Info • Fusarium oxysporum f. sp. lycopersici 4287 v3.0

Status

[March 2023] The Fusarium oxysporum f. sp. lycopersici 4287 v3.0 genome was sequenced with PacBio, assembled with Flye, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

Genome Assembly
Genome Assembly size (Mbp) 55.58
Sequencing read coverage depth 6.59x
# of contigs 45
# of scaffolds 44
# of scaffolds >= 2Kbp 44
Scaffold N50 6
Scaffold L50 (Mbp) 4.14
# of gaps 1
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 6.14, 5.44, 5.19


Some EST libraries were collected during infection stages and therefore included host reads, leading to poor read mapping seen below.

ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 112229289 54963963 49.0%
Other IsoSeq_hq_reads_HWGSY 80035 11526 14.4%
Other IsoSeq_hq_reads_HWGSZ 143223 136923 95.6%
Other RNAseq_contigs 321331 66152 20.6%


Gene Models FilteredModels1
length (bp) of: average median
gene 1863 1559
transcript 1683 1426
exon 550 346
intron 89 56
description:
protein length (aa) 477 385
exons per gene 3.06 2
# of gene models 17629


Collaborators

  • Li-Jun Ma, University of Massachusetts Amherst, USA
  • Michael Freitag, Department of Biochemistry & Biophysics, Oregon State University

Genome Reference(s)

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

Ayhan DH, Abbondante S, Martínez-Soto D, Wu S, Rodriguez-Vargas R, Milo S, Rickelton K, Sohrab V, Kotera S, Arie T, Marshall ME, Rocha MC, Haridas S, Grigoriev IV, Shlezinger N, Pearlman E, Ma L-J
Host-specific adaptation in Fusarium oxysporum correlates with distinct accessory chromosome content in human and plant pathogenic strains.
mBio. 2025 Jun 26;():e0095125. doi: 10.1128/mbio.00951-25

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.