Info • Tricholoma populinum 2016PMI031 v1.0


[June 2020] The 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 Tricholoma populinum 2016PMI031 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 137.00
Sequencing read coverage depth 103.53x
# of contigs 496
# of scaffolds 496
# of scaffolds >= 2Kbp 496
Scaffold N50 45
Scaffold L50 (Mbp) 0.68
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 5.30, 5.03, 4.27

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 101924 99340 97.5%
Ests est.fasta 181698798 180801106 99.5%

Gene Models FilteredModels1
length (bp) of: average median
gene 1599 1331
transcript 1260 1023
exon 224 141
intron 75 57
protein length (aa) 377 296
exons per gene 5.62 4
# of gene models 19692


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.