Info • Cryphonectria parasitica EP155 v2.0
Assembly
v2.0 (March 2010): The assembly release version 2.0 of whole genome shotgun reads was constructed with the Arachne assembler and improved with finishing reads. This release contains 26 main genome scaffolds totaling 43.9 Mb. 5 scaffolds are considered complete telomere to telomere and an additional 6 have a telomere on one end. The remaining 15 scaffolds are smaller and do not contain telomeres. Roughly half of the genome is contained in 4 scaffolds all at least 5.1 Mbp in length.
v1.0 (September 2008): The assembly release version 1.0 of whole genome shotgun reads was constructed with the Arachne assembler, using paired end sequencing reads at a coverage of ~8.54X. After trimming for vector and quality, this genome assembled into 39 main genome scaffolds totaling 43.9 MB. Roughly half of the genome is contained in 5 scaffolds all at least 4.0 Mbp in length.
| Nuclear Genome Assembly: | v1.0 | v2.0 |
| Scaffold count | 39 | 26 |
| All contig count | 536 | 33 |
| Scaffold sequence bases total | 43.9 Mb | 43.9 Mb |
| Scaffolded (large) contig sequence bases total | 43.6 MB | 43.8 MB |
| Estimated % sequence bases in gaps | 0.5 % | 0.2 % |
| Scaffold N50/L50 | 5/4.0 Mb | 4/5.1 Mb |
| Contig N50/L50 | 78/159.5 Kb | 5/4.0 Mb |
| Number of scaffolds > 50.0 Kb: | 20 | 13 |
| % in scaffolds > 50.0 Kb: | 99.6 % | 99.6 % |
Annotation
v2.0 (March 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 and its manual curations were also mapped to the v2.0 assembly and were included in the filtering procedure that determined the initial v2.0 Gene Catalog. After filtering for EST support, completeness and homology support, a total of 11,609 genes were structurally and functionally annotated.
v1.0 (September 2008): Annotation 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 11,184 genes were structurally and functionally annotated.
| Nuclear Genome Annotation: | v1.0 | v2.0 |
| # gene models: | 11,184 | 11,609 |
| Gene density(genes/Mb scaffold): | 254.76 | 264.44 |
| Avg.gene length: | 1783.64 | 1648.61 |
| Avg. protein length: | 465.18 | 422.99 |
| Avg. exon frequency: | 2.96 exons/gene | 2.91 exons/gene |
| Avg. exon length: | 524.67 | 487.09 |
| Avg. intron length: | 120.08 | 122.58 |
| % complete gene models (with start and stop codons): | 89 % | 84 % |
| % genes with homology support: | 86 % | 85 % |
| % genes with Pfam domains: | 50 % | 66 % |
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.
