Info • Jimgerdemannia flammicorona GMNB39

Status

[October 2018] The genome of Jimgerdemannia flammicorona was sequenced at JGI, but assembled and annotated by Ying Chang at Oregon State University. JGI tools were used to automatically annotate predicted proteins. The material used for sequencing of Jimgerdemannia flammicorona resulted in a metagenome. Therefore, assembly was done using Spades v3.12.0 and VizBin (Laczny et al., 2015) was used to separate individual genomes. Maker was then used to annotate the extracted J. flammicorona GMNB39 genome. Please note that Ying does not maintain this copy of the genome and therefore it is not automatically updated.

Summary statistics for the Jimgerdemannia flammicorona GMNB39 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 239.57
Sequencing read coverage depth
# of contigs 33875
# of scaffolds 33875
# of scaffolds >= 2Kbp 26354
Scaffold N50 6348
Scaffold L50 (Mbp) 0.01
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.09, 0.08, 0.07


Gene Models ExternalModels
length (bp) of: average median
gene 1747 1281
transcript 1341 996
exon 305 183
intron 122 100
description:
protein length (aa) 350 259
exons per gene 4.39 3
# of gene models 13653


Collaborators

Ying Chang, Oregon State University, USA

Joseph Spatafora, Oregon State University, USA

Greg Bonito, Michigan State University, USA

Alessandro Desirò, Michigan State University, USA

Genome Reference(s)

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

Chang Y, Desirò A, Na H, Sandor L, Lipzen A, Clum A, Barry K, Grigoriev IV, Martin FM, Stajich JE, Smith ME, Bonito G, Spatafora JW
Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota.
New Phytol. 2019 Apr;222(1):511-525. doi: 10.1111/nph.15613

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.