meridionalis ) is the causal agent of the southern stem canker ( ssc ) disease in soybean . this disease can kill plants from the middle to the end of the growing season resulting in severe yield loss . although ssc commonly occurs in the southern united states , d. aspalathi has been found in some of the northern states , . an isolate of d. aspalathi , ms - ssc91 was isolated from field - grown soybean stem in stoneville , mississippi , usa in 2006 using a modified seed plating procedure . 5-mm pieces , surface - disinfested with 0.5% naocl solution for 3  min , rinsed three times , and placed on acidified potato dextrose agar ( apda ) medium ( difico laboratories , detroit , mi ) adjusted to ph  4.8 with 25% lactic acid after autoclaving . stem samples were placed on each petri dish and incubated at 24  c for 47  days . isolate of ms - ssc91 isolate were white , lanose , and turned tan with age as the typical d. aspalathi previously described . further identification was confirmed by analysis of the its region of rdna amplified by pcr with primers its1 , 5-tccgtaggtgaacctgcgg-3 ' and its4 , 5-tcctccgcttattgatatgc-3 . mycelial plugs ( 4-mm in diameter ) from the margin of a 10-day old culture on apda were punched out with the large ends of disposable micropipette tips ( 200  l ) . the micropipette tip containing the fungal mycelium was subsequently placed over a 3-week old cut soybean stem that was cut at just below the first trifoliolate node . micropipette tips containing plugs of non - infested apda were served as the negative control . two days after inoculation , micropipette tips were removed . at 7  days after inoculation , the main stem length was measured from the soil line to the top of the plant , and the lesion on the stem was measured . the ms - ssc91 isolate has been used to evaluate soybean for resistance to stem canker as part of the usda uniform soybean tests ( http://www.ars.usda.gov/sp2userfiles/place/60661000/uniformsoybeantests/2013soybook.pdf ) . genomic dna of d. aspalathi ms - ssc91 isolate was extracted from a 4-day - old culture using a qiagen dneasy plant mini kit ( qiagen inc . , valencia , ca ) and used to generate paired - end libraries with the truseq dna pcr - free sample preparation kit ( illumina san diego , ca ) according to the manufacturer 's protocol . libraries were sequenced in separate lanes on an illumina hiseq 2000 sequencer using a truseq sbs sequencing kit ( version 3 , illumina ) at the genomics core facility , purdue university , west lafayette , in . after trimming or removing low quality reads or bases with the trimmomatic   and/or fastx_clipper ( http://hannonlab.cshl.edu/fastx_toolkit/ ) using the threshold of base phred score greater than 20 , a total of 126,051,864 paired - end reads and 4,778,811 un - paired reads were retained . the total remaining sequence was 24,801  mb ( approximately 330   coverage of the genome ) . the filtered sequence was assembled with abyss de novo genome assembly software   at kmer  =  80 , and resulted in an assembly with 1873 scaffolds with a minimum size of 2000  bp ( n50  =  86.905  bp ) . the assembly contained 55,035,521 bases and the g  +  c content was 51% . analysis of the completeness of the genome based on the analysis of the 248 ultra - conserved core eukaryotic gene datasets ( cegs ) ( http://korflab.ucdavis.edu/datasets/genome_completeness/index.html#sct2 ) was done with the cegma program . the result showed 242 of the 248 proteins present in the genome sequence with two additional partial genes , indicating that the assembly was 97.6% complete . gene prediction analysis using the augustus software   trained with the parameters of the fungal species fusarium graminearum identified 14,962 genes . the average size of a gene was 1729  bp ; the largest gene was 23  kb . approximately 46% ( 25.8  mb ) of the whole genome sequence was contained in genes . of the 25.8  mb sequences within genes , 22.5  mb were coding sequences . the draft genome of ms - ssc91 represents an important soybean fungal pathogen in the diaporthe - phomopsis complex . meridionalis ) is the causal agent of the southern stem canker ( ssc ) disease in soybean . this disease can kill plants from the middle to the end of the growing season resulting in severe yield loss . although ssc commonly occurs in the southern united states , d. aspalathi has been found in some of the northern states , . an isolate of d. aspalathi , ms - ssc91 was isolated from field - grown soybean stem in stoneville , mississippi , usa in 2006 using a modified seed plating procedure . 5-mm pieces , surface - disinfested with 0.5% naocl solution for 3  min , rinsed three times , and placed on acidified potato dextrose agar ( apda ) medium ( difico laboratories , detroit , mi ) adjusted to ph  4.8 with 25% lactic acid after autoclaving . stem samples were placed on each petri dish and incubated at 24  c for 47  days . isolate of ms - ssc91 isolate were white , lanose , and turned tan with age as the typical d. aspalathi previously described . further identification was confirmed by analysis of the its region of rdna amplified by pcr with primers its1 , 5-tccgtaggtgaacctgcgg-3 ' and its4 , 5-tcctccgcttattgatatgc-3 . mycelial plugs ( 4-mm in diameter ) from the margin of a 10-day old culture on apda were punched out with the large ends of disposable micropipette tips ( 200  l ) . the micropipette tip containing the fungal mycelium was subsequently placed over a 3-week old cut soybean stem that was cut at just below the first trifoliolate node . micropipette tips containing plugs of non - infested apda were served as the negative control . two days after inoculation , micropipette tips were removed . at 7  days after inoculation , the main stem length was measured from the soil line to the top of the plant , and the lesion on the stem was measured . the ms - ssc91 isolate has been used to evaluate soybean for resistance to stem canker as part of the usda uniform soybean tests ( http://www.ars.usda.gov/sp2userfiles/place/60661000/uniformsoybeantests/2013soybook.pdf ) . genomic dna of d. aspalathi ms - ssc91 isolate was extracted from a 4-day - old culture using a qiagen dneasy plant mini kit ( qiagen inc . , valencia , ca ) and used to generate paired - end libraries with the truseq dna pcr - free sample preparation kit ( illumina san diego , ca ) according to the manufacturer 's protocol . libraries were sequenced in separate lanes on an illumina hiseq 2000 sequencer using a truseq sbs sequencing kit ( version 3 , illumina ) at the genomics core facility , purdue university , west lafayette , in . low quality reads or bases with the trimmomatic   and/or fastx_clipper ( http://hannonlab.cshl.edu/fastx_toolkit/ ) using the threshold of base phred score greater than 20 , a total of 126,051,864 paired - end reads and 4,778,811 un - paired reads were retained . the total remaining sequence was 24,801  mb ( approximately 330   coverage of the genome ) . the filtered sequence was assembled with abyss de novo genome assembly software   at kmer  =  80 , and resulted in an assembly with 1873 scaffolds with a minimum size of 2000  bp ( n50  =  86.905  bp ) . the assembly contained 55,035,521 bases and the g  +  c content was 51% . analysis of the completeness of the genome based on the analysis of the 248 ultra - conserved core eukaryotic gene datasets ( cegs ) ( http://korflab.ucdavis.edu/datasets/genome_completeness/index.html#sct2 ) was done with the cegma program . the result showed 242 of the 248 proteins present in the genome sequence with two additional partial genes , indicating that the assembly was 97.6% complete . gene prediction analysis using the augustus software   trained with the parameters of the fungal species fusarium graminearum identified 14,962 genes . the average size of a gene was 1729  bp ; the largest gene was 23  kb . approximately 46% ( 25.8  mb ) of the whole genome sequence was contained in genes . of the 25.8  mb sequences within genes , 22.5  mb were coding sequences . the draft genome of ms - ssc91 represents an important soybean fungal pathogen in the diaporthe - phomopsis complex .
diaporthe aspalathi ( syn . diaporthe phaseolorum var . 
 meridionalis ) is the causal agent of the southern stem canker ( ssc ) disease in soybean . 
 this disease can kill plants from the middle to the end of the growing season resulting in severe yield loss . 
 the mechanisms of ssc disease development and pathogen invasion of soybean are not fully understood . 
 the genome sequence of d. aspalathi has not been described . in this article , we report the successful assembly of the draft genome sequence of a d. aspalathi isolate , designated ms - ssc91 , that was isolated from the stem of a field - grown soybean plant in mississippi , usa in 2006 . 
 this study represents the first reported genome sequence of d. aspalathi in the diaporthe - phomopsis complex . 
 the whole genome shotgun sequence of the ms - ssc91 isolate has been deposited at ddbj / embl / genbank under the accession ljjs00000000 and the sequences could be found at the site http://www.ncbi.nlm.nih.gov / assembly / gca_001447215.1/. the ms - ssc91 genome sequences will provide information on the genetic basis of fungal infection of the soybean stem . 
 it is valuable for studying soybean - fungal interactions and developing new control strategies for this pathogen .