Info • Morchella americana PhC192 v1.0

Status

[July 2021] The Morchella americana PhC192 v1.0 genome was sequenced with PacBio, assembled with Flye, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

We identified polymorphic content, reflected in an assembly and annotation with significant separation of alleles. Many 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 repertiore 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) 63.62
Sequencing read coverage depth
# of contigs 531
# of scaffolds 531
# of scaffolds >= 2Kbp 526
Scaffold N50 21
Scaffold L50 (Mbp) 0.82
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 4.10, 2.42, 2.22


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 59807 54865 91.7%
Ests est.fasta 175108155 171463334 97.9%


Gene Models FilteredModels1
length (bp) of: average median
gene 1856 1595
transcript 1621 1366
exon 438 273
intron 89 66
description:
protein length (aa) 462 365
exons per gene 3.70 3
# of gene models 11032


Collaborators

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.