Info • Lentinula raphanica TFB8682 v1.0

Status

[November 2018] The Lentinula raphanica TFB8682 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 TFB8682 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 38.98
Sequencing read coverage depth 143x
# of contigs 2560
# of scaffolds 2325
# of scaffolds >= 2Kbp 1755
Scaffold N50 269
Scaffold L50 (Mbp) 0.04
# of gaps 235
% of scaffold length in gaps 0.5%
Three largest Scaffolds (Mbp) 0.31, 0.19, 0.19


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 79551 72588 91.2%
Ests est.fasta 178234163 169875955 95.3%


Gene Models FilteredModels1
length (bp) of: average median
gene 1757 1508
transcript 1446 1243
exon 249 153
intron 67 58
description:
protein length (aa) 418 342
exons per gene 5.80 5
# of gene models 14961


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

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.