Info • Phakopsora pachyrhizi MT2006 v1.0


The Phakopsora pachyrhizi MG2006 v1.0 genome was sequenced with PacBio, assembled with MECAT, polished with arrow, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

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 repertiore 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 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 1057.43
Sequencing read coverage depth 142.83x
# of contigs 7465
# of scaffolds 7464
# of scaffolds >= 2Kbp 7464
Scaffold N50 1110
Scaffold L50 (Mbp) 0.22
# of gaps 1
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 3.05, 2.57, 2.17

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 344612 130795 38.0%
Ests est.fasta 1769119900 1451768142 82.1%

Gene Models FilteredModels2
length (bp) of: average median
gene 1532 1223
transcript 1066 783
exon 234 135
intron 133 94
protein length (aa) 319 221
exons per gene 4.56 4
# of gene models 19618


Sébastien Duplessis, INRA, France.



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.