Status
The genome sequence and gene predictions of Fusarium oxysporum f. sp. pisi HDV247 have not been determined by the Joint Genome Institute (JGI), but were downloaded from NCBI on Oct 1, 2019. In order to allow comparative analyses with other fungal genomes sequenced by the JGI, a copy of this genome is incorporated into Mycocosm. Please note that this copy of the genome is not maintained by NCBI and is therefore not automatically updated. JGI tools were used to automatically annotate predicted proteins.
Summary statistics for the Fusarium oxysporum f. sp.
pisi HDV247 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 55.19 |
| Sequencing read coverage depth | 242x |
| # of contigs | 1744 |
| # of scaffolds | 472 |
| # of scaffolds >= 2Kbp | 435 |
| Scaffold N50 | 7 |
| Scaffold L50 (Mbp) | 2.84 |
| # of gaps | 1272 |
| % of scaffold length in gaps | 1.2% |
| Three largest Scaffolds (Mbp) | 5.90, 4.50, 4.45 |
| Gene Models | ExternalModels | |
| length (bp) of: | average | median |
| gene | 2332 | 1959 |
| transcript | 2174 | 1803 |
| exon | 720 | 427 |
| intron | 81 | 56 |
| description: | ||
| protein length (aa) | 457 | 387 |
| exons per gene | 3.02 | 3 |
| # of gene models | 26378 |
Collaborators
Li-Jun Ma, University of Massachusetts Amherst, USA
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Williams AH, Sharma M, Thatcher LF, Azam S, Hane JK, Sperschneider J, Kidd BN, Anderson JP, Ghosh R, Garg G, Lichtenzveig J, Kistler HC, Shea T, Young S, Buck SA, Kamphuis LG, Saxena R, Pande S, Ma LJ, Varshney RK, Singh KB
Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors.
BMC Genomics. 2016 Mar 5;17():191. doi: 10.1186/s12864-016-2486-8
Williams AH, Sharma M, Thatcher LF, Azam S, Hane JK, Sperschneider J, Kidd BN, Anderson JP, Ghosh R, Garg G, Lichtenzveig J, Kistler HC, Shea T, Young S, Buck SA, Kamphuis LG, Saxena R, Pande S, Ma LJ, Varshney RK, Singh KB
Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors.
BMC Genomics. 2016 Mar 5;17():191. doi: 10.1186/s12864-016-2486-8
Links
- JGI EcoGroup Portals: Plant Pathogens
- JGI PhyloGroup Portals: Fungi Dikarya Ascomycota Pezizomycotina Sordariomycetes Hypocreales Nectriaceae Fusarium
Funding
This project was not sequenced at the JGI.
