Status
[April 2018] The nuclear genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity. The mitochondrial genome was sequenced with PacBio and assembled with Falcon.
Summary statistics for the Rhizopogon vulgaris FC72 v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 39.90 |
| Sequencing read coverage depth | 281.22x |
| # of contigs | 1127 |
| # of scaffolds | 1127 |
| # of scaffolds >= 2Kbp | 1050 |
| Scaffold N50 | 71 |
| Scaffold L50 (Mbp) | 0.14 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 1.17, 0.84, 0.81 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 63097 | 57036 | 90.4% |
| Ests | est.fasta | 97221106 | 93774015 | 96.5% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1794 | 1557 |
| transcript | 1459 | 1245 |
| exon | 228 | 145 |
| intron | 64 | 55 |
| description: | ||
| protein length (aa) | 420 | 342 |
| exons per gene | 6.39 | 5 |
| # of gene models | 11905 |
Collaborators
- Francis Martin at MycorWeb
- Peter Kennedy at University of Minnesota
- Amanda Certano at U. Minnesota
- Joseph Spatafora at Oregon State University
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.
