Status
Assembly v2 (28 Dec 2009) is an improved assembly produced by the JGI Finishing Pipeline. 26 scaffolds and 36.6 Mbp were assembled:
Nuclear Genome Assembly v2.0
| Main genome scaffold total | 26 |
| Main genome contig total | 26 |
| Main genome scaffold sequence total | 36.6 Mbp |
| Main genome contig sequence total | 36.6 Mbp |
| Estimated % sequence bases in gaps | 0.0 % |
| Main genome scaffold N50 / L50 | 4 / 4.3 Mbp |
| Main genome contig N50 / L50 | 4 / 4.3 Mbp |
| Number of scaffolds >50 Kbp | 15 |
| % main genome in scaffolds >50 | 99.7% |
| % ESTs aligned to scaffolds | 95% |
Annotation v2 (28 Dec 2009) is a consensus gene set predicted by the JGI Annotation Pipeline, using a variety of cDNA-based, protein-based, and ab initio gene modelers, as well as Annotation v1 genes mapped onto the v2 scaffolds. After filtering for homology and expression support, a total of 11719 genes were structurally and functionally annotated:
Nuclear Genome Annotation v2.0
| # of genes | 11719 |
| Gene density | 320.3 genes / Mbp scaffold |
| Ave.gene length | 1429.3 nt |
| Ave. protein length | 379.5 aa |
| Ave. exon frequency | 3.8 exons / gene |
| % genes with introns | 83% |
| % models with start+stop codons | 85% |
| % genes with NR hits | 82% |
| % genes with Pfam domains | 64% |
| % genes with TM domains | 18% |
| % genes with ESTs | 33% |
| % genes in multigene families | 72% |
The draft assembly release version 1.0 (12 Mar 2009) of whole genome shotgun reads was constructed with Arachne, using paired end sequencing reads at an average coverage of 9.49X. After trimming for vector and quality, the sequencing reads assembled into 23 main genome scaffolds totaling 36.5 MB. Roughly half of the genome is contained in 4 scaffolds all at least 4.3 Mbp in length.
The draft annotation release version 1.0 (12 Mar 2009) of the v1.0 assembly was produced by the JGI Annotation Pipeline, using a variety of cDNA/EST-based, homology-based, and ab initio gene predictors. After filtering for EST and homology support, a total of 10930 genes were structurally and functionally annotated. 83% of the genes have homology support, 61% have Pfam support, and 36% have EST support.
Collaborators
Links
- The Mucor Genome Project
- Phycomyces blakesleeanus NRRL1555 Genome Portal at Joint Genome Institute
- Rhizopus oryzae Database at Broad Institute
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 .
