Info • Phellinus viticola PhevitSig-SM15 v1.0


[June 2020] The Phellinus viticola PhevitSig-SM15 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 Phellinus viticola v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 59.36
Sequencing read coverage depth 245.9x
# of contigs 296
# of scaffolds 296
# of scaffolds >= 2Kbp 296
Scaffold N50 35
Scaffold L50 (Mbp) 0.41
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.06, 1.69, 1.67

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 78231 73277 93.7%
Ests est.fasta 127227597 125748679 98.8%

Gene Models FilteredModels2
length (bp) of: average median
gene 1831 1603
transcript 1493 1281
exon 250 151
intron 70 58
protein length (aa) 437 359
exons per gene 5.98 5
# of gene models 13824



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.