 was more similar to Glyma10g03820, whereas Glyma02g12830, which is located relatively close to Glyma02g15920, had no duplicate genes on chromosome 10. It is possible that the duplication of the same ancestral gene on chromosome 2 resulted in Glyma02g12830 and the ancestor of Glyma10g01450 and Glyma10g03820, which then evolved independently. The intron and exon sequences of the ancestor gene might have elongated or shorten because of various reasons after it split into Glyma02g01420 and Glyma02g15920. Through segmental duplication, the two chromosome segments, one contained in Glyma02g12830 and the other contained in Glyma02g01420 and Glyma02g15920, were independently copied to different parts of chromosome 10. During subsequent evolution, the counterpart of Glyma02g12830 was lost and structures for the counterparts of Glyma02g01420 and Glyma02g15920 changed by deletion or insertion of other fragments or partial sequence repeat variations. Moreover, we noticed that both the Arabidopsis and rice genomes underwent recent duplication events, which also resulted in large-scale expansion of the WRKY gene family in their genomes. Therefore, we also examined the duplicated pattern of WRKY genes in these model species.
The complete sequencing of the Arabidopsis genome revealed numerous large-scale segmental duplications [84]. Previous studies concluded that at least two rounds of duplications probably occurred in the Arabidopsis genome, with many losses and rearrangements leaving a mosaic of "segmental duplications" or "duplication blocks" [74, 84]. Most duplication blocks appear to have originated from one round of polyploidy, as estimated by using various methods, that occurred 20–40 mya, before the evolution of the genus Brassica but after the separation of Brassicaceae from other closely related eudicot families [74]. Results of the present study showed that no apparent tandem duplication events, and rare segmental duplication events (six pairs), exist in the Arabidopsis WRKY gene family. Furthermore, the estimated time of the six pairs of segmental duplicated genes focus on the period of 24–27 mya (Additional file 9). Cannon at el. [72] found nine distinct pairs of duplicated segments and no tandem duplication events in the Arabidopsis WRKY family, which is compatible with our study. Comparison of six pairs of segmental duplicated genes in our study with the results of Blanc et al. [85] suggested that only one pair of genes (At1g13960 and At2g033400) originated from polyploidy in Arabidopsis. Consequently, we speculated that the other five segmental duplicated genes might have derived from independent segmental duplication events. The long period of time over which genome evolution has occurred has provided many opportunities for functional divergence in the genes that arose from duplications. Our results did not reveal evidence that other pairs of WRKY genes in Arabidopsis originated from duplicated blocks. Therefore, most of the Arabidopsis WRKY genes may have lost their paralogous genes after genome duplication [74].
With respect to rice, the expansion patterns of WRKY gene family have been clearly demonstrated. Ramamoorthy et al. [40] predicted 103 genes encoding WRKY transcription factors in rice, and the majority of rice WRKY genes (77.7%; 80 of 103) were detected on duplicated blocks. Of the WRKY genes, 45.6% (47 of 103) of WRKY genes were found to have corresponding coordinates generated by segmental duplications. Furthermore, 35.0% (36 of 103) of the WRKY genes were clustered together with a maximum of 10 extra genes between them, and were regarded as tandemly duplicated genes. The results above were confirmed by Jiang et al. [86]. That is, that both tandem and segmental duplication significantly contributed to the expansion of the WRKY gene family in rice.
All of the evidence suggests that the evolutionary patterns of the WRKY gene family differ between soybean, rice, and Arabidopsis. Species-specific expansion played an important role in the evolution of this family in plants. Segmental duplication appears to be the dominant mechanism for the generation of duplicated genes in soybean, whereas segmental duplication and tandem duplication may play similar roles in the expansion of the rice WRKY gene family. Moreover, although Arabidopsis may have a tetraploid ancestor, the majority of its duplicated genes appear to have been lost throughout evolutionary processes.
Previous studies have demonstrated that members of the WRKY gene family play important roles in the regulation of several plant developmental processes and in responses to various biotic and abiotic stresses. Results of the present study indicate that segmental duplication has likely been the dominant mechanism of gene amplification during the expansion of the WRKY family in soybean. Furthermore, positive selection could be the main driving forces for the functional divergence of duplicated genes, which may have played a critical role in the responses of plants to various stresses throughout their evolutionary history. The results of this study will not only further our understanding of the evolutionary processes of soybean WRKY genes, but will also help to enhance functional genomics studies of WRKY transcription factors in an important model system.
Sequence collection
Seventy WRKY protein sequences downloaded from AtTFDB (http://arabidopsis.med.ohio-state.edu/AtTFDB/) were used to BLAST against the soybean genome database, Phytozome v8.0 (http://www.phytozome.net/soybean), using the BLASTP program. Sequences were selected as candidate proteins if their E value was ≤ 1e-10. For each query sequence, information of the location on chromosomes, genomic sequences, full coding sequences (CDS), and protein sequences were collected from Phytozome, and redundant genes were removed manually. The Simple Modular Architecture Research Tool (SMART; http://smart.embl-heidelberg.de/) was used to confirm each predicted WRKY member.
Phylogenetic tree construction and sequence analysis
The SMART program was used to extract the protein sequences of the WRKY domain for each protein. Multiple sequence alignment of domain sequences of 133 WRKY family proteins from soybean and 70 protein sequences from Arabidopsis was performed using the Clustal X 1.83 program with default parameters, and a phylogenetic tree was generated and viewed using MEGA Version 5.0. Exon and intron organizations of soybean WRKY genes were determined by comparing predicted CDS with their corresponding genomic sequences using GSDS (http://gsds.cbi.pku.edu.cn/) software. Motifs of paralogous WRKY proteins were identified statistically using MEME with default settings, except that the maximum number of motifs to find was set at 10.
RNA-Seq atlas and promoter analysis
RNA-Seq data were introduced to further analyze the expression of GmWRKY genes. Data was normalized using a variation of the reads/Kb/Million method, and Z-score analysis was obtained from SoyBase (http://soybase.org/soyseq/) [44, 87]. A heat map was generated using the GenePattern program (http://www.broadinstitute.org/cancer/software/genepattern/index.html). The cis-acting elements that regulate gene expression are distributed in 300–3000 bp upstream of the coding region, also take into consideration of sequence restriction in PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) and the methods described by Liu et al. [68], therefore, 1500 bp upstream of the coding region were selected as promoter sequence and were downloaded from Phytozome (http://www.phytozome.net) and Soybean Functional Genomics Database (bioinformatics.cau.edu.cn). Then these sequences were submitted to PlantCARE for in silico analysis.
Positive selection and functional divergence
A maximum likelihood method in PAML was applied to test the hypothesis of positive selection in the WRKY gene family [63] under the site model and branch-site model. In the site model, two pairs of models were contrasted to test the selective pressures at codon sites. First, models M0 (one ratio) and M3 (discrete) were compared, using a test for heterogeneity between codon sites in the dN/dS ratio value, ω. The second comparison was M7 (beta) versus M8 (beta + ω > 1). Meanwhile, we introduced the likelihood ratio test (LRT) to compare the two extreme models. When the LRT suggested positive selection, the Bayes empirical Bayes (BEB) method was used to calculate the posterior probabilities that each codon was from the site class of positive selection under models M3 and M8.
The branch-site model assumes that the ω ratio varies between codon sites and that there are four site classes in the sequence. The first class of sites is highly conserved in all lineages with a small ω ratio, ω0. The second class includes neutral or weakly constrained sites for which ω = ω1, where ω1 is near or smaller than 1. In the third and fourth classes, the background lineages show ω0 or ω1, but foreground branches have ω2, which may be greater than 1. When constructing the LRTs, the null hypothesis fixes ω2 = 1, allowing sites evolving under negative selection in the background lineages to be released from constraint and to evolve neutrally on the foreground lineage; the alternative hypothesis constrains ω2 ≥ 1 [64]. Posterior probabilities (Qks) were calculated using the BEB method [65].
The software DIVERGE was used to reveal the functional divergence between members of the WRKY protein family. The coefficients of Type-I and Type-II functional divergence (θ-I and θ-II, respectively) between any two clusters of interest were calculated. A θ-I or θ-II significantly > 0 indicates site-specific altered selective constraints or a radical shift of amino acid physicochemical properties after gene duplication and/or speciation [66]. Moreover, Qk was used to predict critical amino acid residues that were responsible for functional divergence. In this study, we screened the codons (Qk > 0.8) as potential sites that were crucial for functional divergence.
Analysis of WRKY gene expansion patterns and dating the duplication events
In this study, we focused on two patterns of gene expansion: tandem duplication and segmental duplication. Tandem duplications were characterized as multiple members of this family occurring within the same or neighboring intergenic regions, where the WRKY genes were clustered together with a maximum of 10 extra genes between them [40]. Segmental duplications of each WRKY gene within the family in soybean and Arabidopsis genomes were searched in the PGDD (http://chibba.agtec.uga.edu/duplication/). Within the range of 100 kb, the anchors with synonymous substitution rates (Ks) values greater than 1.0 were discarded because of the risk of saturation. Assuming a molecular clock, the Ks values of duplicated genes are expected to be similar over time [88]. Therefore, we used Ks values to estimate the dates of the segmental duplication events. The mean Ks value was calculated for each pair of genes within a duplicated block and was then used to date the duplication events. The approximate date of the duplication event was then calculated using the mean Ks values (T = Ks/2λ), assuming clock-like rates (λ) of synonymous substitution of 1.5 × 10−8 substitutions/synonymous site/year for Arabidopsis[89] and 6.1 × 10−9 for soybean [90].
Authors would like to thank the National Natural Science Foundation of China (30971783) and the Natural Science Foundation of Beijing, China (5132005) for financial support. GY would like to thank Wan Ping, associate professor from school of life sciences, Capital Normal University, for all the help with bioinformatics.
Authors' Affiliations
- Zhang Y, Wang L: The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol. 2005, 5: 1-10.1186/1471-2148-5-1.PubMedPubMed CentralView ArticleGoogle Scholar
- Ishiguro N: Characterization of a cDNA encoding a novel DNA-binding protein, SPF1, that recognizes SP8 sequences in the 5' upstream regions of genes coding for sporamin and β-amylase from sweet potato. Mol Gen Genet. 1994, 244: 563-571.PubMedView ArticleGoogle Scholar
- Rushton PJ, Macdonald H, Huttly AK, Lazarus CM, Hooley R: Members of a new family of DNA binding proteins bind to a conserved cis-element in the promoters of alpha-Amy2 genes. Plant Mol Biol. 1995, 29: 691-702. 10.1007/BF00041160.PubMedView ArticleGoogle Scholar
- Rushton PJ, Torres JT, Parniske M, Wernert P, Hahlbrock K, Somssich IE: Interaction of elicitor-induced DNA-binding proteins with elicitor response elements in the promoters of parsley PR1 genes. EMBO J. 1996, 15: 5690-5700.PubMedPubMed CentralGoogle Scholar
- Cormack RS, Eulgem T, Rushton PJ, Köchner P, Hahlbrock K, Somssich IE: Leucine zipper containing WRKY proteins widen the spectrum of immediate early elicitor-induced WRKY transcription factors in parsley. Biochim Biophys Acta. 2002, 1576: 92-100. 10.1016/S0167-4781(02)00298-1.PubMedView ArticleGoogle Scholar
- De Pater S, Greco V, Pham K, Memelink J, Kijne J: Characterization of a zinc-dependent transcriptional activator from Arabidopsis. Nucleic Acids Res. 1996, 24: 4624-4631. 10.1093/nar/24.23.4624.PubMedPubMed CentralView ArticleGoogle Scholar
- Alexandrova KS, Conger BV: Isolation of two somatic embryogenesis-related genes from orchardgrass (Dactylis glomerata). Plant Sci. 2002, 162: 301-307. 10.1016/S0168-9452(01)00571-4.View ArticleGoogle Scholar
- Chen C, Chen Z: Isolation and characterization of two pathogen-and salicylic acid-induced genes encoding WRKY DNA-binding proteins from tobacco. Plant Mol Biol. 2000, 42: 387-396. 10.1023/A:1006399311615.PubMedView ArticleGoogle Scholar
- Hara K, Yagi M, Kusano T, Sano H: Rapid systemic accumulation of transcripts encoding a tobacco WRKY transcription factor upon wounding. Mol Gen Genet. 2000, 263: 30-37. 10.1007/PL00008673.PubMedView ArticleGoogle Scholar
- Wang Z, Yang P, Fan B, Chen Z: An oligo selection procedure for identification of sequence-specific DNA-binding activities associated with the plant defence response. Plant J. 1998, 16: 515-522. 10.1046/j.1365-313x.1998.00311.x.PubMedView ArticleGoogle Scholar
- Yoda H, Ogawa M, Yamaguchi Y, Koizumi N, Kusano T, Sano H: Identification of early-responsive genes associated with the hypersensitive response to tobacco mosaic virus and characterization of a WRKY-type transcription factor in tobacco plants. Mol Genet Genomics. 2002, 267: 154-161. 10.1007/s00438-002-0651-z.PubMedView ArticleGoogle Scholar
- Ashida Y, Nishimoto M, Matsushima A, Watanabe J, Hirata T: Molecular cloning and mRNA expression of geraniol-inducible genes in cultured shoot primordia of Matricaria chamomilla. Biosci Biotechnol Biochem. 2002, 66: 2511-2514. 10.1271/bbb.66.2511.PubMedView ArticleGoogle Scholar
- Kim CY, Lee SH, Park HC, Bae CG, Cheong YH, Choi YJ, Han C, Lee SY, Lim CO, Cho MJ: Identification of rice blast fungal elicitor-responsive genes by differential display analysis. Mol Plant Microbe Interact. 2000, 13: 470-504. 10.1094/MPMI.2000.13.4.470.PubMedView ArticleGoogle Scholar
- Lambais MR: In silico differential display of defenserelated expressed sequence tags from sugarcane tissues infected with diazotrophic endophytes. Genet Mol Biol. 2001, 24: 103-111. 10.1590/S1415-47572001000100015.View ArticleGoogle Scholar
- Huang T, Duman JG: Cloning and characterization of a thermal hysteresis (antifreeze) protein with DNA-binding activity from winter bitter sweet night shade Solanum dulcamara. Plant Mol Biol. 2002, 48: 339-350. 10.1023/A:1014062714786.PubMedView ArticleGoogle Scholar
- Beyer K, Binder A, Boller T, Collinge M: Identification of potato genes induced during colonization by Phytophthora infestans. Mol Plant Pathol. 2001, 2: 125-134. 10.1046/j.1364-3703.2001.00059.x.PubMedView ArticleGoogle Scholar
- Dellagi A, Helibronn J, Avrova AO, Montesano M, Palva ET, Stewart HE, Toth IK, Cooke DE, Lyon GD, Birch PR: A potato gene encoding a WRKY-like transcription factor is induced in interactions with Erwinia carotovora subsp. atroseptica and Phytophthora infestans and is coregulated with class I endochitinase expression. Mol Plant Microbe Interact. 2000, 13: 1092-1101. 10.1094/MPMI.2000.13.10.1092.PubMedView ArticleGoogle Scholar
- Sun C, Palmqvist S, Olsson H, Borén M, Ahlandsberg S, Jansson C: A Novel WRKY Transcription Factor, SUSIBA2, Participates in Sugar Signaling in Barley by Binding to the Sugar-Responsive Elements of the iso1 Promoter. Plant Cell. 2003, 15: 2076-2092. 10.1105/tpc.014597.PubMedPubMed CentralView ArticleGoogle Scholar
- Marchive C, Mzid R, Deluc L, Barrieu F, Pirrello J, Gauthier A, Corio-Costet MF, Regad F, Cailleteau B, Hamdi S, Lauvergeat V: Isolation and characterization of a Vitis vinifera transcription factor, VvWRKY1, and its effect on responses to fungal pathogens in transgenic tobacco plants. J Exp Bot. 2007, 58: 1999-2010. 10.1093/jxb/erm062.PubMedView ArticleGoogle Scholar
- Eulgem T, Rushton PJ, Robatzek S, Somssich IE: The WRKY superfamily of plant transcription factors. Trends Plant Sci. 2000, 5: 199-206. 10.1016/S1360-1385(00)01600-9.PubMedView ArticleGoogle Scholar
- Yamasaki K, Kigawa T, Seki M, Shinozaki K, Yokoyama S: DNA-binding domains of plant-specific transcription factors: structure, function, and evolution. Trends Plant Sci. 2013, 18: 267-276. 10.1016/j.tplants.2012.09.001.PubMedView ArticleGoogle Scholar
- Rushton PJ, Somssich IE, Ringler P, Shen QJ: WRKY transcription factors. Trends Plant Sci. 2010, 15: 247-258. 10.1016/j.tplants.2010.02.006.PubMedView ArticleGoogle Scholar
- Ulker B, Somssich IE: WRKY transcription factors: from DNA binding towards biological function. Curr Opin Plant Biol. 2004, 7: 491-498. 10.1016/j.pbi.2004.07.012.PubMedView ArticleGoogle Scholar
- Eulgem T, Rushton PJ, Schmelzer E, Hahlbrock K, Somssich IE: Early nuclear events in plant defence signalling: rapid gene activation by WRKY transcription factors. EMBO J. 1999, 18: 4689-4699. 10.1093/emboj/18.17.4689.PubMedPubMed CentralView ArticleGoogle Scholar
- Eulgem T, Somssich IE: Networks of WRKY transcription factors in defense signaling. Curr Opin Plant Biol. 2007, 10: 366-371. 10.1016/j.pbi.2007.04.020.PubMedView ArticleGoogle Scholar
- Ishihama N, Yoshioka H: Post-translational regulation of WRKY transcription factors in plant immunity. Curr Opin Plant Biol. 2012, 15: 431-437. 10.1016/j.pbi.2012.02.003.PubMedView ArticleGoogle Scholar
- Pandey SP, Somssich IE: The Role of WRKY Transcription Factors in Plant Immunity. Plant Physiol. 2009, 4: 1648-1655.View ArticleGoogle Scholar
- Lagacé M, Matton DP: Characterization of a WRKY transcription factor expressed in late torpedo-stage embryos of Solanum chacoense. Planta. 2004, 219: 185-189. 10.1007/s00425-004-1253-2.PubMedView ArticleGoogle Scholar
- Hinderhofer K, Zentgraf U: Identification of a transcription factor specifically expressed at the onset of leaf senescence. Planta. 2001, 213: 469-473. 10.1007/s004250000512.PubMedView ArticleGoogle Scholar
- Pnueli L, Hallak-Herr E, Rozenberg M, Cohen M, Goloubinoff P, Kaplan A, Mittler R: Molecular and biochemical mechanisms associated with dormancy and drought tolerance in the desert legume Retama raetam. Plant J. 2002, 31: 319-330. 10.1046/j.1365-313X.2002.01364.x.PubMedView ArticleGoogle Scholar
- Johnson CS, Kolevski B, Smyth DR: TRANSPARENT TESTA GLABRA2, a Trichome and Seed Coat Development Gene of Arabidopsis, Encodes a WRKY Transcription Factor. Plant Cell. 2002, 14: 1359-1375. 10.1105/tpc.001404.PubMedPubMed CentralView ArticleGoogle Scholar
- Luo M, Dennis ES, Berger F, Peacock WJ, Chaudhury A: MINISEED3 (MINI3), a WRKY family gene, and HAIKU2 (IKU2), a leucine-rich repeat (LRR) KINASE gene, are regulators of seed size in Arabidopsis. Proc Natl Acad Sci U S A. 2005, 48: 17531-17536.View ArticleGoogle Scholar
- Zhang ZL, Xie Z, Zou X, Casaretto J, Ho TH, Shen QJ: A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Plant Physiol. 2004, 134: 1500-1513. 10.1104/pp.103.034967.PubMedPubMed CentralView ArticleGoogle Scholar
- Rushton DL, Tripathi P, Rabara RC, Lin J, Ringler P, Boken AK, Langum TJ, Smidt L, Boomsma DD, Emme NJ, Chen X, Finer JJ, Shen QJ, Rushton PJ: WRKY transcription factors: key components in abscisic acid signaling. Plant Biotechnology J. 2012, 10: 2-11. 10.1111/j.1467-7652.2011.00634.x.View ArticleGoogle Scholar
- Du L, Chen Z: Identification of genes encoding receptor-like protein kinases as possible targets of pathogen- and salicylic acid-induced WRKY DNA-binding proteins in Arabidopsis. Plant J. 2000, 24: 837-847. 10.1046/j.1365-313x.2000.00923.x.PubMedView ArticleGoogle Scholar
- Chen L, Song Y, Li S, Zhang L, Zou C, Yu D: The role of WRKY transcription factors in plant abiotic stresses. Biochim Biophys Acta. 1819, 2012: 120-128.Google Scholar
- Ren X, Chen Z, Liu Y, Zhang H, Zhang M, Liu Q, Hong X, Zhu JK, Gong Z: ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis. Plant J. 2010, 63: 417-429. 10.1111/j.1365-313X.2010.04248.x.PubMedPubMed CentralView ArticleGoogle Scholar
- Seki M, et al: Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J. 2002, 31: 279-292. 10.1046/j.1365-313X.2002.01359.x.PubMedView ArticleGoogle Scholar
- Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K: The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 2007, 50: 347-363. 10.1111/j.1365-313X.2007.03052.x.PubMedView ArticleGoogle Scholar
- Ramamoorthy R, Jiang SY, Kumar N, Venkatesh PN, Ramachandran S: A comprehensive transcriptional profiling of the WRKY gene family in rice under various abiotic and phytohormone treatments. Plant Cell Physiol. 2008, 49: 865-879. 10.1093/pcp/pcn061.PubMedView ArticleGoogle Scholar
- Şahin-Çevik M: A WRKY transcription factor gene isolated from Poncirus trifoliata shows differential responses to cold and drought stresses. Plant Omics. 2012, 5: 438-445.Google Scholar
- Zhou QY, Tian AG, Zou HF, Xie ZM, Lei G, Huang J, Wang CM, Wang HW, Zhang JS, Chen SY: Soybean WRKY-type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stress in transgenic Arabidopsis plants. Plant Biotechnol J. 2008, 6: 486-503. 10.1111/j.1467-7652.2008.00336.x.PubMedView ArticleGoogle Scholar
- Schmutz J, et al: Genome sequence of the palaeopolyploid soybean. Nature. 2010, 14: 178-183.View ArticleGoogle Scholar
- Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G: An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J. 2010, 63: 86-99.PubMedGoogle Scholar
- Dong J, Chen C, Chen Z: Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response. Plant Mol Biol. 2003, 51: 21-37. 10.1023/A:1020780022549.PubMedView ArticleGoogle Scholar
- Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S: PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002, 30: 325-327. 10.1093/nar/30.1.325.PubMedPubMed CentralView ArticleGoogle Scholar
- Sommer H, Saedler H: Structure of the chalcone synthase gene of Antirrhinum majus. Mol Gen Genet. 1986, 202: 429-434. 10.1007/BF00333273.View ArticleGoogle Scholar
- Menkens AE, Schindler U, Cashmore AR: The G-box: a ubiquitous regulatory DNA element in plants bound by the GBF family of bZIP proteins. Trends Biochem Sci. 1995, 20: 506-510. 10.1016/S0968-0004(00)89118-5.PubMedView ArticleGoogle Scholar
- Werneke JM, Chatfield JM, Ogren WL: Alternative mRNA splicing generates the two ribulosebisphosphate carboxylase/oxygenase activase polypeptides in spinach and Arabidopsis. Plant Cell. 1989, 1: 815-825.PubMedPubMed CentralView ArticleGoogle Scholar
- Argüello-Astorga GR, Herrera-Estrella LR: Ancestral Multipartite Units in Light-Responsive Plant Promoters Have Structural Features Correlating with Specific Phototransduction Pathways. Plant Physiol. 1996, 3: 1151-1166.View ArticleGoogle Scholar
- Lois R, Dietrich A, Hahlbrock K, Schulz W: A phenylalanine ammonia-lyase gene from parsley: structure, regulation and identification of elicitor and light responsive cis-acting elements. EMBO J. 1989, 8: 1641-1648.PubMedPubMed CentralGoogle Scholar
- Ibraheem O, Botha CE, Bradley G: In silico analysis of cis-acting regulatory elements in 5' regulatory regions of sucrose transporter gene families in rice (Oryza sativa Japonica) and Arabidopsis thaliana. Comput Biol Chem. 2010, 34: 268-283. 10.1016/j.compbiolchem.2010.09.003.PubMedView ArticleGoogle Scholar
- Jiao Y, Lau OS, Deng XW: Light-regulated transcriptional networks in higher plants. Nat Rev Genet. 2007, 8: 217-230.PubMedView ArticleGoogle Scholar
- Simpson SD, Nakashima K, Narusaka Y, Seki M, Shinozaki K, Yamaguchi-Shinozaki K: Two different novel cis-acting elements of erd1, a clpA homologous Arabidopsis gene function in induction by dehydration stress and dark-induced senescence. Plant J. 2003, 33: 259-270. 10.1046/j.1365-313X.2003.01624.x.PubMedView ArticleGoogle Scholar
- Kim JK, Cao J, Wu R: Regulation and interaction of multiple protein factors with the proximal promoter regions of a rice high pI α-amylase gene. Mol Gen Genet. 1992, 232: 383-393.PubMedView ArticleGoogle Scholar
- Pastuglia M, Roby D, Dumas C, Cock JM: Rapid induction by wounding and bacterial infection of an S gene family receptor-like kinase in Brassica oleracea. Plant Cell. 1997, 9: 49-60.PubMedPubMed CentralView ArticleGoogle Scholar
- Yamaguchi-Shinozaki K, Shinozaki K: Arabidopsis DNA Encoding Two Desiccation-Responsive rd29 Genes. Plant Physiol. 1993, 101: 1119-1120. 10.1104/pp.101.3.1119.PubMedPubMed CentralView ArticleGoogle Scholar
- Freitas FZ, Bertolini MC: Genomic organization of the Neurospora crassa gsn gene: possible involvement of the STRE and HSE elements in the modulation of transcription during heat shock. Mol Genet Genomics. 2004, 272: 550-561. 10.1007/s00438-004-1086-5.PubMedView ArticleGoogle Scholar
- Klotz KL, Lagrimini LM: Phytohormone control of the tobacco anionic peroxidase promoter. Plant Mol Biol. 1996, 31: 565-573. 10.1007/BF00042229.PubMedView ArticleGoogle Scholar
- Pichersky E, Bernatzky R, Tanksley SD, Breidenbach RB, Kausch AP, Cashmore AR: Molecular characterization and genetic mapping of two clusters of genes encoding chlorophyll a/b-binding proteins in Lycopersicon esculentum (tomato). Gene. 1985, 40: 247-258. 10.1016/0378-1119(85)90047-2.PubMedView ArticleGoogle Scholar
- Yang Z: PAML4: A program package for phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007, 24: 1586-1591. 10.1093/molbev/msm088.PubMedView ArticleGoogle Scholar
- Yang Z, Nielsen R: Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol. 2000, 17: 32-43. 10.1093/oxfordjournals.molbev.a026236.PubMedView ArticleGoogle Scholar
- Yang Z: Maximum Likelihood Estimation on Large Phylogenies and Analysis of Adaptive Evolution in Human Influenza Virus A. J Mol Evol. 2000, 51: 423-432.PubMedGoogle Scholar
- Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 1997, 13: 555-556.PubMedGoogle Scholar
- Yang Z: PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol Biol Evol. 2007, 24: 1586-1591. 10.1093/molbev/msm088.PubMedView ArticleGoogle Scholar
- Gu X: Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol. 1999, 16: 1664-1674. 10.1093/oxfordjournals.molbev.a026080.PubMedView ArticleGoogle Scholar
- Gu X: A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. Mol Biol Evol. 2006, 23: 1937-1945. 10.1093/molbev/msl056.PubMedView ArticleGoogle Scholar
- Liu Q, Wang H, Zhang Z, Wu J, Feng Y, Zhu Z: Divergence in function and expression of the NOD26-like intrinsic. BMC Genomics. 2009, 10: 313-10.1186/1471-2164-10-313.PubMedPubMed CentralView ArticleGoogle Scholar
- Liu Q, Zhu H: Molecular evolution of the MLO gene family in Oryza sativa and their functional divergence. Gene. 2008, 409: 1-10. 10.1016/j.gene.2007.10.031.PubMedView ArticleGoogle Scholar
- Wang M, Wang Q, Zhao H, Zhang X, Pan Y: Evolutionary selection pressure of forkhead domain and functional divergence. Gene. 2009, 432: 19-25. 10.1016/j.gene.2008.11.018.PubMedView ArticleGoogle Scholar
- Kong H, Landherr LL, Frohlich MW, Leebens-Mack J, Ma H, dePamphilis CW: Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. Plant J. 2007, 50: 873-885. 10.1111/j.1365-313X.2007.03097.x.PubMedView ArticleGoogle Scholar
- Cannon SB, Mitra A, Baumgarten A, Young ND, May G: The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 2004, 4: 10-10.1186/1471-2229-4-10.PubMedPubMed CentralView ArticleGoogle Scholar
- Yu J, et al: The genomes of Oryza sativa: a history of duplications. PLoS Biol. 2005, 3: e38-10.1371/journal.pbio.0030038.PubMedPubMed CentralView ArticleGoogle Scholar
- Simillion C, Vandepoele K, Van Montagu MC, Zabeau M, Van de Peer Y: The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2002, 99: 13627-13632. 10.1073/pnas.212522399.PubMedPubMed CentralView ArticleGoogle Scholar
- Du J, Tian Z, Sui Y, Zhao M, Song Q, Cannon SB, Cregan P, Ma J: Pericentromeric Effects Shape the Patterns of Divergence, Retention, and Expression of Duplicated Genes in the Paleopolyploid Soybean. Plant Cell. 2012, 24: 21-32. 10.1105/tpc.111.092759.PubMedPubMed CentralView ArticleGoogle Scholar
- Edger PP, Pires JC: Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Res. 2009, 17: 699-717. 10.1007/s10577-009-9055-9.PubMedView ArticleGoogle Scholar
- Wu C, Washida H, Onodera Y, Harada K, Takaiwa F: Quantitative nature of the Prolamin-box, ACGT and AACA motifs in a rice glutelin gene promoter: minimal cis-element requirements for endosperm-specific gene expression. Plant J. 2000, 23: 415-421. 10.1046/j.1365-313x.2000.00797.x.PubMedView ArticleGoogle Scholar
- Duan MR, Nan J, Liang YH, Mao P, Lu L, Li L, Wei C, Lai L, Li Y, Su XD: DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein. Nucleic Acids Res. 2007, 35: 1145-1154. 10.1093/nar/gkm001.PubMedPubMed CentralView ArticleGoogle Scholar
- Maeo K, Hayashi S, Kojima-Suzuki H, Morikami A, Nakamura K: Role of conserved residues of the WRKY domain in the DNA-binding of tobacco WRKY family proteins. Biosci Biotechnol Biochem. 2001, 65: 2428-2436. 10.1271/bbb.65.2428.PubMedView ArticleGoogle Scholar
- Church GM, Sussman JL, Kim SH: Secondary structural complementarity between DNA and proteins. Proc Natl Acad Sci U S A. 1977, 74: 1458-1462. 10.1073/pnas.74.4.1458.PubMedPubMed CentralView ArticleGoogle Scholar
- Lynch M, Force A: The Probability of Duplicate Gene Preservation by Subfunctionalization. Genetics. 2000, 154: 459-473.PubMedPubMed CentralGoogle Scholar
- Lynch M, O'Hely M, Walsh B, Force A: The probability of preservation of a newly arisen gene duplicate. Genetics. 2001, 159: 1789-1804.PubMedPubMed CentralGoogle Scholar
- He X, Zhang J: Rapid subfunctionalization ccompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics. 2005, 169: 1157-1164. 10.1534/genetics.104.037051.PubMedPubMed CentralView ArticleGoogle Scholar
- Arabidopsis Genome Iniative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000, 14: 796-815.View ArticleGoogle Scholar
- Blanc G, Wolfe KH: Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution. Plant Cell. 2004, 16: 1679-1691. 10.1105/tpc.021410.PubMedPubMed CentralView ArticleGoogle Scholar
- Jiang SY, González JM, Ramachandran S: Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice. PLoS One. 2013, 8: e63551-10.1371/journal.pone.0063551.PubMedPubMed CentralView ArticleGoogle Scholar
- Severin AJ, et al: RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome. BMC Plant Biol. 2010, 10: 160-10.1186/1471-2229-10-160.PubMedPubMed CentralView ArticleGoogle Scholar
- Shiu SH, Karlowski WM, Pan R, Tzeng YH, Mayer KF, Li WH: Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell. 2004, 16: 1220-1234. 10.1105/tpc.020834.PubMedPubMed CentralView ArticleGoogle Scholar
- Blanc G, Wolfe KH: Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell. 2004, 16: 1667-1678. 10.1105/tpc.021345.PubMedPubMed CentralView ArticleGoogle Scholar
- Lynch M, Conery JS: The evolutionary fate and consequences of duplicate genes. Science. 2000, 290: 1151-1155. 10.1126/science.290.5494.1151.PubMedView ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


text:
Vishwas, Shazia unhappy with AAP, rift out in open
Differences within the Aam Aadmi Party (AAP) are out in the open, with two founding members publicly expressing displeasure over ticket distribution in the 19-month-old outfit gearing up for its Lok Sabha poll debut.india Updated: Mar 13, 2014 01:39 IST
Hindustan Times
Differences within the Aam Aadmi Party (AAP) are out in the open, with two founding members publicly expressing displeasure over ticket distribution in the 19-month-old outfit gearing up for its Lok Sabha poll debut.
India's youngest party has faced rebellion at a number of places but the grouse is common — new recruits getting priority over "old hands". Questions have also been raised about some controversial names finding way into the list of candidates. AAP has so far named 187 candidates for the 543 Lok Sabha seats.
While Kumar Vishwas took a swipe at "dirty water" flowing into "clean river", Shazia Ilmi refused to be pitted against Congress president Sonia Gandhi in Rae Bareli even after the party brass' insistence. AAP was borne out of Anna Hazare's anti-corruption stir of which Vishwas and Ilmi were a part.
Party chief Arvind Kejrwal's tweet on Tuesday that talked about "forces realigning after my attack on Modi" and "relationship getting redefined" added another twist to the simmering discontent.
In the past, Kumar has praised BJP's PM candidate Narendra Modi, who has come in for severe criticism from Kejriwal.
Vishwas, who will take on Congress vice-president Rahul Gandhi in Amethi, tweeted on Monday, "If dirty water falls into a clean river, devotees would be scared to take bath." The poet-turned-politician, said party sources, was extremely unhappy with newcomers being picked to fight elections.
He also warned the party against fielding controversial figures. While he could not be reached for comments, he told some news channels, "Yes I had certain issues with the party and I have passed them on the Arvind, and Manish Sisodia."
Ilmi is upset over not being fielded from the Capital. "I'm not contesting from Rae Bareilly(sic)...I never agreed to nor do I now...i have been denying this for last two months," she tweeted Tuesday.
Talking to reporters, she denied there was rift in the party, but conceded she wanted to contest from Delhi, and not from Uttar Pradesh, where she would be an outsider. She was keen on New Delhi seat but the party named investigative journalist Aashish Khetan, who was not even an AAP member, party sources said.
The party had to face protests when it fielded Ashutosh, a former journalist, from Chandni Chowk within days of him joining AAP.
First Published: Mar 13, 2014 01:30 IST


text:
Awareness- Maya Freelon Assante
Maya Freelon Asante looks at global issues, including war, poverty, waste, beauty, and aging, and makes works which demonstrate her passion to share about these issues. She takes tissue paper, uses water to transfer the pigments onto another paper, and the presses. She makes Tissue Ink Monoprints which look at deterioration and the idea of us staining our history and future.
Process- Week of 5/23/16
Finished last project! very relieved. Happy with how it turned out but wish i had prepared more fabric to have made the bottom have thicker.
Process- Week of 5/16/16
More work, its going slow but i like how it looks.
I visited the VMFA with friends just for the fun of it and was drawn to the exhibit on women from abstract expressionism. I remember really enjoying learning about this movement in class, and so it was neat to get to see a different focus of this movement and see pieces in person. I noticed that the colors used seemed to be more dull or timid than many of what I remember we looked at in class, which was interesting. Much more pastel and muted colors than i was expecting. Part of this could have just been which pieces were specifically chosen, and so i think planning an exhibition is a relay important step of displaying artwork and a message.
Process- Week of 5/9/16
Started next project. Excited as to how it might work out. Cut, died, and started tying fabric.
Awareness- Paul Anthony Smith
Paul Anthony Smith works with mixed media to create unified works. He uses printmaking and sculpture in combination with his photography to create interesting works. His pieces come from inspiration from his home country, Jamaica, transforming images of his community in the process.
Connect- Talking Politics
The role which art can play in politics and politics can play in art is one which is fluid and yet very rarely transparent. While there is often a connection, it can be difficult to tell what role art should play in political world. Talking Politics 2008, is an article which takes 6 artists connected to politics through their art of varied backgrounds, and leads them in an open discussion about the role art plays in the world, specifically in relation to politics.
One of the main themes that came out of this article was the growing nature of the connection between aesthetically pleasing and social commentary artwork. These artists have found that they overlap, its rarely just one or the other. One mentioned that "visual art's aesthetic dimension helps clarify its meaning." (Talking Politics 2008, pg 3) The connection between the two is valid, and is essential for greater understanding now, as well as to serve as documentation for the future. Artists recognize that they must be smart in how they present their piece, making it visually interesting so people will then spend the time to get involved with the work and determine deeper meaning from it. This concept really made me think about how much art might have been made in the past, that had a good meaning, but lacked the pizzazz for the piece to be considered later in history. I felt like there was also interesting commentary in the article about the art market, and sales. Art has to be profitable, and sometimes I think an artist must choose between their values and being successful. If the rest of the world feels a certain way, it's easier for artists to fit in, rather than find a way in.
Earlier in the year we read an article about protest art. In one of Jimmy Howerton's articles in response from Q1, he really mentions some ideas which connect to those mentioned in this article. He mentions how many news stations are sectioned out on what they report on based on their political standing. That people avoid others opinions, causing us to become more polarized. I feel like that idea is mentioned in this, when the artists are talking about selling work. If you give in to the wants of a group of people, and only make art for them, you can be successful. But is it worth it to give up what you value? Art is "highly monetized" (pg 5) and people will sometimes make art just to make money, like with protest art and the news stations who streamline their opinions to only fit their viewers' ideals.
Overall, I think the article did a great job in giving readers a variety of perspectives. At sometimes it was difficult to read due to the nature of the open table, but it was informative. I think the art world really needs to think about, moving forward, the reason why we should create art. It should ahve a purpose, one that encourages discussion and questioning, rather than simply agreeing and staying safe on your side of the court.
Process- Week of 4/18/16
Got lots done on my home project. Like how it turned out. I really like the texture, but wish I had spent more time on the colors.
Process- Week of 4/11/16
Finished up 2nd Q3 project. I like how this turned out, wish it were a little longer or had more fabric.
Awareness- Susie Ganch
Susie Ganch is American born to Hungarian parents. Her work consists of things from small intricate jewelry, to large filling sculptures. Her sculptures are large, and are made of lots of tiny pieces assembled together. She lives in Richmond now, and works as a teacher, sculptor, and jeweler. Her work focuses on permeability and interconnectedness.
Charlotte Wilmouth, born and raised in Richmond, VA. This site is for my work and things which inspire me to try something new. This is a blog for my art.
May 2016


text:
We service the Greater New Jersey Area providing Mold inspections,air and surface testing, VOC testing,water screening and Sanitization plans. All inspections done by a CMI(certified Mold Inspector).
EIS uses the latest and best technology available for our testing services to ensure our customers receive the most accurate results they deserve. All testing is done by certified laboratories that provide accurate and professional analysis.
EIS is family owned and operated, fully insured, and provides all results in writing including lab report. All interactions between EIS and their customers are 100% confidential. Immediate service, call today.
Sign up to hear from us about specials, sales, and events.
683 gallows hill rd, Cranford, NJ 07016, US
Monday - Friday: 9am - 5pm
Saturday: By appointment
Sunday: Closed
If customers can't find it, it doesn't exist. Clearly list and describe the services you offer. Also, be sure to showcase a premium service.
Having a big sale, on-site celebrity, or other event? Be sure to announce it so everybody knows and gets excited about it.
Are your customers raving about you on social media? Share their great stories to help turn potential customers into loyal ones.
Running a holiday sale or weekly special? Definitely promote it here to get customers excited about getting a sweet deal.
Have you opened a new location, redesigned your shop, or added a new product or service? Don't keep it to yourself, let folks know.
Customers have questions, you have answers. Display the most frequently asked questions, so everybody benefits.


text:
Assistant Professor - Marketing - Behavioural Research
Job description
Requisition Title: Assistant Professor - Marketing - Behavioural Research - 1802940
The Rotman School of Management at the University of Toronto invites applications for a full-time tenure-stream appointment in Marketing specializing in Behavioural Research. The appointment will be at the rank of Assistant Professor and will commence July 1, 2019.
Applicants for this position must have a Ph.D. in Marketing or a related discipline or be near completion by date of appointment or shortly thereafter. In addition, applicants must have a strong theoretical and methodological background in Behavioural Research, typically with training and interest in psychology, and an ability to apply this knowledge to important questions and issues in Marketing.
We seek individuals with demonstrated excellence in research and creative professional work, and a demonstrated excellence for teaching.
For this position, excellence in research is evidenced primarily by the quality of the submitted dissertation, the job market paper or a research pipeline that is at high international levels, presentations at top conferences, presenting research at other highly ranked schools and other documents submitted for review, as well as strong letters of reference from referees of high standing. The successful candidate for this position is expected to pursue independent, innovative research at the highest international level, and to publish articles in internationally recognised top-tier academic journals in the field of Marketing. Individuals that can publish or have been previously published in the Journal of Consumer Research, the Journal of Marketing Research, Marketing Science, Management Science, and the Journal of Marketing and journals of similar calibre and international standing are preferred. Other noteworthy activities in Marketing that contribute to the visibility and prominence of the discipline are assets.
In addition, published articles in internationally recognised top-tier academic journals in the field of psychology are an asset.
Applicants should have a demonstrated excellence for teaching, as evidenced by a strong ability to integrate both theory and practice through effective communication and presentation skills, and previous experience with graduate supervision or a willingness to undertake graduate supervision, engaging activities that will stimulate and challenge the intellectual capacity of faculty and students, and a demonstrated mastery of his or her subject area. Evidence of teaching experience may include a record of prior teaching experience but can also be assessed by the quality of the invited classroom presentation exhibited by the candidate.
Select applicants will be invited to present their research at the Rotman School to faculty and students.
The Rotman School of Management has a strong research oriented faculty that is supportive of serious scholarship and committed to the professional development of its faculty. Within the University of Toronto the Area has close ties with the departments of Psychology, Statistics and Economics. All Rotman Marketing Ph.D. students complete graduate level courses in at least one of these departments. The Marketing Area provides a stimulating and supportive research environment and a strong commitment to excellence in both research and teaching.
Salaries are competitive and commensurate with qualifications and experience.
U of T is Canada's largest university and has an international research reputation. The Rotman School operates an undergraduate Commerce program, a Graduate Diploma in Professional Accounting, a full-time, part-time and executive MBA program, a Master of Finance, a Master of Financial Risk Management, and a Ph.D. program.
Rotman is situated in the heart of Canada's corporate and financial centre, and the world's most diverse city. Rotman's core values reflect this diversity and, as such, we have a preference for candidates with demonstrated experience and interest in promoting a diverse and inclusive research and teaching environment. For more information about the Rotman School and its core values, please visit: http://www.rotman.utoronto.ca/Connect/AboutRotman/OurValues
Applications must be submitted online using the link below. No paper applications or supporting documents will be accepted. Applicants must submit a curriculum vitae, cover letter, a research statement, job market paper, sample publications (if any), and a teaching statement.
By the closing date, August 13, 2018 applicants should arrange to have three letters of reference (on letterhead, signed and scanned) sent directly via email by the writers to:
Nitin Mehta
Area Coordinator and Chair Recruiting Committee Marketing
Rotman School of Management
University of Toronto
Email: [email protected]
Please note: Submission guidelines can be found at: http://uoft.me/how-to-apply.
All applications must be received online by August 13, 2018.
The University of Toronto is strongly committed to diversity within its community and especially welcomes applications from racialized persons/persons of colour, women, Indigenous/Aboriginal People of North America, persons with disabilities, LGBTQ persons, and other who may contribute to the further diversification of ideas.
As part of your application, you will be asked to complete a brief Diversity Survey. This survey is voluntary. Any information directly related to you is confidential and cannot be accessed by search committees or human resources staff. Results will be aggregated for institutional planning purposes. For more information, please see http://uoftme/UP.
All qualified candidates are encouraged to apply; Canadians and permanent residents will be given priority.
Job Field: Tenure Stream
Faculty / Division: Joseph L. Rotman School of Management
Department: Rotman School of Management
Campus: St. George (downtown Toronto)
Job Posting: Jul 5, 2018
Job Closing: August 13, 2018, 11:59pm EST