Status
[July 2015] The Setosphaeria turcica genome was
sequenced using the Illumina platform and assembled with AllPathsLG
release version R49403 (Gnerre
et al., 2010).
Mitochondrial genome was assembled separately and is available in
the downloads section.
Summary statistics for the Setosphaeria turcica NY001 v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 38.42 |
| Sequencing read coverage depth | 93.8x |
| # of contigs | 1823 |
| # of scaffolds | 489 |
| # of scaffolds >= 2Kbp | 417 |
| Scaffold N50 | 45 |
| Scaffold L50 (Mbp) | 0.23 |
| # of gaps | 1334 |
| % of scaffold length in gaps | 6.0% |
| Three largest Scaffolds (Mbp) | 1.75, 1.20, 0.88 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | RNNotator assembled Illumina ESTs | 34363 | 31720 | 92.3% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1624 | 1379 |
| transcript | 1499 | 1257 |
| exon | 595 | 382 |
| intron | 85 | 58 |
| description: | ||
| protein length (aa) | 420 | 337 |
| exons per gene | 2.52 | 2 |
| # of gene models | 13422 |
Collaborators
Gillian Turgeon, Cornell University
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
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
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.
