Info • Lentinula raphanica INPA1701G ss19 v1.0

Status

[December 2017] The Lentinula raphanica INPA1701G ss19 genome was sequenced with PacBio, assembled with Falcon, 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 INPA1701G ss19 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 49.07
Sequencing read coverage depth 58.15x
# of contigs 77
# of scaffolds 77
# of scaffolds >= 2Kbp 76
Scaffold N50 15
Scaffold L50 (Mbp) 1.28
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.15, 2.13, 2.08


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 46254 45414 98.2%
Ests est.fasta 102761045 102615771 99.9%


Gene Models FilteredModels1
length (bp) of: average median
gene 1725 1461
transcript 1403 1182
exon 242 148
intron 69 58
description:
protein length (aa) 419 339
exons per gene 5.80 4
# of gene models 16189


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.