Info • Mycena galopus ATCC-62051 v1.0

Status

The Mycena galopus ATCC 62051 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Rnnotator. The mitochondrial genome was sequenced with PacBio technology and assembled with Celera.

Mycena galopus ATCC-62051 is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. 796 of the 1364 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 Mycena galopus ATCC-62051 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 211.36
Sequencing read coverage depth 80.0955730724134x
# of contigs 1364
# of scaffolds 1364
# of scaffolds >= 2Kbp 1355
Scaffold N50 110
Scaffold L50 (Mbp) 0.49
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 3.65, 3.42, 2.16


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 69408 65078 93.8%
Ests est.fasta 133977271 133240761 99.5%


Gene Models FilteredModels2
length (bp) of: average median
gene 1487 1221
transcript 1144 939
exon 211 135
intron 80 55
description:
protein length (aa) 346 274
exons per gene 5.42 4
# of gene models 49694


Collaborators

Genome Reference(s)

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

Miyauchi S, Kiss E, Kuo A, Drula E, Kohler A, Sánchez-García M, Morin E, Andreopoulos B, Barry KW, Bonito G, Buée M, Carver A, Chen C, Cichocki N, Clum A, Culley D, Crous PW, Fauchery L, Girlanda M, Hayes RD, Kéri Z, LaButti K, Lipzen A, Lombard V, Magnuson J, Maillard F, Murat C, Nolan M, Ohm RA, Pangilinan J, Pereira MF, Perotto S, Peter M, Pfister S, Riley R, Sitrit Y, Stielow JB, Szöllősi G, Žifčáková L, Štursová M, Spatafora JW, Tedersoo L, Vaario LM, Yamada A, Yan M, Wang P, Xu J, Bruns T, Baldrian P, Vilgalys R, Dunand C, Henrissat B, Grigoriev IV, Hibbett D, Nagy LG, Martin FM
Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits.
Nat Commun. 2020 Oct 12;11(1):5125. doi: 10.1038/s41467-020-18795-w

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.