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The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually-recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic/genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) and higher levels of SNVs than those reported for humans, plants, and P. infestans. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single nucleotide variant (SNV) sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.
Phytophthora capsici is a virulent, hemibiotrophic pathogen of vegetable crops, inflicting significant losses worldwide (Leonian 1922; Erwin and Ribeiro 1996; Gevens et al. 2008; Lamour and Kamoun 2009; Meitz et al. 2010; Lamour et al. 2011). It's main hosts are peppers and cucurbits and during the last ninety years P. capsici has spread geographically as agricultural cultivation of these hosts has intensified; dynamically adapting to fungicides and new hosts (Leonian 1922; Erwin and Ribeiro 1996; Lamour and Hausbeck 2001; Hausbeck and Lamour 2004; Gevens et al. 2008; Hurtado-Gonzales et al. 2008; Lamour and Kamoun 2009; Meitz et al. 2010; Lamour et al. 2011; Gobena et al. 2012). Like other members of this destructive genus (e.g. the late blight pathogen P. infestans and the sudden oak death pathogen P. ramorum), P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts (Lamour and Hausbeck 2001; Hausbeck and Lamour 2004; Lamour and Kamoun 2009) (Fig. 1B–G). In addition, P. capsici often features meiosis between two mating types, producing thick-walled oospores that remain dormant for years, making it very difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation (Fig. 1A). Members of this genus are notoriously plastic in field and laboratory scenarios and we examined the molecular basis for rapid adaptation in P. capsici through genome sequencing, development of a high-density genetic map, and integrative genomic/genetic characterization of P. capsici field isolates and intercross progeny. Development of these tools and subsequent analyses revealed significant mitotic loss of heterozygosity (LOH) in clonally propagated field isolates as well as multiple sexual progeny. Follow-up tests revealed a strong association of LOH with changes in mating type and loss of pathogenicity.
Assembling the nuclear genome of a diploid organism with frequent nucleotide variants can be difficult and a partially inbred line of P. capsici (LT1534) was developed for sequencing (Supplementary Fig. 1) (Hurtado-Gonzales and Lamour 2009; Gobena et al. 2012). The 64 Mbp reference genome was assembled using Arachne from 30X paired and singleton 454 FLX and Titanium genomic DNA reads, 5X Sanger paired reads, 56,448 Sanger ESTs, and 1,260 full-length cDNA sequences. This resulted in 917 scaffolds and an N50 of 706 kbp (Supplementary Table 1). The size of the P. capsici genome is intermediate among the sequenced oomycetes, larger than Albugo and Pythium ultimum (up to 45 Mbp) (Levesque et al. 2010; Kemen et al. 2011), but more compact than P. ramorum, P. sojae, Hyaloperonospora arabidopsis and P. infestans at 65, 95, 100, and 240 Mbp, respectively (Tyler et al. 2006; Haas et al. 2009; Baxter et al. 2010). The P. capsici draft genome had fewer scaffolds and/or larger scaffold N50, which may reflect hybrid assembly or fewer repeat sequences in P. capsici (19%) than P. infestans, P. sojae or P. ramorum (74%, 39%, and 28%, respectively) (Tyler et al. 2006; Haas et al. 2009). Like other Phytophthora species, the majority of P. capsici repeats were retrotransposons (84%) with long terminal repeats, of which 57% were Gypsy elements. The mitochondrial genome (80,148 bp) was assembled in 4 scaffolds.
Gene model prediction using a training set of 16.4 million sequencing-by-synthesis mRNA-sequences from nine life stages predicted 19,805 genes supported by cDNA sequences (50%) or previously identified proteins (75%) (Supplementary Tables 2 and 3). After excluding 2,682 genes with homology to transposable elements, P. capsici had a similar gene content to P. infestans, P. sojae and P. ramorum (17,797, 16,988 and 14,451, respectively) (Tyler et al. 2006; Haas et al. 2009) and had slightly more core eukaryotic genes identified compared to these other species (Supplementary Fig. 2). The non-repetitive gene density in P. capsici (268/Mbp) was higher than other Phytophthora species (74/Mbp in P. infestans, 179/Mb in P. sojae and 222/Mb in P. ramorum) (Tyler et al. 2006; Haas et al. 2009).
Genome comparisons revealed almost perfect scaffold-level synteny between the gene models of P. capsici, P. ramorum and P. sojae, with very little duplication (Fig. 2A, B). There was also extensive synteny with P. infestans genes (Supplementary Fig. 3). The genome organization of P. capsici was similar to other Phytophthora species, with ⅔ of the genes located in gene-rich blocks that have a conserved order and few repeats (median intergenic distance 351 bp), separated by relatively gene-poor regions without order conservation and more repetitive sequences (median intergenic distance ~3kb; Fig. 2C) (Haas et al. 2009). Like P. infestans, the 365 predicted P. capsici genes without a homolog resided predominantly in gene-poor genomic regions (Fig. 2C) (Haas et al. 2009; Raffaele et al. 2010).
Seventy eight percent of the predicted P. capsici genes clustered into 2,483 candidate multigene families. Among these families, there are cytoplasmic effector genes of the RxLR type including homologs of known avirulence genes in P. infestans (Whisson et al. 2007; Dou et al. 2008; Boutemy et al. 2011). P. capsici had 357 RxLR effector genes, which is a similar to the numbers reported for P. sojae and P. ramorum, whereas P. infestans had > 500 (Tyler et al. 2006; Haas et al. 2009). Phytophthora capsici also had 29 putative full length and 70 pseudogenes for Crinkling and Necrosis (CRN) effectors, an ancient class of intracellular effector proteins that share a highly conserved N-terminal domain, required for translocation, and diverse C-terminal effector domains (Haas et al. 2009). While markedly fewer than in P. infestans, the majority of predicted CRN effector domains were conserved between species.
Nucleotide diversity was assessed in seven P. capsici field isolates (including parental isolates TN1 and TN2) and an isolate of the sister species P. tropicalis by restriction-site associated DNA (RAD) sequencing (Supplementary Table 4) (Baird et al. 2008). Between 5 and 9 million sequencing-by-synthesis reads, flanked by a SgrAI restriction site, were generated per isolate (Table S5). The reads were aligned to the P. capsici reference genome and covered ~2.3 Mbp at a depth of ≥30-fold (Kim et al. 2009; Baranzini et al. 2010; Bell et al. 2011). The SNV density among P. capsici isolates was 23.4/kb (range 16.9 – 25.9/kb) and between P. capsici and the closely related species P. tropicalis was 51.7/kb (Supplementary Tables 6 and 7; Supplementary Figs. 4 and 5). This is much higher than the SNV diversity observed among P. infestans strains (0.65/Kb average) and between P. infestans T30-4 and species in its clade (7.67/Kb average) (Raffaele et al. 2010). The nucleotide diversity (π) was 0.012 (range 0.009 – 0.016), ~16-fold higher than H. sapiens and ~4-fold higher than obtained by RAD in natural stickleback populations and most outbred plant species. The threespined stickleback (Gasterosteus aculeatus L.) is an outcrossing species of fish studied to better understand adaptive evolution (Hohenlohe et al. 2010).
In addition, the inheritance of SNV's was examined in 65 putative F1 intercross progeny by PstI-based RAD (Supplementary Figs. 1 and 6; Supplementary Table 8). Of these 65 isolates, two were found to be clonally derived from the TN2 parent and three additional isolates were clonal to progeny isolates. The remaining 60 true F1 progeny were genotyped at bi-allelic sites exhibiting either a di- or tri-modal distribution where the peaks corresponded to homozygous reference alleles, heterozygotes, and homozygous alternate alleles (Supplementary Fig. 7) (Kim et al. 2009). Genotypes were imputed at 500,352 nucleotides with ≥10 uniquely aligned reads in ≥55 progeny. Homozygosity was inferred when >90% reads displayed one allele, and heterozygosity when 20–80% of reads displayed one allele. We have previously shown such genotype imputation to be >99% accurate (Kim et al. 2009; Baranzini et al. 2010; Bell et al. 2011). Forty-five percent (9,254) of SNVs showing Mendelian inheritance were in coding regions, and 3,382 (37%) of these were non-synonymous (Supplementary Fig. 8a, Supplementary Table 10). The distribution of mutations in Phytophthora clade 1c species is in a similar range with 35% of SNV's in coding regions, 41% of which are non-synonymous (Raffaele et al. 2010). This was surprising since there is typically extensive purifying selection on genes. A parsimonious explanation of these findings is that rates of mutation relative to generation times are much greater in P. capsici than higher eukaryotes.
A total of 20,568 SNVs were either polymorphic in the parents and had Mendelian segregation (χ2≥0.05), or were homozygous for opposite alleles in the parents and heterozygous in progeny that did not exhibit loss of heterozygosity (LOH) (marker spacing 3,111 bp; Supplementary Table 9). A genetic map was developed using markers on the 108 scaffolds that had sufficient SNVs for independent genetic linkage analysis in the F1 progeny. Of these, 92 scaffolds had SNV's that were inherited as a single co-segregating block, while markers on 15 scaffolds broke into 2 blocks and markers on the largest scaffold (Scaffold 1) broke into three blocks (Supplementary Table 11; Supplementary Fig. 9). Scaffold-level linkage groups were inherited with LOD scores of ≥7. Following scaffold-level linkage analysis, a genetic map of P. capsici was constructed with 1,136 SNVs that had segregation patterns <95% similar. The genetic map was 1,654 centiMorgans (cM) in length and comprised eighteen linkage groups accounting for 84% (54Mbp) of the reference genome and containing ~90% of the predicted genes (Fig. 3; Supplementary Table 12). The order for the majority of markers was the same on the genetic and physical maps. Genetic linkage analysis localized the mating type locus to a ~300kb critical region on scaffold block 4.1 in LG10.
Integrated genomic and genetic analysis allowed assessment of chromosomal variation among the 65 putative F1 intercross progeny. Twenty-three F1 isolates and two clonal isolates contained regions with LOH. LOH was identified by homozygosity at all markers in ≥ 2 adjacent (linked) RAD sequences that were incompatible with parental genotypes (Supplementary Fig. 10; Supplementary Table 13). The minimum length of LOH tracts varied from 299 bp to >1 Mbp. LOH occurred in 14 of the 18 LGs and in 59 scaffolds or scaffold blocks. Fifty-four percent (11,048) of SNVs exhibited LOH in at least one isolate and the LOH was bidirectional. The frequency and distribution of LOH tracts varied among isolates and 36.5% (19.7 Mbp) of the genome was affected by LOH in at least one isolate. Two isolates (TN37 and TN47) had LOH exceeding 10% of the genome (Supplementary Table 14). Interestingly, LOH showed bias toward gene-rich regions (Supplementary Fig. 8B, C). Given the requirements of informative parental genotypes, at least two adjacent RAD tags to be affected, and that LOH was sought only in the mapped genome, the true extent of LOH is likely to be considerably higher.
Sub-chromosomal mitotic LOH has several molecular mechanisms including deletions (resulting in hemizygosity) and translocations (resulting in homozygosity) associated with homologous and non-homologous recombination or gene conversion (Chamnanpunt et al. 2001; Cvitanich et al. 2006). Of note, mutagenesis-induced LOH in P. capsici was not associated with sub-chromosomal deletions (Hulvey et al. 2010). In only one of 12 isolates was LOH due to hemizygosity as assessed by batched, normalized sequence coverage plots (Bell et al. 2011) (Fig. 4A–C). Forty-five percent (4,967) of the marker nucleotides exhibiting LOH were exonic, 17% (1,911) were in coding regions and 3.5% (391) were predicted to be non-synonymous, affecting 264 genes. Phenotypic consequences of genome diversity were sought among F1 progeny. Five F1 isolates switched mating type from A2 to A1 between assessments in 2005 and RAD sequencing in 2010, while one switched from A1 to A2 (Fig. 5A). Isolates were in storage for most of this interval and were sub-cultured < 10 times. Four of the isolates that switched from A2 to A1 had >800 Kbp tracts of LOH encompassing a region that appears to contain the mating type locus (or loci) on LG10 (Fig. 5A). TN25, which changed from A1 to A2, did not exhibit LOH at the mating type locus but did have >1.6 Mbp LOH in LG16. However, A1 mating type isolates TN37 and TN70 had similar LOH on LG16, but did not change mating type. Thus, LOH at the mating type locus was associated with mating type switch in four of six isolates.
LOH was also associated with a loss of pathogenicity to pepper and cucumber fruit. Between tests in 2005 and 2011, progeny isolates TN37 and TN47 became unable to infect wounded or un-wounded fruit (Fig. 5B). In 2011, host cells consistently elicited a strong hypersensitive response (cell necrosis) at point of inoculation, suggesting loss of a factor necessary for infection, such as an Avh protein. This is characteristic of Phytophthora Avh proteins, which evolve rapidly in a presumed host-pathogen arms race (Tyler et al. 2006; Whisson et al. 2007; Jiang et al. 2008; Haas et al. 2009). These isolates had similar growth rates in vitro in 2005 and 2011 even after substantial LOH (Supplementary Table 14). Indeed, the TN37 and TN47 genomes each had > 10% LOH and share an LOH tract on LG1 (17_31,860 – 17_870,195 and 105_51,382 – 105_63734; Supplementary Tables 13–14). A plausible explanation is that LOH changed the expression or expressed sequence of one or more P. capsici effectors in the avirulent isolates.
In summary, the genome sequence of P. capsici was typical for the genus in organization and gene content. A prototypical, dense genetic map indicated the recombination rate of P. capsici to be 38.7 kbp/cM, an order of magnitude less than yeast, but 30-fold higher than H. sapiens (Li and Freudenberg 2009). SNV density and diversity among P. capsici genomes was much higher than in other eukaryotes and coding and non-synonymous variants were remarkably common. This suggests that germline mutation rates may be much higher in P. capsici than in H. sapiens, Saccharomyces cerevisiae, Drosophila melanogaster and P. infestans, or that purifying selection was less (Baranzini et al. 2010). The overall SNV diversity for the seven P. capsici field isolates was similar, but markedly different from the P. tropicalis isolate. The isolates from Peru and Argentina appear to be part of long-lived, widely dispersed clonal lineages where, unlike the situation for the North America isolates, sexual recombination may be rare (Hurtado-Gonzales et al. 2008; Gobena et al. 2012). Interestingly, the isolates from Peru and Argentina share the most polymorphic loci and may be derived from a common, invasive population or widely dispersed clonal lineage. The high level of SNV diversity in P. capsici has practical implications for research. The SNV's can be used to finely map segregating phenotypes in larger populations of progeny, conduct sensitive analyses of population structure and overall dynamics, and to track the fate of numerous heterozygous loci during asexual growth (e.g. tracking LOH).
Phytophthora capsici populations are often characterized by high levels of diversity and rapid adaptation (Leonian 1922; Erwin and Ribeiro 1996; Lamour and Hausbeck 2001; Hausbeck and Lamour 2004; Gevens et al. 2008; Hurtado-Gonzales et al. 2008; Lamour and Kamoun 2009; Meitz et al. 2010; Lamour et al. 2011; Gobena et al. 2012). In addition to elevated genetic diversity, P. capsici genomes also had a remarkably high frequency of mitotic LOH occurring more commonly in gene rich areas. Mitotic genomic instability was also recently described in P. ramorum (Vercauteren et al. 2011), suggesting LOH may be a general characteristic of oomycetes. Here we show loss of pathogenicity and mating type switches are likely phenotypic consequences of mitotic LOH. For the latter, the evidence for causality of LOH was strong: four of five progeny that switched from the A2 to the A1 mating type had tracts of LOH spanning the region where mating type maps in this cross. This was reminiscent of the mating type locus in the fungus Candida albicans, where a repressor suppresses switching to the mating-competent form (Morschhauser 2010). Loss of mating type heterozygosity relieves this repression, ensuring that only mating type homozygous cells are mating-competent. An ability to switch mating type has important consequences, particularly in northern latitudes where survival of the winter or fallow months requires thick-walled, sexually-produced oospores (Lamour et al. 2011). It also provides a mechanism to introgress mutations efficiently into a population (Supplementary Figure 10). The fungicide mefenoxam, for example, is strongly inhibitory to P. capsici and has been widely used in some areas. Mefenoxam resistance is inherited in P. capsici as a single incompletely dominant trait (Lamour and Hausbeck 2000; Lamour and Hausbeck 2001). Mating type switches in a rare, partially resistant field isolate will double the chances for outcrossing. In addition to aiding introgression of a novel resistance allele by sexual reproduction, LOH could directly catalyze the conversion to full resistance. Using the SNV markers presented here, it should be possible to detect instances of LOH within naturally occurring isolates.
The dramatic expansion of repeated sequences observed in several pathogen lineages of oomycetes (P. infestans, H. arabidopsidis) and fungi (Puccinia graminis f. sp. tritici, Melampsora larci-populina, Blumeria graminis) was proposed to contribute to fast adaptation (Haas et al. 2009; Spanu et al. 2010). A clear correlation was indeed observed between the rate of gene evolution and the amount of flanking repeats (Raffaele et al. 2010). By contrast, the P. capsici genome is rather compact, with a relatively low repeat content, and yet shows remarkable plasticity. This plasticity may be due in part to LOH which represents an alternative mechanism for rapidly generating diversity, preferentially affecting gene dense regions. Previous studies suggest a role for LOH in adaptive evolution (Rosenberg 2011). It has, for example, been associated with oncogenesis and embryonic stem cell adaptation in H. sapiens (Narva et al. 2010), and fluconazole resistance in C. albicans (Forche et al. 2011). Here we extend these observations, suggesting that the co-occurrence of frequent mitotic LOH and high nucleotide diversity in genes may provide a general mechanism for rapid adaptation in P. capsici. In addition, LOH may contribute to the difficulties encountered when studying oomycetes in the laboratory (e.g. loss of pathogenicity and virulence) and the overall success of oomycetes as plant pathogens.
Three in vitro crosses were completed to produce a moderately inbred isolate for sequencing the reference genome (Hurtado-Gonzales and Lamour 2009). Crosses include an F1, and two recurrent backcrosses (BC1 and BC2). An isolate from the BC2 progeny was chosen for genome sequencing based on growth rate and asexual and sexual spore production (Hurtado-Gonzales and Lamour 2009). The initial cross was between an A1 isolate recovered from cucumber in Michigan in 1997 (TN1) and an A2 isolate recovered from pumpkin in Tennessee in 2004 (TN2). The backcrosses were to the TN2 parent. Crosses were made by co-culturing the parental isolates on V8-juice agar plates, incubating the plates for 8 to 12 weeks in darkness, and then separating the sexual oospores from the subtending asexual mycelium and other asexual spores (sporangia and zoospores) through mechanical shearing and an enzyme treatment to destroy the asexual material (Lamour and Hausbeck 2000). The enzymes not only destroy the asexual material; they stimulate oospore germination. Germinating oospores were harvested using a 5μl pipette while looking at the spores under a light microscope. Once harvested, the germinated spores are placed onto V8 media, sub-cultured to produce mycelium for DNA and to conduct mating type analysis, and then stored long term (3 to 5 years) in water with sterile hemp seeds.
The progeny from all of the crosses were genotyped using AFLP markers, tested for mating type, assessed for growth rate on agar media, and assayed for pathogenicity and virulence on detached pepper (variety Early Jalapeno) and cucumber fruit (various varieties) (Hurtado-Gonzales and Lamour 2009). All fruit inoculations were conducted on two fruit and the experiments repeated twice. Pathogenicity was assessed by placing a 7mm plug of mycelium at both a wounded and non-wounded site. Wounded sites are distal and non-wounded sites proximal to the stem end of the fruit. Pathogenicity to pepper fruit was assessed in 2005 and 2011. Sixty-nine progeny from the F1 were further analyzed using a focused re-sequencing strategy (outlined below). In addition, the mating type was tested at three different time intervals: within 6 months of the cross, at the time of the focused re-sequencing, and one year following the re-sequencing.
High quality genomic DNA was prepared from the isolate selected for genome sequencing using a phenol/chloroform protocol. Aliquots from the same batch of DNA were submitted to 454 Inc. (Branford, CT) and to the Joint Genome Institute (JGI, Walnut Creek, CA) for 454- and Sanger-based sequencing, respectively. A total of 2,451,737 random shotgun genomic reads, 2,022,402 paired-end reads (2.3 Kb), and 833,606 paired-end reads (18.0 Kb) were produced using the 454 Titanium chemistry. In addition, 197,306 random genomic paired-end reads from a 6.3Kb plasmid library, 146,588 paired-end reads from a 34.7Kb fosmid library and 65,000 ESTs were produced at the JGI using Sanger sequencing. Additionally, 1,260 full-length cDNA sequences were generated by Sanger sequencing and cDNA sequence assembly.
The sequence reads were assembled using a modified version of Arachne v.20071016 (Jaffe et al. 2003) with parameters maxcliq1=100, n_haplotypes=2 and BINGE_AND_PURGE=True. The output of this assembly was passed through Rebuilder and SquashOverlaps with parameters to merge adjacent assembled alternative haplotypes, and subsequently run through another complete Arachne assembly process to finalize the assembly. Prior to assembly, redundant 454 pairs (defined as at least 98% identical across their length) were removed and a single pair retained. An error correction step was applied to all 454 data that attempted to set bps to equal the Sanger sequence. This was accomplished by shredding the Sanger sequence to a similar size as the 454 reads and then aligning these shredded reads and the 454 simultaneously. Where the 454 read sequence had no support we changed the 454 read sequence to match the Sanger read sequence. This removed many of the 454 sequence errors (primarily indels and occasional bp substitutions) and coalesced the haplotyopes if the Sanger data was all from one haplotype. Error correction was also applied during the Arachne assembly process by screening each scaffold against bacterial proteins, organelle sequences and GenBank using Megablast against Genbank NR and blastp against a set of known microbial proteins. Twenty-eight scaffolds identified as prokaryotic contamination were removed. We classified additional scaffolds as mitochondrion (4), small repetitive (6), alternative haplotyope (17), and less than 1kb (1050). The final assembly consists of 971 scaffold sequences, with half of the genome contained in 29 scaffolds of at least 705.7 kb in length and contigs greater than 34.6kb. Scaffolds ranged in size from 1 kb to 2.1 Mb with an N50 of 705.7 kb (Supplementary Table 1). The genome size was tested using the approach outlined by Baxter with nt by nt coverage calculated by aligning back to the reference (Baxter et al. 2010). This resulted in an estimated genome size of approximately 55 Mbp. We also estimated the genome size by measuring the percentage of all reads that were captured by the assembly using a high quality 10,000 read subset (average quality >= 35, length >= 100 and no missing bases) and extrapolating genome size if the assembly had captured all the reads. We extrapolated up from the genome size that doesn't include gaps (56.1 Mb) and 97.44% of the reads were captured leading to an estimated genome size of approximately 57 Mbp. Both estimates likely underestimate the genome size due to over alignment of repeat copies, possibly explaining the discrepancy between our gapped genome size (64.1 Mb) and these lower estimates of total genome size. Nevertheless, both estimates are similar to the non-gapped genome size (56.1 Mb) suggesting that the assembly is missing very little of the non-repetitive genome.
In addition, total RNA was isolated from different growth conditions (rich media, starvation, and sporulating), pooled, and submitted to both 454 and the JGI for Sanger cDNA and EST sequencing. At the JGI, ESTs were produced as previously described with the following modification: 2 cDNA libraries were constructed and sequenced and the size ranges of the cDNA library inserts were 0.6k–2kb and >2kb (Jeffries et al. 2007).
The genome assembly of Phytophthora capsici LT1534 was annotated using the JGI Annotation Pipeline, which combines several gene predictors: A) cDNA-based gene models were derived from 1260 full-length cDNAs and 11,090 consensus sequences clustered from 56,448 ESTs, and then mapped to genomic sequence, B) protein-based gene models were predicted using FGENESH+ (Salamov and Solovyev 2000) and GeneWise (Birney et al. 2004) seeded by BLASTx alignments of genomic sequence against sequences from the NCBI non-redundant protein set nr, and C) ab initio gene models were predicted using FGENESH trained on the set of putative full-length genes and reliable protein-based models. GeneWise models were completed using scaffold data to find start and stop codons. ESTs, EST clusters, EST contigs, and full length cDNAs were used to verify, complete, and extend the gene models. Because multiple gene models per locus were often generated, a single representative gene model for each locus was chosen based on homology and EST support, and used for further analysis. This led to a filtered set of 19,805 gene models (including 2,682 genes with homology to transposable elements) with their properties and support by different lines of evidence summarized in Supplementary Tables 2 and 3. All gene-based analyses were done on the full 19,805 gene set. A total of 56,448 ESTs are available in Genbank under the title "DOE Joint Genome Institute Phytophthora capsici EST project". An additional 1260 full length cDNAs are available in Genbank under the title "DOE Joint Genome Institute Phytophthora capsici cDNA project". The genome sequence is available at http://genome.jgi-psf.org/Phyca11/Phyca11.home.html.
All predicted gene models were functionally annotated by the JGI Annotation Pipeline using InterProScan (Zdobnov and Apweiler 2001) and hardware-accelerated double-affine Smith-Waterman alignments (http://www.timelogic.com/) against highly curated databases such as SwissProt (Bairoch et al. 2005), KEGG (Ogata et al. 1999), and Pfam (Bateman et al. 2004). KEGG hits were used to map EC numbers (Bairoch 2000), and InterPro, KEGG, and SwissProt hits were used to map GO terms (Ashburner et al. 2000). In addition, predicted proteins were annotated according to KOG classification (Koonin et al. 2004). Protein targeting predictions were made with signalP (Nielsen et al. 1999) and TMHMM (Krogh et al. 2001). Finally, all proteins were aligned by BLASTp to proteins in nr and to each other; after the latter analysis the alignment scores were used as a distance metric for clustering by MCL (http://www.micans.org/mcl/) into a first draft of 2,483 candidate multigene families. The same method was used to group genes with those of other Phytophthora species. We used BLASTP to identify Crinkler (CRN) coding genes from the P. capsici gene model set (Supplementary Table 16). For this purpose, 16 well characterized CRN proteins from P. infestans were searched against the P. capsici protein data set. Sequences with significant hits (E= <10-5) were retrieved and a non-redundant CRN-like protein set was created (Win et al. 2006). CRN-like protein sequences were manually examined for the presence of LFLAK motifs and C-terminal effector domains. To determine whether candidates are full length or pseudogenes, we aligned our CRN candidates with previously characterized CRNs. CRN proteins of at least 250 amino acid residues or more and that aligned with both the N and C-terminal domains of PiCRNs were considered full length (Haas et al. 2009). Finally, we used SignalP3.0 to identify predicted secretion signals for all CRN candidates (Supplementary Table 16). Candidate RxLR effectors were mined via the protocol outlined previously (Haas et al. 2009). In brief, all open reading frames greater than 210 nucleotides (70 AA) from the genome were generated and translated to amino acid coding sequences. Those containing an RXLR ( Arg - Anything - Leu - Arg) between 30 – 60 amino acids from the start, a signal peptide score greater than .9, and a cleavage site prior to the RXLR are considered effectors (Supplementary Table 17).
The CEGMA pipeline was used to compare the completeness and continuity of six Oomycete genomes (Parra et al. 2007). CEGMA checks the completeness and continuity of genome assemblies on the basis of 248 core eukaryotic genes. Here, we compared the CEGMA analyses (without KOG 69) for the genomes of P. sojae, P. ramorum, P. infestans, Pythium ultimum, and Hyaloperonospora arabidopsis to the draft genome of P. capsici reported here (Supplementary Table 15).
Transposon-like coding sequences were identified by searching the annotated protein-coding sequences of P. capsici against databases of transposon sequences with TransposonPSI (http://transposonpsi.sf.net). Nucleotide sequences corresponding to the coding regions of the annotated protein coding genes were searched against the TransposonPSI collection of transposon protein sequences using BLASTX. This included ORFs derived from mobile elements discovered in other sequenced Phytophthora genomes. In addition, the P. capsici protein sequences were searched against a collection of PSI-BLAST profiles corresponding to common families of transposable elements, including Gypsy-retrotransposons and Piggybac-transposons. Any P. capsici annotated coding sequence identified by having a BLAST E-value of at most 1e-10 was identified and reported, yielding 2,682 candidate gene annotations with transposon homology (see: Pcap.annot_transposon_mining.maxE_1e-10.txt.gz). Transposon family (PSI-BLAST) and top transposon protein BLASTX match are provided. Scaffolds, gene models clusters, and annotations thereof, may be accessed at the JGI P. capsici portal (http://www.jgi.doe.gov/capsici/) (Grigoriev et al. 2012).
Restriction site Associated DNA (RAD) sequencing was employed to identify and genotype single base substitutions in 7 field isolates (including the parents TN1 and TN2) and 69 progeny (TN3 – TN71) of the F1 cross (Baird et al. 2008). Briefly, genomic DNA was digested with the 6bp recognition restriction endonuclease PstI or the 8bp recognition SgrAI (Floragenex, Inc.). The digested DNA was sheared to between 200 and 500 bp and adaptors ligated which contained sequencing priming sites and an isolate-specific 5bp tag (Baird et al. 2008). Between 5 and 9 million sequencing-by-synthesis reads of length 72 nt were generated per isolate using an Illumina GAII sequencer (Supplementary Fig. 6, Supplementary Tables 5 and 8). The short reads abutting the restriction site are referred to as RAD tags. The RAD approach reduces complexity by focusing the sequencing to the regions directly adjacent (left and right) to a restriction site and the isolate-specific 5bp tags allow multiplexed sequencing. Reads were aligned to the P. capsici reference, covering ~2 million nucleotides at a depth of ≥30-fold (Supplementary Tables 5 and 8) (Kim et al. 2009; Baranzini et al. 2010; Bell et al. 2011).
Alignments of the RAD sequence and subsequent variant detection were carried out using the Genomic Short-read Nucleotide Alignment Program (GSNAP (Wu and Nacu 2010)) and the Alpheus pipeline (Miller et al. 2008), as described (Kim et al. 2009; Baranzini et al. 2010; Bell et al. 2011). Reads were aligned to the P. capsici genome assembly (version 11) and alignments retained that matched the genome with 95% identity or higher and that had ≤5 equally high scoring alignments. Reads with equally good hits to more than one genomic region, reflecting repeat content or redundancy in the assembly, were not considered uniquely aligned. Four isolates were excluded from analysis due to insufficient aligned reads (Supplementary Fig. 6). Read count–based allele frequencies of bi-allelic nucleotide variants had a tri-modal distribution, with peaks corresponding to homozygous reference alleles, heterozygotes, and homozygous alternate alleles (Supplementary Fig. 7) (Kim et al. 2009).
Potential segregating SNV sites were identified in the parents and progeny using the following criteria: ≥10X unique sequence coverage, an average quality score ≥20 and an alternate allele frequency ≥20% within unique reads. This pool of potential segregating sites was then analyzed across all lines and SNV genotyping criteria were developed based on a visual assessment of the distribution of alternate alleles at different levels of unique sequence coverage (Supplementary Fig. 7). SNVs were genotyped at the identified segregating SNV sites for all lines with at least 10X unique coverage where alternate allele frequency within unique reads was <10% (homozygous for the reference allele), >20% and <80% (heterozygous), or >90% (homozygous for the alternate allele). Our final pool of markers was limited to loci with 5 or fewer missing genotypes in the progeny. This approach does not enrich or bias for gene rich areas of the genome.
Nucleotide density and diversity was calculated for SNV sites in the SgrAI RAD tags from the P. capsici parents and five additional unrelated isolates (two of which represent very large clonal populations in Peru and Argentina) and a P. tropicalis isolate. Heterozygosity and homozygosity were distinguished by allele frequency cutoffs of 15% and 85% and there was no requirement for number of missing genotypes in the isolates. SNV diversity was calculated as previously described (Begun et al. 2007).
Loss of Heterozygosity (LOH) was assessed using graphical genotypes constructed by ordering the SNV loci according to (i) the genetic linkage of markers in the individual scaffolds and (ii) the genetic linkage of markers from all scaffolds together (see below). The minimum tracts of LOH were calculated for regions with continuous, uninterrupted switching of loci to either the reference or alternate allele (homozygosity) in a way that is impossible by normal meiosis or clonal reproduction (Judd and Petes 1988). To avoid minor genotyping errors, LOH was only assigned for tracts where the switched loci spanned at least two different sequencing sites. In addition, the junction of LOH versus non-LOH in an isolate with good sequence coverage was analyzed to compare the coverage on either side of the junction.
Genetic similarity of the parents and progeny was assessed in JMP Genomics by analyzing a relationship matrix for our final pool of markers using a Fast Ward Hierarchical clustering at the default settings. Alleles were assumed to be identical by descent. Putative clones were confirmed using the graphical genotypes. Genetic similarity analyses revealed three clonal lineages. One clonal lineage contained the parent isolate TN2 and the (mistaken) F1 progeny TN3 and TN50. Two other clonal lineages were derived from true F1 progeny and included isolates TN56, TN57, and TN63 in one clonal lineage and isolates TN8 and TN11 in another clonal lineage (Supplementary Fig. 11). This was not surprising since occasional sporangia survive the enzymatic treatment used to destroy asexual propagules, and premature oospore germination can produce sporangia that appear to be discrete oospore progeny. A single isolate of each lineage was retained for genetic linkage analysis. Apomixis, which occurred in other crosses stemming from these parents, is another possible explanation for the clones of the TN2 parent (Hurtado-Gonzales and Lamour 2009).
Putative segregating markers were analyzed using a Chi-square test for simple Mendelian inheritance (5% significance). A total of 20,568 SNVs were either polymorphic in the parents and had Mendelian segregation (χ2≥=0.05), or were homozygous for opposite alleles in the parents and heterozygous in progeny that did not exhibit LOH. These were used for genetic linkage analysis (average marker spacing 3,111 bp; Supplementary Table 9).
A total of 3,141 SNVs exhibited segregation ratios <5% by χ2-test. Some of these clustered in blocks and may reflect gene conversion, as described in other Phytophthora species (Chamnanpunt et al. 2001; Cvitanich et al. 2006). An additional ~100 loci were heterozygous in both parents and all progeny and may reflect assembly artifacts, copy number variants or obligate heterozygosity.
Mendelian markers were further analyzed using JoinMap 4.1 at the default settings for a CP type cross (heterogeneously heterozygous with phase unknown) (van Ooijen 2011). Initially, markers from individual scaffolds were analyzed to determine if they are inherited as a linked unit (expected if the scaffold is assembled correctly). If a scaffold broke into more than one piece, the pieces are referred to as scaffold blocks. Following this, markers from all the scaffolds, or scaffold blocks, were analyzed together to produce a linkage map. The LGs were further refined to include only markers with segregation patterns <95% similar and to exclude isolates showing any LOH within the LG. Markers are named with the scaffold number followed by the nucleotide position on the scaffold. Additional information was included for the markers used in JoinMap 4.1 to designate the three possible segregation scenarios: hk = heterozygous in both parents, nn = Parent 1 is homozygous and Parent 2 is heterozygous, and lm = Parent 1 is heterozygous and Parent 2 is homozygous.
The SNV genotyping error rates were assessed for both parents (TN1 and TN2) at 95 polymorphic sites in portions of 30 genes across 14 linkage groups by Sanger sequencing of PCR products. Of these 190 genotypes, all but 5 were confirmed. The 5 genotypes that differed occurred on a single gene that switched to homozygosity at all 5 sites.
Sequences, assembly and annotations are available via the JGI Genome Portal at http://jgi.doe.gov/capsici and at DDBJ/EMBL/GenBank under the accession ADVJ00000000.
This work was supported by grants to SFK from the National Science Foundation (05-512), US Department of Agriculture, and Joint Genome Institute Community Sequencing Program. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. JM was supported in part by NIH grant RR016480. SR was supported by a Marie Curie Fellowship (contract 255104). RStam and EH were supported by the BBSRC and Royal Society of Edinburgh. LC, JW and SK were supported by the Gatsby Charitable Foundation. RSharma and MT are supported by the LOEWE Initiative of the state of Hesse. KL was supported by a grant from the UTIA AgResearch program. We thank Paul Richardson and Eddy Rubin for JGI support in genome sequencing.
AUTHOR CONTRIBUTIONSManuscript Preparation: KHL, SFK, JM, SK, EH, SR, IVG, AK, RStam, AKB, MT; Crosses, phenotypic analyses, and genetic analyses: KHL, DG, OPH, ASavidor, JH, and DS; Genomic or Transcriptomic Sequencing: JK, JA, EAL, SFK, JM, DLD, CD, OC, CSH; Assembly: JS, DP; Annotation: AK, ASalamov, IVG; Alignments and variant detection: NAM, BJR, JM KHL; Analysis: KHL, JM, SFK, SK, EH, DS, SR, LMC, AK, IVG, AKB, RSD, SF, ASavidor, DG, OPH, JH, RSharma, RStam, DS, MT, JW, BJH, CD, CSH, OC.
PubMed Central Canada is a service of the Canadian Institutes of Health Research (CIHR) working in partnership with the National Research Council's national science library in cooperation with the National Center for Biotechnology Information at the U.S. National Library of Medicine(NCBI/NLM). It includes content provided to the PubMed Central International archive by participating publishers.


text:
Top Definition
a nark; someone who snitches
I saw the girl steal the pizzas, however, I'm not going to be a taddle-tail and tell the boss who did it.
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subset: commoncrawl


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The Ultimate Doomsday To-Do List
You never know exactly what the future holds, so we might as well get to doing fantastic stuff while the gettings good.
Whether you fall on the "December 21 will be the end of us, just as the Mayan calendar predicted," end of the spectrum or you're in noted astrophysicist Neil deGrasse Tyson's camp (the one that's based in science and assures us that the world is set to keep on spinning), it's impossible to avoid mention of the prediction that the world will come to its end this month. Is the apocalypse a laughing matter? No. Does it seem likely to actually happen? Also no. Does it, however, provide an excellent impetus for writing up a Doomsday To-Do list, an itinerary of completely fun activities that you should probably do anyway? Why, yes! Let's fun things up, while we still can!
- Find a new hero, and emulate his or her accomplishments. Let's just say that Mayor Cory Booker has set the bar pretty danged high in terms of being an awesome human, and most of us in the VN office are obsessed with his do-goodery.
- Get yourself a tub of Celeste's Best cookie dough. What happens after it's open is up you.
- Donate more money than you normally would to your favorite animal organization. If the world ends, you won't need the cash anyway, and if it doesn't you can start off the New Year having done something great!
- If you are a lady, have a lady day. For me, this means going to the Korean spa and paying intensely muscular women to scrub the living daylights out of my skin, after sitting in a piping hot steam room for hours. Maybe it means something different to you (but really, this is one of the most amazing uses your time could possibly have).
- Re-read all of Calvin and Hobbes. All of it. Every panel. Pretty much everything that's good about humanity, imagination, and philosophy (not to mention comics) are in those pages.
- Adopt a companion animal. Do you really want to spend your last days on the planet not cuddling an amazing dog? Really?
- Host a really rocking dinner party. According to The New York Times, the art of the dinner party is going the way of the dodo. Before we all become extinct, let's dress up, gather friends, ply them with cocktails, and share an incredible meal.
- Speaking of dressing up, if there's a bit of extra cash leftover after you've given your chunk to animal organizations, splurge on a new coat from Vaute Couture, new shoes from Brave GentleMan, or a new Matt & Nat bag. Might as well support vegan companies while you can, yes?
- Order one of every single candy and caramel from Obsessive Confection Disorder. Do it.
- Say it. There's definitely someone in your life whom you silently appreciate, and now's the time to stop the silence. Could be your neighbor who always says hello, your long-suffering mother, or someone you think is too famous/busy/far away to want to hear from little ol' you. Forget that noise, and make some that sounds like, "Thanks for what you do."
- Send a present to someone who isn't expecting it. You know what always fits just right? A dozen vegan cinnamon rolls from Cinnaholic, complete with the recipient's favorite frosting flavors.
- If you are a gentleman, have a gent's day. As we already covered, I'm not a dude, so I really can't recommend anything too specific here, but I will say that it's always a good idea to read comic books (pretty much anything by Alan Moore) and/or re-watch all of Star Trek: The Next Generation.
- Say yes. The friend you have that you're always just a tad too busy to visit? Accept his or her invitation to drinks and catch up.
- Speaking of drinks, find out what your favorite one is. Yes, this will take a lot of research, so pace yourself a bit. Are you a Mojito gal? A Moscow Mule man? A straight-from-the-bottle-the-world-is-ending-do-you-really-think-I-have-time-to-concoct-a-cocktail-right-now whiskey drinker? Find out!
- Make the VN Signature Mac 'n' Cheese. Now.
- Grab a gaggle of friends, find a karaoke bar, and get cozy. Might as well make some memories, right? If the world ends, your potential shame will be short-lived, and if it doesn't, your friends can remember your on-stage bravery for years to come. Win-win.
- Celebrate the holidays—all of them. Decorate the heck out of your home, go nuts with streamers, whip up your favorite latkes to enjoy under a Christmas tree while dressed as your favorite superhero before you shoot off (legal!) fireworks and hunt for dark chocolate bunnies. Repeat the next day, because, why not?
- Read a favorite book out loud. The writing of a beloved author is even more magical when actually verbalized.
- Get some. (In the immortal words of Monty Python, "Wink, wink. Say no more.")
- Buy yourself a Moleskin 18-month planner (the preferred planner of the VN staff). Fill it with the successes for the next year that you'd have in your absolute wildest dreams. If the planet goes kaput, you'll have spent some time considering a dream life. If we happen to get a bit more time walking around, work on making those goals reality!
- Dance. A lot. With someone you like.
10 Vegan Reasons We're Dreaming of Fall
Lattes, whipped cream, root veggies, and pumpkin spice everything, here we come!
Read More »
Two Sisters and Their Vegan Weddings
What do you get when you combine two creative sisters, two dashing grooms, and two different but equally vegan weddings?
Read More »
How to Build the Ultimate Veggie Burger
Two succulent patties, extra cheese, and all the vegan bacon under the sun—our fantasy burger is the best way to say adieu to summer.
Read More »
Vegan Weddings 2016 (Jac Reasor & Jae Russell)
Dating site OKCupid is to thank for this Latin-inspired wedding.
Read More »
How to Nail Your Ultimate Summer Look By Labor Day
Miles from a beach? Dont worry, as weve got all the best vegan products to make you look your summer best.
Read More »
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- Top 3 Vegan Parenting Myths, Busted


text:
Otford transport
Map key
- National rail stations Hide
Click on train stations below to view on map
Completely London
Click on train stations below to view on map
The entire team at KFH has been not only highly professional and impressive but also a great pleasure to deal with. Selling a house can be a very stressful time, but KFH has made the experience so far smooth, quick, trouble free and a financial success beyond our expectations.
Craig C - Seller


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interactive book
This project received 7 bids from talented freelancers with an average bid price of $147 USD.Get free quotes for a project like this
Project Budget$30 - $250 USD
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Project Description
interactive book up to 30 pages
html 5
flipping from left to right
audio and video enabling
highlighting the text read while playing the audio
Please submit previous examples of ebook you did otherwise your bid won't be considered.
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text:
- ITV Report
- ITV Report
The Duke of Edinburgh in Devonport
Live updates
- ITV Report
Nuclear submarine re-opens after refit
A museum that is a submarine has re-opened after a facelift. HMS Courageous in Devonport Naval Base tells the story of naval nuclear powerRead the full story ›
Brazen thief steals phone from side of police station
The wall box phone from Devonport Police station has been stolen.
The crime was publicised by local PC, Dan Box, on Twitter - who urged those who knew anything to contact police.
This is not a wind up! The Devonport police station wall phone has gone missing. Any sightings give us a call....just not at Devonport!
The phone is on the side of the station and allows passerby's to contact staff quickly.
The station in Fore Street is home to officers from all the main strands of policing, including emergency response officers, the local neighbourhood team and the crime investigation department.
Plymouth crew exercises freedom of Welsh town
Devonport-based HMS Monmouth has made a return visit to her "home town" for the first time in three years.
The ship was given the Freedom of the town of Monmouth in 2004 and on Sunday (21 March) the crew exercised this right by parading through the town in the traditional style, bayonets fixed, drums beating and colours flying. They were cheered by hundreds of residents.
The ship leaves Cardiff on Thursday (24 March) to return to her base port of Plymouth for routine maintenance ahead of intensive operational training in the summer.
- ITV Report
Gunshots in Devonport? Just practice rifle salutes
If you live in Devonport and think you hear gunshots this afternoon and tomorrow morning, you might be right.Read the full story ›
- ITV Report
The Duke of Edinburgh in Devonport
A gallery of images from The Duke of Edinburgh's visit to Devonport Naval Base in his role as Captain General of the Royal MarinesRead the full story ›
Duke of Edinburgh due to visit Devonport
The Duke of Edinburgh is due to meet with Royal Marines at Devonport today.
He'll be presenting long service and good conduct awards, as well as meeting injured servicemen and women. Prince Philip will then officially open the new Mercury building at the naval base.
As part of his visit, the Duke will view amphibious craft equipment, including landing craft and raiding craft.
Hundreds of migrants rescued in Mediterranean by Plymouth ship
A Devonport-based ship has rescued more than 400 migrants in the Mediterranean.
HMS Enterprise has been helping with the Royal Navy's operation to counter migrant smugglers. The people they rescued are being cared for on-board the ship before being transferred to a Norwegian support vessel.
Teenage boy due to be sentenced over Devonport fire
A 14-year-old boy is due to be sentenced later, after destroying a block of flats when he built a homemade bunsen burner in Plymouth.
Twenty families were unable to return to their homes, following the fire at flats on Clowance Street in June.
The teenager has admitted starting the fire, which caused millions of pounds worth of damage
£500 million to Plymouth's rival dockyard
Plymouth has been left out of a government plan that will see £500 million go to one of Devonport's rival dockyards - Faslane on the Clyde.
Alongside Portsmouth and Devonport, Faslane is one of three major naval hubs, and is the home of Britain's Trident nuclear deterrent.
The money will go towards a 10-year infrastructure project which is expected to begin in 2017. The plans include building sea walls and jetties, and will create thousands of jobs.
Two submarines from Devonport will also be moved up to Faslane in 2020.
Have you seen these teenagers? Police release efit after pregnant woman attacked
Police are looking for two teenagers after an attack on a pregnant woman in Plymouth last month.
The 24-year-old woman, who was 17 weeks pregnant, suffered back and internal injuries after she was pushed in the stomach and had her purse grabbed.
The attack happened on Evelyn Street, in the St Budeaux area of the city late on Friday July 31st.
Both suspects are described as being 14 or 15.
"I would like to reassure residents that this is an unusual and isolated incident which is rare for this quiet residential area of Plymouth."


text:
'Who's the Boss' Cast Reunites for EW
The stars of the iconic series sit down to a family dinner to eat, drink, and talk about what it's like to appear on a show that broke all the rules and redefined the concept of family
'Westworld': EW review
Can 'Allied' survive the Brad Pitt-Angelina Jolie breakup?
Pitt's divorce from Jolie threatens to overwhelm the publicity campaign for his awards-season spy movie. That's not necessarily the worst thing.
'Westworld': Meet the Characters
Latest News
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- 'Luke Cage' premiere recap: 'Moment of Truth' Aired on Friday, Sep 30
- 'How to Get Away With Murder' recap: 'There Are Worse Things Than Murder' Aired on Thursday, Sep 29
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Located in New York City, SCEPA is at the center of a network of leaders dedicated to progressive and innovative education and ideas.
SCEPA faculty are investigating the economics of climate change, from mitigation proposals to implementation.
SCEPA focuses on the U.S. economy, with an awareness of the global context of domestic economic developments.
A research institute within The New School's Economics Department, SCEPA is dedicated to collaboration between today's experts and tomorrow's leading economists.
SCEPA is working to reform a retirement system that is failing Americans.
- On Capitol Hill
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Our projects are designed to empower policy makers to create positive change. With a focus on collaboration and outreach, we provide original, standards-based research on key policy issues.
SCEPA joined with the Economic Policy Institute on Capitol Hill to brief congressional staff and policy experts on tax expenditures, or incentives given through the tax code without scrutiny by Congress.
SCEPA economists are working on the prospects for a more progressive economic order to emerge from the shock of the recession. They have published papers and documents that place current events in a longer-term context as well as policy proposals to deal with short-term concerns. They are also documenting the emerging discussion of how the discipline of economics is reacting to the Great Recession and the questioning of conventional economic analysis.
Lance Taylor, a SCEPA Faculty Fellow, presents an overview of his new book, Maynard's Revenge, in a Google Tech Talk.
The book, published this November by Harvard University Press, is a timely analysis of mainstream macroeconomics, posing the need for a more useful and realistic economic analysis that can provide a better understanding of the ongoing global financial and economic crisis.
The government spends $143 billion through tax breaks in an effort to expand pension coverage and security. Yet, over half of the American workforce does not have a pension. Retirement insecurity hurts business plans, workers' lives and retiree well-being. Reform is needed.
SCEPA's Guaranteeing Retirement Income Project, sponsored by the Rockefeller Foundation and in collaboration with Demos and the Economic Policy Institute, has a plan to guarantee safe and secure retirement income for all Americans.
VIDEO: Climate Policies After Paris
- Details
Representatives from over 155 countries gathered at the United Nations on Earth Day 2016 to sign the historic COP21 climate change agreement negotiated in Paris last year.
Now what?
The backbone of the agreement is a commitment to limit global warming to under two degrees Celsius above preindustrial levels. To do so would require a worldwide switch from fossil fuels to renewable energy.
Ottmar Edenhofer, co-chair of the Intergovernmental Panel on Climate Change (IPCC), joined SCEPA's Economics of Climate Change lecture series to share his road map for bringing the Paris agreement to life. His presentation discussed how the agreement will change the institutional landscape of global climate governance and how to bring the economics and politics of climate stability to action.
Edenhofer is a leading international expert on climate policy at the Technical University of Berlin. He is director of the Mercator Research Institute on Global Commons and Climate Change, a fellow of the German Academy of Sciences, and deputy director and chief economist of the Potsdam Institute for Climate Impact Research.
The event was be followed by a reception featuring the premiere of "The Warming Earth," a jazz piece composed by Rich Shemaria.
"Climate Policies After Paris" is hosted by SCEPA's Economics of Climate Change Project and generously sponsored by the Tishman Enviromental and Design Center (TEDC), the Institute for New Economic Thinking (INET), the Fritz Thyssen Foundation and the German Research Foundation (DFG).
April Unemployment Report for Workers Over 55
- Details
Self-Employment Is No Solution for the Older Unemployed
A smaller share of older workers are officially looking for work. The unemployment rate for workers aged 55 to 64 was 3.6% in April, down 0.3 percentage points from March. Older men's unemployment decreased from 4.0% to 3.8%, and older women's unemployment decreased from 3.8% to 3.6%.
Older workers have lower official unemployment rates than the national average, but face stagnating wages, growing long-term unemployment, physically demanding jobs, and age discrimination. One widely-advocated solution is for the unemployed to create their own jobs by becoming self-employed.
But this is wishful thinking. The existing self-employed are workers who have, to a greater or lesser extent, chosen self-employment rather than entered it as a last resort. It does not follow that if the older unemployed attempt to become self-employed, they will succeed. Analysis of Health and Retirement Study (HRS) data, a nationally representative survey of older Americans shows:
- Few unemployed workers over 55 enter self-employment – only 5.7% during the period 2010-2012.
- The low rate of entry to self-employment likely reflects a lack of resources, rather than insufficient entrepreneurial zeal among older unemployed workers.
Median household-level financial assets of unemployed workers over 55 are only $2,000. In contrast, newly self-employed older workers have average financial assets of $25,000, and older employees $10,000. Unemployed workers are also less likely to have housing wealth to draw on. Only 71% of older unemployed workers are homeowners, compared with 87% of the newly self-employed and 83% of employees, and unemployed homeowners have less housing equity than the newly self-employed and employees. With only $2,000 to start a business and little collateral, the older unemployed are unlikely to be able to finance viable businesses. Instead, self-employment likely means taking insecure, low-paid work in the gig economy.
America's older workers should be able to choose to leave the labor force after a lifetime of work. Policy proposals that call for cutting Social Security benefits by raising the retirement age leave people at the mercy of a labor market unfriendly to older workers. Guaranteed Retirement Accounts (GRAs) open a path to retirement security by providing all workers retirement savings plans with guaranteed growth.
VIDEO: The Future of Capitalism
- Details
Yanis Varoufakis delivered SCEPA's annual Robert Heilbroner Memorial Lecture, "The Future of Capitalism" on Monday, April 25th, 2016.
We all know Varoufakis as the former Greek Finance Minister and media sensation who stood up to Europe in the fight against austerity. His lecture highlighted themes his new book, "And The Weak Suffer What They Must?," including the origins of a crisis that has affected not only Greece, but all of Europe.
The lecture was followed by a panel discussion featuring New School Professor of Economics Mark Setterfield and economics student Ebba Boye.
Follow the conversation on Twitter with @SCEPA_economics using #YanisTNS.
Varoufakis' career has spanned academia, public service, and the private sector. After three decades in academia, he was elected to the Hellenic Parliament in 2015 as a member of the Syriza Party and became Minister of Finance in Alexis Tsipras' government. He currently serves as professor of economics at the University of Athens and as a consultant for the Valve Corporation.
SCEPA's Robert Heilbroner Memorial Lecture on the Future of Capitalism:
The Heilbroner lecture honors the work of Robert Heilbroner, who was both a student and a professor in the economics department of The New School for Social Research. This event is dedicated to understanding questions of economic justice and how the profit-seeking activities of private firms might also serve broader social goals. To use Heilbroner's words, "capitalism's uniqueness in history lies in its continuously self-generated change, but it is this very dynamism that is the system's chief enemy."
The event was free and open to the public.


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Watto's Junk Yard / Re: Rebel scum mods are gone!« on: January 4, 2005, 05:42 PM »
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text:
Matt Taibbi Joins Occupy Wall Street for Anti-Corporate Protest
Matt Taibbi speaking to Occupy Wall Street protesters today.
Occupy Wall Street protesters held their biggest march so far this year today as part of a nationwide "Shut Down the Corporations" day of action.
Several hundred occupiers gathered in Bryant Park this morning before marching east on 42nd Street to the global headquarters of Pfizer Pharmaceuticals, targeted because the company is a member of the American Legislative Exchange Council.
When the marchers returned to Bryant Park, Rolling Stone writer Matt Taibbi delivered a lecture explaining the origins of the mortgage crisis and the role played by Bank of America.
Taibbi said the financial industry sowed the seeds for the economic crisis when it began repackaging high-risk mortgages into triple-A-rated mortgage-backed securities.
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"That's what these guys did," Taibbi said. "They turned a bunch of oregano into high-grade weed and they sold it all around the world."
Compounding the crisis, of course, were the credit default swaps major banks bought, essentially betting that the toxic derivatives they were selling would fail.
"It's sort of like selling a lot full of cars with no brakes and then buying life insurance on all the drivers," Taibbi said.
All the major financial institutions are implicated in these shady dealings, Taibbi said, but Bank of America is the worst. "They're like a Zelig of the white-collar crime era," he said. "They're involved in everything."
Taibbi called for criminal investigation into Bank of America's behavior, and an end to federal support for the institution. "We've got to put pressure on our elected officials to disallow any further state support of Bank of America," he said.
Given Bank of America's precarious financial situation, cutting off the taxpayer support could bring the bank crashing down, Taibbi said. "We have to figure out a way to unwind these corrupt companies in a way that doesn't destroy the rest of us."
The rest of the day's action was typical Occupy Wall Street fare: hundreds of protesters streaming through the streets, chased and herded by police on scooters and on foot attempted to divert and break up the demonstration.
A heavy police presence and metal barricades kept the occupiers away from the Bank of America tower across the intersection from Bryant Park, so instead they visited Bank of America retail branches throughout the neighborhood. The branches closed their doors when the protesters drew near, and police rushed to put themselves between the banks and the march.
At one point, a member of the OWS Direct Action working group expressed frustration at the disorganization of the march. "But it's okay," she said. "We're learning for May 1st."
Here's video of Taibbi's talk, via Tim Pool:
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5 star hotel
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3.06 mi from Orange County Museum of Art
Best Rooms: For the best ocean views, book an Ocean room and request to be placed in the 400s wing.
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Address2011 North Highland Avenue Los AngelesSee nearby area
For rates, enter dates/guests
Description provided by property
Just 2 blocks from Hollywood Boulevard and the well-known Walk of Fame, this hotel offers warmly decorated rooms with free Wi-Fi and a cable TV. It features an outdoor pool and on-site restaurant.
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Hollywood history hangs in the thick air at Musso & Frank Grill, Tinseltown's oldest eatery (since 1919). Charlie Chaplin used to...
Yamashiro Farmers Market
The best farmers market views in LA are yours from Yamashiro's spectacular perch. In addition to organic produce, expect tasty prepared...