[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.