Status
v2.0 (November 2011): This improved Cochliobolus heterostrophus C5 genome sequence assembly v2.0 was assembled using Phrap, from whole genome shotgun and paired end sequencing reads, and improved by manual finishing and fosmid clone sequencing. The nuclear genome sequence from this draft assembly was annotated using the JGI Genome Annotation Pipeline and custom analyses. Gene models and manual annotations from the v1.0 assembly were mapped forward to the v2.0 assembly using the fgenesh gene modeler and sequence similarity cutoffs.
Summary statistics for the Cochliobolus heterostrophus C5
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 36.46 |
| Sequencing read coverage depth | Improved |
| # of contigs | 88 |
| # of scaffolds | 68 |
| # of scaffolds >= 2Kbp | 68 |
| Scaffold N50 | 7 |
| Scaffold L50 (Mbp) | 1.84 |
| # of gaps | 20 |
| % of scaffold length in gaps | 0.4% |
| Three largest Scaffolds (Mbp) | 4.21, 3.37, 2.54 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | EstClusters | 88751 | 72109 | 81.2% |
| Ests | ESTs | 309728 | 281924 | 91.0% |
| Other | GenBank | 162 | 100 | 61.7% |
| Gene Models | FilteredModels4 | |
| length (bp) of: | average | median |
| gene | 1580 | 1365 |
| transcript | 1423 | 1224 |
| exon | 535 | 320 |
| intron | 97 | 59 |
| description: | ||
| protein length (aa) | 428 | 355 |
| exons per gene | 2.66 | 2 |
| # of gene models | 13336 |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F, Hesse CN, Kosti I, LaButti K, Lindquist EA, Lucas S, Salamov AA, Bradshaw RE, Ciuffetti L, Hamelin RC, Kema GH, Lawrence C, Scott JA, Spatafora JW, Turgeon BG, de Wit PJ, Zhong S, Goodwin SB, Grigoriev IV
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi.
PLoS Pathog. 2012;8(12):e1003037. doi: 10.1371/journal.ppat.1003037
Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar R, Martin J, Schackwitz W, Grimwood J, MohdZainudin N, Xue C, Wang R, Manning VA, Dhillon B, Tu ZJ, Steffenson BJ, Salamov A, Sun H, Lowry S, LaButti K, Han J, Copeland A, Lindquist E, Barry K, Schmutz J, Baker SE, Ciuffetti LM, Grigoriev IV, Zhong S, Turgeon BG
Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens.
PLoS Genet. 2013;9(1):e1003233. doi: 10.1371/journal.pgen.1003233
Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F, Hesse CN, Kosti I, LaButti K, Lindquist EA, Lucas S, Salamov AA, Bradshaw RE, Ciuffetti L, Hamelin RC, Kema GH, Lawrence C, Scott JA, Spatafora JW, Turgeon BG, de Wit PJ, Zhong S, Goodwin SB, Grigoriev IV
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi.
PLoS Pathog. 2012;8(12):e1003037. doi: 10.1371/journal.ppat.1003037
Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar R, Martin J, Schackwitz W, Grimwood J, MohdZainudin N, Xue C, Wang R, Manning VA, Dhillon B, Tu ZJ, Steffenson BJ, Salamov A, Sun H, Lowry S, LaButti K, Han J, Copeland A, Lindquist E, Barry K, Schmutz J, Baker SE, Ciuffetti LM, Grigoriev IV, Zhong S, Turgeon BG
Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens.
PLoS Genet. 2013;9(1):e1003233. doi: 10.1371/journal.pgen.1003233
Funding
The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
