Info • Russula decolorans Maridalen v1.0

Status

[November 2022] The Russula decolorans 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. The mitochondrial genome was assembled separately and is available in the Download tab.

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) 57.04
Sequencing read coverage depth 135.06x
# of contigs 394
# of scaffolds 394
# of scaffolds >= 2Kbp 394
Scaffold N50 46
Scaffold L50 (Mbp) 0.29
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.96, 1.66, 1.46


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 55484 51845 93.4%
Ests est.fasta 121513437 120166045 98.9%


Gene Models FilteredModels1
length (bp) of: average median
gene 1983 1657
transcript 1612 1329
exon 256 159
intron 72 58
description:
protein length (aa) 464 362
exons per gene 6.29 5
# of gene models 12065


Collaborators

  • Petr Baldrian, Institute of Microbiology of the Czech Academy of Sciences, Czech Republic

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.