Info • Polychytrium aggregatum JEL109 v1.0


[May 2019] The Polychytrium aggregatum JEL109 v1.0 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

This genome is likely diploid, and this is reflected in an assembly and annotation with significant separation of alleles. Many of the 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 repertiore 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 Polychytrium aggregatum JEL109 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 64.92
Sequencing read coverage depth 279.61x
# of contigs 461
# of scaffolds 461
# of scaffolds >= 2Kbp 457
Scaffold N50 41
Scaffold L50 (Mbp) 0.39
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.62, 1.46, 1.42

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 29833 26279 88.1%
Ests est.fasta 64266015 62436535 97.2%

Gene Models FilteredModels1
length (bp) of: average median
gene 2435 2035
transcript 1698 1423
exon 312 173
intron 167 148
protein length (aa) 486 386
exons per gene 5.45 4
# of gene models 10690


Genome Reference(s)


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.