Info • Pisolithus croceorrhizus subspA 74A v1.0

Status

[August 2018] (August 2018) The Pisolithus croceorrhizus 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 mitochondrial genome was assembled separately and is available on the Download page.

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 subspA 74A v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 80.71
Sequencing read coverage depth 56.17x
# of contigs 576
# of scaffolds 576
# of scaffolds >= 2Kbp 565
Scaffold N50 95
Scaffold L50 (Mbp) 0.26
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.06, 0.98, 0.92


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 113614 103335 91.0%
Ests est.fasta 125355415 124458158 99.3%


Gene Models FilteredModels2
length (bp) of: average median
gene 1675 1396
transcript 1336 1098
exon 222 141
intron 70 56
description:
protein length (aa) 388 303
exons per gene 6.01 5
# of gene models 15799


Funding

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.