Info • Serendipita sp. 407 v1.0


[November 2017] The Serendipita sp. 407 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.


Serendipita sp. 407 is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. 177 of the 192 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 Serendipita sp. 407 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 40.69
Sequencing read coverage depth 123.05x
# of contigs 192
# of scaffolds 192
# of scaffolds >= 2Kbp 192
Scaffold N50 8
Scaffold L50 (Mbp) 1.67
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 4.96, 2.92, 2.78

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 63047 57617 91.4%
Ests est.fasta 142688842 141314104 99.0%

Gene Models FilteredModels1
length (bp) of: average median
gene 1950 1673
transcript 1624 1387
exon 274 161
intron 68 56
protein length (aa) 472 390
exons per gene 5.93 5
# of gene models 10738



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.