Status
Assembly v11 (20 Aug 2010) is a hybrid assembly of 454 and Sanger gDNA reads. A total of 917 scaffolds and 64.0 Mbp were assembled using Arachne:
| Nuclear Genome Assembly: | v11.0 | v1.0 |
| Scaffold count: | 917 | 1406 |
| All Contig count: | 10760 | 36297 |
| Scaffold sequence bases total(Mbp): | 64.0 | 107.8 |
| Scaffolded Contig sequence bases total(Mbp): | 56.0 Mb | 63.2 Mb |
| Estimated % sequence bases in gaps: | 12.5% | 40.9% |
| Scaffold N50 / L50 (# / kbp): | 29 / 706 | 28 / 439 |
| Contig N50 / L50 (# / kbp): | 397 / 35 | 1574 / 10 |
| Number of scaffolds > 50.0 Kb: | 140 | 302 |
| % in scaffolds > 50.0 Kb: | 91.9% | 79.7% |
| % assembly masked by repeats: | 14.4% | 0.2% |
| # finished cDNAs: | 1260 | 1260 |
| % finished cDNAs that align with assembly: | 97.1% | 83.1% |
Annotation v11 (20 August 2010) of the v11.0 assembly was produced by the JGI Annotation Pipeline, using a variety of cDNA-based, protein-based, and ab initio gene predictors. After filtering for EST and protein homology support, a total of 19805 genes were structurally and functionally annotated.
| Nuclear Genome Annotation: | v11.0 | v1.0 |
| # gene models: | 19805 | 17414 |
| Gene density(# / Mbp scaffold): | 309 | 162 |
| Avg.gene length (nt): | 1253 | 1625 |
| Avg. protein length (aa) : | 314 | 381 |
| Avg. exon frequency (# / gene): | 2.20 | 2.62 |
| % genes with intron: | 50% | 58% |
| % complete models (with start+stop codons): | 69% | 72% |
| % genes with EST support: | 50% | 53% |
| % genes with nr support: | 75% | 76% |
| % genes with Pfam domains: | 47% | 42% |
| % genes with transmembrane domain: | 15% | 18% |
| % genes in multigene family: | 78% | 79% |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Lamour KH, Mudge J, Gobena D, Hurtado-Gonzales OP, Schmutz J, Kuo A, Miller NA, Rice BJ, Raffaele S, Cano LM, Bharti AK, Donahoo RS, Finley S, Huitema E, Hulvey J, Platt D, Salamov A, Savidor A, Sharma R, Stam R, Storey D, Thines M, Win J, Haas BJ, Dinwiddie DL, Jenkins J, Knight JR, Affourtit JP, Han CS, Chertkov O, Lindquist EA, Detter C, Grigoriev IV, Kamoun S, Kingsmore SF
Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici.
Mol Plant Microbe Interact. 2012 Oct;25(10):1350-60. doi: 10.1094/MPMI-02-12-0028-R
Lamour KH, Mudge J, Gobena D, Hurtado-Gonzales OP, Schmutz J, Kuo A, Miller NA, Rice BJ, Raffaele S, Cano LM, Bharti AK, Donahoo RS, Finley S, Huitema E, Hulvey J, Platt D, Salamov A, Savidor A, Sharma R, Stam R, Storey D, Thines M, Win J, Haas BJ, Dinwiddie DL, Jenkins J, Knight JR, Affourtit JP, Han CS, Chertkov O, Lindquist EA, Detter C, Grigoriev IV, Kamoun S, Kingsmore SF
Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici.
Mol Plant Microbe Interact. 2012 Oct;25(10):1350-60. doi: 10.1094/MPMI-02-12-0028-R
Funding
The work conducted by the U.S. Department of Energy Joint Genome
Institute, a DOE Office of Science User Facility, is supported by
the Office of Science of the U.S. Department of Energy under
Contract No. DE-AC02-05CH11231.
