Due to a planned NERSC power outage, JGI portals will be unavailable 6:00am PDT July 10 - 11:59pm PDT July 14. System Status updates available here.
Info • Cantharellales sp. MUCL 035158 v1.0

Status

[March 2020] The Cantharellales sp. MUCL 035158 v1.0 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

Cantharellales sp. MUCL 035158 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 repertoire 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 Cantharellales sp. MUCL 035158 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 53.37
Sequencing read coverage depth 177.55x
# of contigs 522
# of scaffolds 522
# of scaffolds >= 2Kbp 522
Scaffold N50 17
Scaffold L50 (Mbp) 0.70
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 3.51, 2.48, 2.26


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 65471 61397 93.8%
Ests est.fasta 166024014 163811215 98.7%


Gene Models FilteredModels1
length (bp) of: average median
gene 2038 1771
transcript 1586 1378
exon 243 148
intron 84 67
description:
protein length (aa) 455 381
exons per gene 6.53 5
# of gene models 12467


Collaborators

Petr Baldrian, Institute of Microbiology of the CAS, Czech Republic

Francis M. Martin, INRA, France.

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.