Info • Pisolithus microcarpus 441 v2.0

Status

[June 2020] The genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was 1) sequenced with 454 and assembled with MIRA, 2) sequenced with Illumina and assembled with Trinity, and 3) 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 microcarpus 441 v2.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 77.25
Sequencing read coverage depth 92.52x
# of contigs 151
# of scaffolds 151
# of scaffolds >= 2Kbp 151
Scaffold N50 16
Scaffold L50 (Mbp) 1.41
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 5.23, 4.07, 3.94


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests JGI_Illumina_RNA_reads 182469908 181839809 99.7%
Other INRA_454_RNA_contigs 59500 41022 68.9%
Other INRA_454_RNA_reads 195303 167395 85.7%
Other JGI_Illumina_RNA_contigs 103874 97981 94.3%
Other JGI_Pacbio_RNA_consensii 56744 54605 96.2%
Other JGI_Pacbio_RNA_reads 1022219 994447 97.3%


Gene Models FilteredModels1
length (bp) of: average median
gene 1630 1337
transcript 1302 1044
exon 227 149
intron 71 56
description:
protein length (aa) 383 295
exons per gene 5.73 4
# of gene models 16766


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.