Info • Lentinula lateritia RV95-379 v1.0

Status

[July 2020] The Lentinula lateritia RV95-379 v1.0 genome was sequenced with Illumina, assembled with SPAdes, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

Post-assembly BLAST analysis identified bacterial, and to a lesser degree fungal, contamination best matching bacterium Ralstonia picketii and Tolypocladium inflatum, respectively. From the 4126 initial scaffolds, we detected and removed the 466 (5,667,835 bp) Ralstonia sequences. Also, we removed nine non-target fungal mitochondrial (20,452 bp) and 63 other bacterial (169,568 bp) sequences. Six scaffolds (30,194 bp) were removed based on the tetramer principal component analysis. This clean-up process resulted in the 3582 sequences of the genome (39,474,067 bp).

Four Ralstonia genomes were used as references based on the highest similarity with the NCBI nt database (https://ftp.ncbi.nlm.nih.gov/blast/db/). Ralstonia pickettii 12J (GCA_000020205.1) Ralstonia pickettii 12D (GCA_000023425.1) Ralstonia insidiosa FC1138 (GCA_001653935.1) Ralstonia insidiosa ATCC 49129 (GCA_001663855.1).

Summary statistics for the Lentinula lateritia RV95-379 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 39.47
Sequencing read coverage depth 96.49x
# of contigs 3663
# of scaffolds 3582
# of scaffolds >= 2Kbp 2303
Scaffold N50 282
Scaffold L50 (Mbp) 0.04
# of gaps 81
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.29, 0.23, 0.20


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 59290 54744 92.3%
Ests est.fasta 134027970 133504847 99.6%


Gene Models FilteredModels1
length (bp) of: average median
gene 1793 1534
transcript 1466 1242
exon 241 147
intron 66 57
description:
protein length (aa) 430 348
exons per gene 6.09 5
# of gene models 13702


Collaborators

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.