[September 2020] [June 2020] The Phakopsora pachyrhizi PPUFV02 genome was sequenced with the PromethION platform of Oxford nanopore technology (Oxford, UK) by KeyGene N.V. (Wageningen, The Netherlands). The longest reads were assembled with Minimap2 and Miniasm pipeline. The most contiguous assembly was observed with the longest 30X Nanopore reads. To improve the consensus, error correction was performed three times with Racon using all the Nanopore reads. The resulting assembly was polished with the 50x Illumina PCR-free 150 bp PE reads mapped with bwa and Pilon, repeated three times.

Phakopsora pachyrhizi PPUFV02 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.