Status
Assembly v2 (1 March 2010) is an improved assembly produced by the JGI Finishing Pipeline. 80 scaffolds and 53.9 Mbp were assembled:
Nuclear Genome Assembly v2.0
| Main genome scaffold total | 80 |
| Main genome contig total | 350 |
| Main genome scaffold sequence total | 53.9 Mbp |
| Main genome contig sequence total | 53.4 Mbp |
| Estimated % sequence bases in gaps | 1.1 % |
| Main genome scaffold N50 / L50 | 11 / 1.5 Mbp |
| Main genome contig N50 / L50 | 41 / 370.4 kbp |
| Number of scaffolds >50 Kbp | 51 |
| % main genome in scaffolds >50 | 99.4 % |
| % ESTs aligned to scaffolds | 98 % |
Annotation v2 (1 March 2010) 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 to the v2 scaffolds. After filtering for homology and expression support, a total of 16528 genes were structurally and functionally annotated:
Nuclear Genome Annotation v2.0
| # of genes | 16528 |
| Gene density | 306.4 genes / Mbp scaffold |
| Ave.gene length | 1627.7 nt |
| Ave. protein length | 352.8 aa |
| Ave. exon frequency | 4.5 exons / gene |
| % genes with introns | 89 % |
| % models with start+stop codons | 90 % |
| % genes with NR hits | 67 % |
| % genes with Pfam domains | 44 % |
| % genes with TM domains | 16 % |
| % genes with ESTs | 33 % |
| % genes in multigene families | 76 % |
Assembly v1 (September 2006): The assembly release version 1.0 of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of ~7.49X. After trimming for vector and quality, 506287 reads assembled into 475 main genome scaffolds totaling 55.9 Mbp. Roughly half of the genome is contained in 15 scaffolds all at least 1.0 MB in length.
Annotation v1 (November 2006): The draft annotation, version 1.0, includes a total of 14,792 gene models predicted and functionally annotated using the JGI Annotation Pipeline.
Collaborators
- DOE Joint Genome Institute,
- Luis Corrochano at the University of Sevilla, Spain
- Ed Braun at the University of Florida
- Scott Baker at the Pacific Northwest National Laboratory
Links
- The Phycomyces Web Site
- Mucor circinelloides CBS277.49 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 .
