Info • Fusarium oxysporum f.sp. cubense II5 v2.0


[December 2020] The genome sequence of Fusarium oxysporum f.sp. cubense II5 were not determined by the Joint Genome Institute (JGI), but were provided by Li-Jun Ma and Yong Zhang on Oct 14, 2020. This genome was sequenced with PacBio and illumina, assembled with Canu v1.8 followed by polishing by Quiver using Illumina sequences, and annotated with the JGI Annotation Pipeline.

Summary statistics for the Fusarium oxysporum f.sp. cubense II5 v2.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 49.43
Sequencing read coverage depth 341.0x
# of contigs 67
# of scaffolds 53
# of scaffolds >= 2Kbp 53
Scaffold N50 5
Scaffold L50 (Mbp) 4.48
# of gaps 14
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 6.69, 6.51, 5.26

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 1104761 33247 3.0%
Ests est.fasta 141461436 51469578 36.4%

Gene Models FilteredModels1
length (bp) of: average median
gene 1775 1567
transcript 1626 1431
exon 555 344
intron 80 56
protein length (aa) 469 400
exons per gene 2.93 2
# of gene models 16048


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


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.