Info • Lentinula aciculospora JLM2183 v1.0

Status

[February 2021] The Lentinula aciculospora JLM2183 v1.0 genome was sequenced with PacBio, assembled with HiCanu, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

The genome is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. Many of the scaffolds are very similar to larger scaffolds and are predicted to constitute an alternate or secondary haplotype. To represent these primary and secondary haplotypes in the Portal, we have created 'primary alleles' and 'secondary alleles' gene model tracks, comprising the models found on each haplotype. The goal of the GeneCatalog (GC) is to produce a non-redundant set of models which captures the full functional repertiore of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.

Summary statistics for the Lentinula aciculospora JLM2183 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 110.95
Sequencing read coverage depth 19.29x
# of contigs 290
# of scaffolds 290
# of scaffolds >= 2Kbp 290
Scaffold N50 25
Scaffold L50 (Mbp) 1.19
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 5.75, 4.35, 4.27


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 67963 60140 88.5%
Ests est.fasta 425647019 421526312 99.0%


Gene Models FilteredModels2
length (bp) of: average median
gene 1888 1635
transcript 1535 1316
exon 235 142
intron 66 57
description:
protein length (aa) 447 366
exons per gene 6.53 5
# of gene models 11469


Collaborators

Genome Reference(s)

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.