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Info • Lentinula edodes B17 v1.3

Status

The Lentinula edodes B17 genome sequence and gene models were not determined by the Joint Genome Institute (JGI), but were provided by Hojin Ryu on Sep 24, 2020. Please note that this copy of the genome is not maintained by the author and is therefore not automatically updated. In order to allow comparative analyses with other fungal genomes sequenced by the JGI, a copy of this genome is incorporated into MycoCosm. The JGI Annotation Pipeline was used to add functional annotation to this genome.

We combined three gene predictions and generated the FilteredModels1 gene track by selecting plausible gene models: two versions provided by the author and the one we predicted using the Braker with the L. edodes RNA-seq (Sequence Reads Archive: SRR7439932). In order to ensure this genome is comparable to those sequenced by the JGI, we applied filters to remove if present: 1) transposable elements, 2) pseudogenes, 3) alternative transcripts and overlapping models, 4) alleles on secondary scaffolds and 5) unsupported short models. All published models are available in the ExternalModels track.

Summary statistics for the Lentinula edodes B17 v1.3 release are below.
Genome Assembly
Genome Assembly size (Mbp) 46.10
Sequencing read coverage depth 61.0x
# of contigs 122
# of scaffolds 30
# of scaffolds >= 2Kbp 30
Scaffold N50 5
Scaffold L50 (Mbp) 3.66
# of gaps 92
% of scaffold length in gaps 0.4%
Three largest Scaffolds (Mbp) 5.85, 5.33, 5.31


Gene Models FilteredModels1
length (bp) of: average median
gene 1586 1331
transcript 1178 975
exon 184 113
intron 77 58
description:
protein length (aa) 393 325
exons per gene 6.40 5
# of gene models 13943


Genome Reference(s)

Funding

This project was not sequenced at the JGI.