Info • Trichoderma virens Gv29-8 v2.0

Status

Assembly

v2.0 (May 2010). The assembly release version 2.0 is an improved assembly that has undergone gap closure and is now in 93 main genome contigs with no gaps. Roughly half of the genome is contained in 8 scaffolds all at least 1.8 MB in length.

v1.0 (Dec 2007): The assembly release version 1.0 of whole genome shotgun reads was constructed with the JGI assembler, JAZZ, using paired end sequencing reads at an Avgrage coverage of ~8.05X. After trimming for vector and quality, 445,647 reads assembled into 135 main genome scaffolds totaling 38.8 MB. Roughly half of the genome is contained in 9 scaffolds all at least 1.7 MB in length.

Nuclear Genome Assembly: v1.0 v2.0
Scaffold count: 135 93
All Contig count: 587 93
Scaffold sequence bases total: 38.8 Mb 39.0 Mb
Scaffolded (Large) Contig sequence bases total: 38.6 Mb 39.0 Mb
Estimated % sequence bases in gaps: 0.4% 0.0%
Scaffold N50/L50: 9/1.7 Mb 8/1.8 Mb
Contig N50/L50: 66/173.9 Kb 8/1.8 Mb
Number of scaffolds > 50.0 Kb: 48 43
% in scaffolds > 50.0 Kb: 97.7% 97.8%

Annotation

v2.0 (May 2010): Annotation of the v2.0 assembly was produced by the JGI Annotation Pipeline, using a variety of homology-based and ab initio gene predictors. The v1.0 gene catalog along with its manual curations was mapped to the v2.0 assembly and included in filtering. After filtering for EST support, completeness and homology support, a total of 12,427 genes were structurally and functionally annotated.

v1.0 (Dec 2007) of the v1.0 assembly was produced by the JGI Annotation Pipeline, using a variety of homology-based and ab initio gene predictors. After filtering for EST support, completeness and homology support, a total of 11,655 genes were structurally and functionally annotated.

Nuclear Genome Annotation: v1.0 v2.0
# gene models: 11,655 12,427
Gene density: 300.39 318.64
Avg.gene length: 1714 nt 1711 nt
Avg. protein length: 480 aa 471 aa
Avg. exon frequency: 2.98 exons/gene 2.93 exons/gene
Avg. exon length: 507 nt 515 nt
Avg. intron length: 104 nt 106 nt
% complete gene models (with start and stop codons): 84% 86%
% genes with homology support: 90% 90%
% genes with Pfam domains: 54% 61%

Genome Reference(s)

Please cite the following publication(s) if you use the data from this genome in your research:

Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Döhren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gómez-Rodríguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernández-Oñate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lübeck M, Lübeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV
Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma.
Genome Biol. 2011;12(4):R40. doi: 10.1186/gb-2011-12-4-r40

Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396.