Status
[September 2020] The Cryomyces antarcticus CBS 116301 v3.0 genome was sequenced with PacBio, assembled with HiCanu version 2.0, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.
Cryomyces antarcticus CBS 116301 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.
Genome Assembly | |
Genome Assembly size (Mbp) | 51.66 |
Sequencing read coverage depth | 32.75x |
# of contigs | 262 |
# of scaffolds | 262 |
# of scaffolds >= 2Kbp | 262 |
Scaffold N50 | 24 |
Scaffold L50 (Mbp) | 0.69 |
# of gaps | 0 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 2.09, 1.76, 1.53 |
ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
EstClusters | ESTclusters | 33028 | 32249 | 97.6% |
Ests | est.fasta | 49805129 | 49642727 | 99.7% |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 1847 | 1602 |
transcript | 1657 | 1418 |
exon | 527 | 318 |
intron | 90 | 62 |
description: | ||
protein length (aa) | 472 | 387 |
exons per gene | 3.15 | 3 |
# of gene models | 9404 |
Collaborators
Stephen B Goodwin, Purdue University, USA
Joseph Spatafora, Oregon State University, USA
Genome Reference(s)
Gomez-Gutierrrez Sandra V., Sic-Hernandez Wily R., Haridas Sajeet, LaButti Kurt, Eichenberger Joanne, Kaur Navneet, Lipzen Anna, Barry Kerrie, Goodwin Stephen B., Gribskov Michael, Grigoriev Igor V.
Comparative genomics of the extremophile Cryomyces antarcticus and other psychrophilic Dothideomycetes
Front. Fungal Biol.. 2024;5: doi: 10.3389/ffunb.2024.1418145
Links
- 1000 Fungal Genomes Project
- JGI PhyloGroup Portals: Fungi Dikarya Ascomycota Pezizomycotina Dothideomycetes