Status
[March 2023] The Fusarium oxysporum f. sp. lycopersici 4287 v3.0 genome was sequenced with PacBio, assembled with Flye, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 55.58 |
| Sequencing read coverage depth | 6.59x |
| # of contigs | 45 |
| # of scaffolds | 44 |
| # of scaffolds >= 2Kbp | 44 |
| Scaffold N50 | 6 |
| Scaffold L50 (Mbp) | 4.14 |
| # of gaps | 1 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 6.14, 5.44, 5.19 |
Some EST libraries were collected during infection stages and therefore included host reads, leading to poor read mapping seen below.
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 112229289 | 54963963 | 49.0% |
| Other | IsoSeq_hq_reads_HWGSY | 80035 | 11526 | 14.4% |
| Other | IsoSeq_hq_reads_HWGSZ | 143223 | 136923 | 95.6% |
| Other | RNAseq_contigs | 321331 | 66152 | 20.6% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1863 | 1559 |
| transcript | 1683 | 1426 |
| exon | 550 | 346 |
| intron | 89 | 56 |
| description: | ||
| protein length (aa) | 477 | 385 |
| exons per gene | 3.06 | 2 |
| # of gene models | 17629 |
Collaborators
- Li-Jun Ma, University of Massachusetts Amherst, USA
- Michael Freitag, Department of Biochemistry & Biophysics, Oregon State University
Links
- JGI PhyloGroup Portals: Fungi Dikarya Ascomycota Pezizomycotina Sordariomycetes Hypocreomycetidae Hypocreales Nectriaceae Fusarium
- JGI EcoGroup Portals: Plant Pathogens
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.
