Info • Phakopsora pachyrhizi K8108 v2.0


[February 2020] The Phakopsora pachyrhizi K8108 v2.0  genome was sequenced with PacBio, assembled with MECAT, and polished with arrow at Syngenta and annotated with the JGI Annotation Pipeline. An alternative gene prediction set, determined by Syngenta is also available .
Phakopsora pachyrhizi is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. Many of the smaller scaffolds are very similar to larger scaffolds and are predicted to constitute an alternate or secondary haplotype. To represent these primary and secondary haplotypes in the Portal, we have created 'primary alleles' and 'secondary alleles' gene model tracks, comprising the models found on each haplotype. The goal of the GeneCatalog (GC) is to produce a non-redundant set of models which captures the full functional repertoire of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.

Summary statistics for the Phakopsora pachyrhizi K8108 v2.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 1082.91
Sequencing read coverage depth 64x
# of contigs 6507
# of scaffolds 6505
# of scaffolds >= 2Kbp 6505
Scaffold N50 900
Scaffold L50 (Mbp) 0.28
# of gaps 2
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 3.03, 2.54, 2.54

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 244030 25609 10.5%
Ests est.fasta 449553900 168432797 37.5%

Gene Models FilteredModels2
length (bp) of: average median
gene 1637 1340
transcript 1151 836
exon 249 144
intron 136 95
protein length (aa) 337 235
exons per gene 4.62 4
# of gene models 18216


Project management:





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.