Status
The Phytophthora cinnamomi var. cinnamomi genome was sequenced using the Illumina platform , 454 platform and Sanger sequencing. Each fastq file was QC filtered for artifact/process contamination and subsequently assembled with AllPathsLG release version R41043 (Gnerre et al., 2010).
Summary statistics for the Phytophthora cinnamomi var
cinnamomi v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 77.97 |
| Sequencing read coverage depth | 69.6x |
| # of contigs | 9537 |
| # of scaffolds | 1314 |
| # of scaffolds >= 2Kbp | 840 |
| Scaffold N50 | 89 |
| Scaffold L50 (Mbp) | 0.26 |
| # of gaps | 8223 |
| % of scaffold length in gaps | 25.3% |
| Three largest Scaffolds (Mbp) | 1.21, 1.09, 0.99 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | EstClusters2 | 61542 | 50305 | 81.7% |
| Other | RNAseq_assemblies | 40282 | 34236 | 85.0% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1303 | 907 |
| transcript | 1123 | 788 |
| exon | 536 | 288 |
| intron | 166 | 79 |
| description: | ||
| protein length (aa) | 348 | 233 |
| exons per gene | 2.10 | 1 |
| # of gene models | 26131 |
Collaborators
Wayne Reeve Ph.D., Centre for Phytophthora Science and Management, Murdoch University, School of Biological Science, Perth, Australia
Links
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.
