Info • Fusarium oxysporum Fo5176 v1.0

Status

[December 2020] The genome sequence of Fusarium oxysporum Fo5176 were not determined by the Joint Genome Institute (JGI), but were downloaded from NCBI on Oct 14, 2020. This genome was sequenced with Illumina NovaSeq and PacBio Sequel, assembled with HGAP v. 4, Juicer v. 1.5 and Juicebox v. 1.11.08, and annotated with the JGI Annotation Pipeline.

Summary statistics for the Fusarium oxysporum Fo5176 release are below.
Genome Assembly
Genome Assembly size (Mbp) 67.98
Sequencing read coverage depth 120.0x
# of contigs 25
# of scaffolds 19
# of scaffolds >= 2Kbp 19
Scaffold N50 7
Scaffold L50 (Mbp) 4.09
# of gaps 6
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 6.73, 5.89, 5.48


RNA was obtained from an infection time course experiment. The presence of host cell RNA accounts for the poor mapping statistics below.

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 268462 35889 13.4%
Ests est.fasta 270291508 79835372 29.5%


Gene Models FilteredModels1
length (bp) of: average median
gene 1738 1478
transcript 1552 1326
exon 519 315
intron 95 57
description:
protein length (aa) 458 378
exons per gene 2.99 2
# of gene models 19130


Collaborators

  • Li-Jun Ma, University of Massachusetts Amherst, USA

Genome Reference(s)

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

Fokkens L, Guo L, Dora S, Wang B, Ye K, Sánchez-Rodríguez C, Croll D
A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem.
G3 (Bethesda). 2020 Oct 5;10(10):3549-3555. doi: 10.1534/g3.120.401375

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.