Info • Trichoderma atroviride 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 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.

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

Links

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.