[February 2023] PacBio sequencing data was provided by Henrique De Paoli at the Agile BioFoundry (ABF). The Pichia kudriavzevii YB-431 genome was assembled together with CANU v2.2 at JGI. Mitochondrial genome was assembled separately and is available in the downloads section.
This Pichia kudriavzevii assembly is likely diploid, and this is reflected in an assembly and annotation with significant separation of alleles. 139 of the 144 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. The transcriptome data used to support the genome annotation was retrieved from Issatchenkia orientalis IO21 (IsorIO21_1).