Info • Pisolithus tinctorius Marx 270 v2.0

Status

[June 2020] The genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was both 1) sequenced with Illumina and assembled with Trinity, and 2) sequenced with PacBio and clustered with IsoSeq. The mitochondrial genome was assemblied 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 tinctorius Marx 270 v2.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 92.53
Sequencing read coverage depth 131.85x
# of contigs 224
# of scaffolds 224
# of scaffolds >= 2Kbp 224
Scaffold N50 17
Scaffold L50 (Mbp) 1.37
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 6.75, 6.55, 4.45


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests JGI_Illumina_RNA_reads 124358787 123980484 99.7%
Other JGI_Illumina_RNA_contigs 93928 87958 93.6%
Other JGI_Pacbio_RNA_consensii 53567 52596 98.2%
Other JGI_Pacbio_RNA_reads 1362383 1347960 98.9%


Gene Models FilteredModels1
length (bp) of: average median
gene 1639 1352
transcript 1311 1047
exon 228 148
intron 71 56
description:
protein length (aa) 383 297
exons per gene 5.74 4
# of gene models 16924


Genome Reference(s)

Please cite the following publication(s) if you use the data from this genome in your research:

Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canbäck B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Doré J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Högberg N, Johansson T, Khouja HR, LaButti K, Lahrmann U, Levasseur A, Lindquist EA, Lipzen A, Marmeisse R, Martino E, Murat C, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm RA, Perotto S, Peter M, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A, Tunlid A, Grigoriev IV, Hibbett DS, Martin F
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.
Nat Genet. 2015 Apr;47(4):410-5. doi: 10.1038/ng.3223

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

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.