Info • Pisolithus tympanobaculus R1 v1.0


[March 2023] The Pisolithus tympanobaculus R1 v1.0 genome was sequenced with PacBio, assembled with Flye, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

This genome is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. Some 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 repertoire of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.

Genome Assembly
Genome Assembly size (Mbp) 98.41
Sequencing read coverage depth 99.14x
# of contigs 1026
# of scaffolds 1026
# of scaffolds >= 2Kbp 1022
Scaffold N50 174
Scaffold L50 (Mbp) 0.17
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.71, 0.70, 0.68

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 116447 103582 89.0%
Ests est.fasta 130376298 128840329 98.8%

Gene Models FilteredModels1
length (bp) of: average median
gene 1706 1414
transcript 1364 1104
exon 234 149
intron 73 56
protein length (aa) 408 317
exons per gene 5.82 5
# of gene models 17658


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.