Info • Phellopilus nigrolimitatus SigPhenig9 v1.0


[March 2018] The Phellopilus nigrolimitatus SigPhenig9 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.

This Phellopilus nigrolimitatus assembly is likely partially diploid, and this is reflected in an assembly and annotation with significant separation of alleles. 555 of the 696 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.

Summary statistics for the Phellopilus nigrolimitatus v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 56.76
Sequencing read coverage depth 140.98x
# of contigs 696
# of scaffolds 696
# of scaffolds >= 2Kbp 690
Scaffold N50 35
Scaffold L50 (Mbp) 0.34
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.65, 2.27, 1.64

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 95256 90768 95.3%
Ests est.fasta 109150148 108128203 99.1%

Gene Models FilteredModels1
length (bp) of: average median
gene 1770 1525
transcript 1424 1212
exon 246 151
intron 74 61
protein length (aa) 410 334
exons per gene 5.78 5
# of gene models 14792


Sundy Maurice, University of Oslo, Norway

Håvard Kauserud, University of Oslo, Norway

Francis M. Martin, INRA, France.

Genome Reference(s)


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.