Info • Pichia kudriavzevii YB-431


[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).

Genome Assembly
Genome Assembly size (Mbp) 22.61
Sequencing read coverage depth 84x
# of contigs 144
# of scaffolds 144
# of scaffolds >= 2Kbp 144
Scaffold N50 7
Scaffold L50 (Mbp) 0.40
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.81, 2.78, 2.55

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 6869 5520 80.4%
Ests est.fasta 124808228 121743159 97.5%

Gene Models FilteredModels1
length (bp) of: average median
gene 1949 1632
transcript 1891 1607
exon 1450 1296
intron 193 56
protein length (aa) 549 448
exons per gene 1.30 1
# of gene models 4748


Henrique DePaoli - Agile BioFoundry, LBNL


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.