Info • Issatchenkia orientalis ATCC PTA-6658 v2.0


[November 2018] The Issatchenkia orientalis ATCC PTA-6658 genome was sequenced using PacBio and assembled together with Falcon version 1.8.8. The Falcon assembly was run through Falcon unzip version 0.4.0 to further phase the haplotypes in the assembly. Mitochondrial genome was assembled separately and is available in the downloads section.
This Issatchenkia orientalis assembly is likely partially diploid, and this is reflected in an assembly and annotation with significant separation of alleles. 128 of the 135 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.

Summary statistics for the Issatchenkia orientalis v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 23.08
Sequencing read coverage depth 1233.53x
# of contigs 135
# of scaffolds 135
# of scaffolds >= 2Kbp 134
Scaffold N50 6
Scaffold L50 (Mbp) 1.28
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.87, 2.71, 1.89

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 9627 6695 69.5%
Ests est.fasta 191344953 183093893 95.7%

Gene Models FilteredModels1
length (bp) of: average median
gene 1720 1466
transcript 1667 1430
exon 1203 1011
intron 141 80
protein length (aa) 489 407
exons per gene 1.39 1
# of gene models 4909


Huimin Zhao, University of Illinois , USA

Yasuo Yoshikuni, Joint Genome Institute, USA


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.