Info • Morchella fluvialis PhC 265 v3.0


[June 2020] The Morchella fluvialis PhC 265 v3.0 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 fluvialis PhC 265 v3.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 55.01
Sequencing read coverage depth 115.84x
# of contigs 108
# of scaffolds 108
# of scaffolds >= 2Kbp 108
Scaffold N50 12
Scaffold L50 (Mbp) 1.73
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 4.17, 3.56, 3.50

Note: lower than expected mapping of EST clusters is attributed to a small read percentage contributing to the creation of unmatched contigs. Unmapped RNA reads hit organisms in the target genus and bacteria.

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 89285 54711 61.3%
Ests est.fasta 197533317 188673673 95.5%

Gene Models FilteredModels1
length (bp) of: average median
gene 1789 1523
transcript 1562 1316
exon 426 266
intron 87 65
protein length (aa) 444 348
exons per gene 3.66 3
# of gene models 11113



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.