Info • Ceratobasidium sp. 379 v1.0


[July 2020] The Ceratobasidium sp. 379 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.

The genome is likely a polymorphic dikaryon, and this is 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 Ceratobasidium sp. 379 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 83.87
Sequencing read coverage depth 74.98x
# of contigs 534
# of scaffolds 534
# of scaffolds >= 2Kbp 533
Scaffold N50 59
Scaffold L50 (Mbp) 0.36
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.16, 1.91, 1.72

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 45078 42520 94.3%
Ests est.fasta 55771257 55244133 99.1%

Gene Models FilteredModels1
length (bp) of: average median
gene 1876 1622
transcript 1486 1275
exon 220 141
intron 70 56
protein length (aa) 443 364
exons per gene 6.75 5
# of gene models 17852



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.