Info • Lentinula edodes W1-26 v1.0


[February 2019] The genome sequence and gene prediction of Lentinula edodes W1-26 were not determined by the JGI, but were downloaded from ShiitakeGDB and have been published (PubMed: 27500531). Please note that this copy of the genome is not maintained by the author and is therefore not automatically updated. This copy of the genome does not include the mitochondrial chromosome or genes. The JGI Annotation Pipeline was used to add additional functional annotation to the author's chromosomes and proteins.

The downloaded GFF3 file contained alternative models on a locus tagged with ".t2", ".t3", ".t4", and so on. We created the FilteredModels track so as to represent only non-overlapping genes, and the GeneCatalog was built based on the FilteredModels. Moreover, we discarded gene models having internal stops and transposable element-derived genes. As a result, 12,538 gene models were finally presented. All gene models before filtering can be found in ExternalModels track.

Summary statistics for the Lentinula edodes W1-26 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 41.83
Sequencing read coverage depth 232x
# of contigs 1164
# of scaffolds 340
# of scaffolds >= 2Kbp 303
Scaffold N50 41
Scaffold L50 (Mbp) 0.30
# of gaps 824
% of scaffold length in gaps 2.5%
Three largest Scaffolds (Mbp) 1.37, 1.05, 1.00

Gene Models FilteredModels2
length (bp) of: average median
gene 2248 1961
transcript 1860 1619
exon 267 156
intron 67 58
protein length (aa) 475 387
exons per gene 6.95 6
# of gene models 12538

Genome Reference(s)


This project was not sequenced at the JGI.