Status
Summary statistics for the Phytophthora sojae v3.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 82.60 |
| Sequencing read coverage depth | 8 |
| # of contigs | 1643 |
| # of scaffolds | 83 |
| # of scaffolds >= 2Kbp | 83 |
| Scaffold N50 | 4 |
| Scaffold L50 (Mbp) | 7.61 |
| # of gaps | 780 |
| % of scaffold length in gaps | 4.0% |
| Three largest Scaffolds (Mbp) | 13.39, 11.59, 10.77 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | ABI RNAseq assemblies | 27804 | 21124 | 76.0% |
| ESTs | Sanger ESTs | 7850 | 6869 | 87.5% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1421 | 992 |
| transcript | 1181 | 843 |
| exon | 494 | 272 |
| intron | 174 | 79 |
| description: | ||
| protein length (aa) | 379 | 273 |
| exons per gene | 2.39 | 2 |
| # of gene models | 26584 |
Collaborators
Brett Tyler, Ph.D., Virginia Bioinformatics Institute, Virginia Polytechnic and State University
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL
Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.
Science. 2006 Sep 1;313(5791):1261-6. doi: 10.1126/science.1128796
Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL
Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.
Science. 2006 Sep 1;313(5791):1261-6. doi: 10.1126/science.1128796
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.
