Status
[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 |
description: | ||
protein length (aa) | 549 | 448 |
exons per gene | 1.30 | 1 |
# of gene models | 4748 |
Collaborators
Henrique DePaoli - Agile BioFoundry, LBNL
Links
- JGI PhyloGroup Portals: Fungi Dikarya Ascomycota Saccharomycotina Saccharomycetes Saccharomycetales Pichiaceae