Info • Stephanosporaceae sp. PMI 697 v1.0


[January 2023] The Stephanosporaceae sp. PMI 697 v1.0 genome was sequenced with PacBio, assembled with Flye, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

This genome is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. Some 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 repertoire of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.

Genome Assembly
Genome Assembly size (Mbp) 81.11
Sequencing read coverage depth 85.36x
# of contigs 780
# of scaffolds 780
# of scaffolds >= 2Kbp 778
Scaffold N50 112
Scaffold L50 (Mbp) 0.20
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.99, 0.76, 0.71

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 69597 65956 94.8%
Ests est.fasta 147727648 144476931 97.8%

Gene Models FilteredModels1
length (bp) of: average median
gene 1979 1686
transcript 1634 1388
exon 253 154
intron 65 54
protein length (aa) 479 385
exons per gene 6.45 5
# of gene models 15305


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.