Info • Russula emetica Přilba v1.0

Status

[March 2019] The genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity. The mitochondrial genome was sequenced separately and is available on the Download page.

The DNA sample source is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. Many of the smaller 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.

The RNA sample has some insect contamination.

Summary statistics for the Russula emetica Přilba v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 55.12
Sequencing read coverage depth 148.51x
# of contigs 444
# of scaffolds 444
# of scaffolds >= 2Kbp 440
Scaffold N50 29
Scaffold L50 (Mbp) 0.53
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.80, 1.79, 1.78


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 123500 95918 77.7%
Ests est.fasta 133807398 132001375 98.7%


Gene Models FilteredModels1
length (bp) of: average median
gene 1693 1448
transcript 1377 1146
exon 248 159
intron 71 59
description:
protein length (aa) 402 321
exons per gene 5.55 4
# of gene models 13215


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.