Info • Lactarius quietus S23C v1.0

Status

(May 2016) The Lactarius quietus S23C genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline.

Lactarius quietus S23C is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. 1404 of the 2812 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 Lactarius quietus S23C v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 115.90
Sequencing read coverage depth 97x
# of contigs 2812
# of scaffolds 2812
# of scaffolds >= 2Kbp 2746
Scaffold N50 325
Scaffold L50 (Mbp) 0.09
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.08, 0.90, 0.81


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 56406 52661 93.4%
Ests est.fasta 180107308 177774464 98.7%
Ests NCBI_ESTs 453 203 44.8%


Gene Models FilteredModels1
length (bp) of: average median
gene 1556 1268
transcript 1233 1001
exon 224 146
intron 73 57
description:
protein length (aa) 358 272
exons per gene 5.52 4
# of gene models 18943


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.