Info • Russula sp. KIS8R TL3126 v1.0

Status

[December 2024] The Russula sp. KIS8 v1.0 genome was sequenced with PacBio, assembled with Flye, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity.

This genome is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. Some 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 repertoire of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.

Genome Assembly
Genome Assembly size (Mbp) 72.42
Sequencing read coverage depth 27.49x
# of contigs 1946
# of scaffolds 1946
# of scaffolds >= 2Kbp 1942
Scaffold N50 218
Scaffold L50 (Mbp) 0.08
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.78, 0.75, 0.75


The transcriptome was contaminated with animal and bacteria RNA, resulting in a low mapping rate.
ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 213091 87700 41.2%
Ests est.fasta 116979304 113021415 96.6%


Gene Models FilteredModels1
length (bp) of: average median
gene 1906 1622
transcript 1549 1284
exon 260 157
intron 74 59
description:
protein length (aa) 446 348
exons per gene 5.96 5
# of gene models 13876


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.