Status
[December 2019] The Erysiphe pisi Palampur-1 genome was sequenced using PacBio reads and assembled with Falcon (pb-assembly 0.0.2, falcon-kit 1.2.3, pypeflow 2.1.0). Mitochondrial genome was assembled separately using Flye version 2.4 and is available in the downloads section. Post assembly analysis identified low level insect contamination best matching Tyrophagus putrescentiae (full ITS 99.2% match). Contaminant insect was identified and removed from the main assembly prior to release.
Summary statistics for the Erysiphe pisi Palampur-1 v2.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 76.36 |
| Sequencing read coverage depth | 229.38x |
| # of contigs | 538 |
| # of scaffolds | 533 |
| # of scaffolds >= 2Kbp | 492 |
| Scaffold N50 | 43 |
| Scaffold L50 (Mbp) | 0.56 |
| # of gaps | 5 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 1.77, 1.55, 1.38 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 419203 | 151045 | 36.0% |
| Ests | est.fasta | 275456466 | 165688487 | 60.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1650 | 1409 |
| transcript | 1488 | 1241 |
| exon | 514 | 300 |
| intron | 87 | 58 |
| description: | ||
| protein length (aa) | 426 | 336 |
| exons per gene | 2.89 | 3 |
| # of gene models | 7543 |
Collaborators
Mary Wildermuth, University of California, Berkeley.
Links
- JGI PhyloGroup Portals: Fungi Dikarya Ascomycota Pezizomycotina Leotiomycetes
- 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.
