Status
[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.
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 |
description: | ||
protein length (aa) | 390 | 306 |
exons per gene | 5.99 | 5 |
# of gene models | 15058 |
Collaborators
Genome Reference(s)
Plett JM, Miyauchi S, Morin E, Plett K, Wong-Bajracharya J, de Freitas Pereira M, Kuo A, Henrissat B, Drula E, Wojtalewicz D, Riley R, Pangilinan J, Andreopoulos W, LaButti K, Daum C, Yoshinaga Y, Fauchery L, Ng V, Lipzen A, Barry K, Singan V, Guo J, Lebel T, Costa MD, Grigoriev IV, Martin F, Anderson IC, Kohler A
Speciation underpinned by unexpected molecular diversity in the mycorrhizal fungal genus Pisolithus.
Mol Biol Evol. 2023 Feb 22;():. doi: 10.1093/molbev/msad045