Info • Plectosphaerella cucumerina RP01 v1.0

Status

[December 2017] The Plectosphaerella cucumerina RP01 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 Plectosphaerella cucumerina v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 36.52
Sequencing read coverage depth 141.27x
# of contigs 11
# of scaffolds 11
# of scaffolds >= 2Kbp 11
Scaffold N50 3
Scaffold L50 (Mbp) 6.49
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 7.95, 7.80, 6.49


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 27719 27303 98.5%
Ests est.fasta 117868249 37513830 31.8%


Gene Models FilteredModels1
length (bp) of: average median
gene 1839 1610
transcript 1695 1480
exon 602 376
intron 81 59
description:
protein length (aa) 482 409
exons per gene 2.82 2
# of gene models 12956


Collaborators

Francis M. Martin, INRA, France.

Joseph Spatafora, Oregon State University, USA

Genome Reference(s)

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

Mesny F, Miyauchi S, Thiergart T, Pickel B, Atanasova L, Karlsson M, Hüttel B, Barry KW, Haridas S, Chen C, Bauer D, Andreopoulos W, Pangilinan J, LaButti K, Riley R, Lipzen A, Clum A, Drula E, Henrissat B, Kohler A, Grigoriev IV, Martin FM, Hacquard S
Genetic determinants of endophytism in the Arabidopsis root mycobiome.
Nat Commun. 2021 Dec 10;12(1):7227. doi: 10.1038/s41467-021-27479-y

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.