Info • Morchella steppicola PhC 289 v1.0

Status

[July 2020] The Morchella steppicola PhC 289 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.

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.

Summary statistics for the Morchella steppicola PhC 289 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 81.03
Sequencing read coverage depth 143.55x
# of contigs 341
# of scaffolds 341
# of scaffolds >= 2Kbp 341
Scaffold N50 25
Scaffold L50 (Mbp) 1.05
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.55, 2.47, 2.17


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 55537 50904 91.7%
Ests est.fasta 175310515 174414521 99.5%


Gene Models FilteredModels1
length (bp) of: average median
gene 1802 1556
transcript 1567 1341
exon 429 271
intron 91 66
description:
protein length (aa) 446 354
exons per gene 3.65 3
# of gene models 11718


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.