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 29 main genome contigs with no gaps. Roughly half of the genome is contained in 6 scaffolds all at least 2.0 MB in length.
v1.0 (June 2008): 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 ~8.26X. After trimming for vector and quality, 430,655 reads assembled into 50 main genome scaffolds totaling 36.1 MB. Roughly half of the genome is contained in 6 scaffolds all at least 2.0 MB in length.
v2.0 (May 2010). The assembly release version 2.0 is an improved assembly that has undergone gap closure and is now in 29 main genome contigs with no gaps. Roughly half of the genome is contained in 6 scaffolds all at least 2.0 MB in length.
v1.0 (June 2008): 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 ~8.26X. After trimming for vector and quality, 430,655 reads assembled into 50 main genome scaffolds totaling 36.1 MB. Roughly half of the genome is contained in 6 scaffolds all at least 2.0 MB in length.
| Nuclear Genome Assembly: | v1.0 | v2.0 |
| Scaffold count: | 50 | 29 |
| All Contig count: | 304 | 29 |
| Scaffold sequence bases total: | 36.1 Mb | 36.1 Mb |
| Scaffolded (Large) Contig sequence bases total: | 36.0 Mb | 36.1 Mb |
| Estimated % sequence bases in gaps: | 0.2% | 0.0% |
| Scaffold N50/L50: | 6/2.0 Mb | 6/2.0 Mb |
| Contig N50/L50: | 43/275.5 Kb | 6/2.0 Mb |
| Number of scaffolds > 50.0 Kb: | 22 | 20 |
| % in scaffolds > 50.0 Kb: | 99.7% | 99.8% |
Annotation
2.0 (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 11,863 genes were structurally and functionally annotated.
v1.0 (June 2008) 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 11,193 genes were structurally and functionally annotated.
2.0 (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 11,863 genes were structurally and functionally annotated.
v1.0 (June 2008) 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 11,193 genes were structurally and functionally annotated.
| Nuclear Genome Annotation: | v1.0 | v2.0 |
| # gene models: | 11193 | 11863 |
| Gene density: | 310 | 329 |
| Avg.gene length: | 1748 nt | 1800 nt |
| Avg. protein length: | 473 aa | 455 aa |
| Avg. exon frequency: | 2.93 exons/gene | 2.86 exons/gene |
| Avg. exon length: | 529 nt | 561 nt |
| Avg. intron length: | 103 nt | 108 nt |
| % complete gene models (with start and stop codons): | 89% | 89% |
| % genes with homology support: | 89% | 89% |
| % genes with Pfam domains: | 53% | 60% |
Collaborators
- Christian Kubicek, Vienna University of Technology, Austria
- Scott Baker, PNNL
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
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.
