Info • Coprinopsis sp. MPI-PUGE-AT-0042 v1.0

Status

[February 2019] The Coprinus phaeopunctatus MPI-PUGE-AT-0042 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.

Coprinus phaeopunctatus MPI-PUGE-AT-0042 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.

Summary statistics for the Coprinus phaeopunctatus v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 121.01
Sequencing read coverage depth 38.95x
# of contigs 486
# of scaffolds 486
# of scaffolds >= 2Kbp 486
Scaffold N50 54
Scaffold L50 (Mbp) 0.61
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 4.23, 2.99, 2.98


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 78858 70128 88.9%
Ests est.fasta 180634624 179313295 99.3%


Gene Models FilteredModels1
length (bp) of: average median
gene 1698 1453
transcript 1388 1170
exon 261 162
intron 74 56
description:
protein length (aa) 412 336
exons per gene 5.31 4
# of gene models 27373


Collaborators

Francis M. Martin, INRA, France.

Joseph Spatafora, Oregon State University, USA

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.