Status
[April 2019] The Lentinula raphanica JLM1587 genome was sequenced with Illumina technology, assembled sequentially with Velvet and AllPathsLG, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.
Summary statistics for the Lentinula raphanica JLM1587
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 38.60 |
| Sequencing read coverage depth | 141.8x |
| # of contigs | 2424 |
| # of scaffolds | 2238 |
| # of scaffolds >= 2Kbp | 1702 |
| Scaffold N50 | 279 |
| Scaffold L50 (Mbp) | 0.04 |
| # of gaps | 186 |
| % of scaffold length in gaps | 0.5% |
| Three largest Scaffolds (Mbp) | 0.26, 0.22, 0.18 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 106223 | 98138 | 92.4% |
| Ests | est.fasta | 276035814 | 257019119 | 93.1% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1754 | 1496 |
| transcript | 1435 | 1223 |
| exon | 247 | 149 |
| intron | 68 | 58 |
| description: | ||
| protein length (aa) | 421 | 344 |
| exons per gene | 5.82 | 5 |
| # of gene models | 14701 |
Collaborators
- David Hibbett, Clark University
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Sierra-Patev Sean, Min Byoungnam, Naranjo-Ortiz Miguel, Looney Brian, Konkel Zachary, Slot Jason C., Sakamoto Yuichi, Steenwyk Jacob L., Rokas Antonis, Carro Juan, Camarero Susana, Ferreira Patricia, Molpeceres Gonzalo, Ruiz-Dueñas Francisco J., Serrano Ana, Henrissat Bernard, Drula Elodie, Hughes Karen W., Mata Juan L., Ishikawa Noemia Kazue, Vargas-Isla Ruby, Ushijima Shuji, Smith Chris A., Donoghue John, Ahrendt Steven, Andreopoulos William, He Guifen, LaButti Kurt, Lipzen Anna, Ng Vivian, Riley Robert, Sandor Laura, Barry Kerrie, Martínez Angel T., Xiao Yang, Gibbons John G., Terashima Kazuhisa, Grigoriev Igor V., Hibbett David
A global phylogenomic analysis of the shiitake genus <i>Lentinula</i>
Proc. Natl. Acad. Sci. U.S.A.. 2023;120(10): doi: 10.1073/pnas.2214076120
Sierra-Patev Sean, Min Byoungnam, Naranjo-Ortiz Miguel, Looney Brian, Konkel Zachary, Slot Jason C., Sakamoto Yuichi, Steenwyk Jacob L., Rokas Antonis, Carro Juan, Camarero Susana, Ferreira Patricia, Molpeceres Gonzalo, Ruiz-Dueñas Francisco J., Serrano Ana, Henrissat Bernard, Drula Elodie, Hughes Karen W., Mata Juan L., Ishikawa Noemia Kazue, Vargas-Isla Ruby, Ushijima Shuji, Smith Chris A., Donoghue John, Ahrendt Steven, Andreopoulos William, He Guifen, LaButti Kurt, Lipzen Anna, Ng Vivian, Riley Robert, Sandor Laura, Barry Kerrie, Martínez Angel T., Xiao Yang, Gibbons John G., Terashima Kazuhisa, Grigoriev Igor V., Hibbett David
A global phylogenomic analysis of the shiitake genus <i>Lentinula</i>
Proc. Natl. Acad. Sci. U.S.A.. 2023;120(10): doi: 10.1073/pnas.2214076120
Links
- JGI PhyloGroup Portals: Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricales Lentinula
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.
