Info • Pisolithus croceorrhizus ssp. 2 72 v1.0


[October 2018] The Pisolithus croceorrhizus ssp. 2 72 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity.

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 Pisolithus croceorrhizus ssp. 2 72 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 76.51
Sequencing read coverage depth 213.39x
# of contigs 718
# of scaffolds 718
# of scaffolds >= 2Kbp 704
Scaffold N50 117
Scaffold L50 (Mbp) 0.20
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.98, 0.93, 0.88

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 116423 104540 89.8%
Ests est.fasta 146176937 145061344 99.2%

Gene Models FilteredModels2
length (bp) of: average median
gene 1674 1401
transcript 1337 1098
exon 223 143
intron 69 56
protein length (aa) 390 306
exons per gene 5.99 5
# of gene models 15058


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.