Info • Hypoxylon rubiginosum ER1909 v1.0

Status

[June 2019] The Hypoxylon rubiginosum ER1909 v1.0 genome was sequenced with Illumina, assembled with SPAdes, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

Summary statistics for the Hypoxylon rubiginosum ER1909 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 44.16
Sequencing read coverage depth 90.53x
# of contigs 484
# of scaffolds 472
# of scaffolds >= 2Kbp 337
Scaffold N50 30
Scaffold L50 (Mbp) 0.44
# of gaps 12
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.79, 1.41, 1.23


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 39530 37323 94.4%
Ests est.fasta 114450163 113242832 98.9%


Gene Models FilteredModels1
length (bp) of: average median
gene 1994 1762
transcript 1828 1606
exon 612 388
intron 85 64
description:
protein length (aa) 485 407
exons per gene 2.99 3
# of gene models 13953


Collaborators

Genome Reference(s)

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

Franco MEE, Wisecaver JH, Arnold AE, Ju YM, Slot JC, Ahrendt S, Moore LP, Eastman KE, Scott K, Konkel Z, Mondo SJ, Kuo A, Hayes RD, Haridas S, Andreopoulos B, Riley R, LaButti K, Pangilinan J, Lipzen A, Amirebrahimi M, Yan J, Adam C, Keymanesh K, Ng V, Louie K, Northen T, Drula E, Henrissat B, Hsieh HM, Youens-Clark K, Lutzoni F, Miadlikowska J, Eastwood DC, Hamelin RC, Grigoriev IV, U'Ren JM
Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes.
New Phytol. 2022 Feb;233(3):1317-1330. doi: 10.1111/nph.17873

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.