Status
[September 2017] [Aug 2017] This draft assembly was produced using Roche (454) reads, Sanger-sequenced fosmids, and shredded consensi from Velvet-assembled Illumina (Solexa) reads in March 2011. This is an updated annotation of the same assembly using RNA-seq reads from various growth conditions to improve gene calling.
Summary statistics for the Setosphaeria turcica Et28A v2.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 43.01 |
| Sequencing read coverage depth | 58.1x |
| # of contigs | 1959 |
| # of scaffolds | 407 |
| # of scaffolds >= 2Kbp | 407 |
| Scaffold N50 | 8 |
| Scaffold L50 (Mbp) | 2.14 |
| # of gaps | 1552 |
| % of scaffold length in gaps | 11.1% |
| Three largest Scaffolds (Mbp) | 4.03, 3.60, 3.52 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 12641 | 11668 | 92.3% |
| Ests | est.fasta | 323923661 | 100790539 | 31.1% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1631 | 1361 |
| transcript | 1490 | 1236 |
| exon | 563 | 348 |
| intron | 88 | 57 |
| description: | ||
| protein length (aa) | 452 | 369 |
| exons per gene | 2.65 | 2 |
| # of gene models | 12028 |
Collaborators
Gillian Turgeon, Cornell University
Stephen Goodwin, USDA-ARS
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.
