Info • Xylaria nigripes YMJ 653 v1.0

Status

[August 2019] The Xylaria nigripes YMJ 653 v1.0 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

Summary statistics for the Xylaria nigripes v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 34.60
Sequencing read coverage depth 895.41x
# of contigs 64
# of scaffolds 64
# of scaffolds >= 2Kbp 64
Scaffold N50 12
Scaffold L50 (Mbp) 1.10
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.42, 1.85, 1.70


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 50110 48750 97.3%
Ests est.fasta 157039332 154696974 98.5%


Gene Models FilteredModels1
length (bp) of: average median
gene 2067 1843
transcript 1876 1662
exon 619 372
intron 96 70
description:
protein length (aa) 487 406
exons per gene 3.03 3
# of gene models 8815


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.