Info • Issatchenkia orientalis SD108 v2.0


[November 2018] The Issatchenkia orientalis SD108 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. 119 of the 130 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) 21.69
Sequencing read coverage depth 1095.4x
# of contigs 130
# of scaffolds 130
# of scaffolds >= 2Kbp 130
Scaffold N50 7
Scaffold L50 (Mbp) 0.93
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.61, 2.46, 1.91

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 11520 7323 63.6%
Ests est.fasta 214732929 208056410 96.9%

Gene Models FilteredModels1
length (bp) of: average median
gene 1724 1483
transcript 1674 1442
exon 1207 1029
intron 133 71
protein length (aa) 490 409
exons per gene 1.39 1
# of gene models 4925


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.