Status
(version 1.0, June 2011) This draft release was produced using Sanger reads, shredded consensus from velvet assembled illumina data, Roche (454) standard and Roche (454) paired end. Gap closure with gapResolution closed 164 gaps (24%) in initial assembly.
Summary statistics for the Cochliobolus sativus v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 34.42 |
| Sequencing read coverage depth | 42.43x |
| # of contigs | 478 |
| # of scaffolds | 157 |
| # of scaffolds >= 2Kbp | 157 |
| Scaffold N50 | 7 |
| Scaffold L50 (Mbp) | 1.79 |
| # of gaps | 321 |
| % of scaffold length in gaps | 3.5% |
| Three largest Scaffolds (Mbp) | 3.64, 3.03, 2.70 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | EST_clusters | 214773 | 28700 | 13.4% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1691 | 1460 |
| transcript | 1545 | 1322 |
| exon | 587 | 361 |
| intron | 91 | 58 |
| description: | ||
| protein length (aa) | 444 | 367 |
| exons per gene | 2.63 | 2 |
| # of gene models | 12250 |
Collaborators
- Igor Grigoriev, Joint Genome Institute
- Shaobin Zhong, North Dakota State University
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
Links
- Cochliobolus heterostrophus C5
- Mycosphaerella fijiensis v2.0
- Mycosphaerella graminicola v2.0
- Alternaria brassicicola
- Pyrenophora tritici-repentis
- Stagonospora nodorum SN15
- Dothistroma septosporum
- Septoria musiva
- Leptosphaeria maculans
- Hysterium pulicare
- Rhytidhysteron rufulum
- Setosphaeria turcica
- Baudoinia compniacensis
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.
