Info • Serendipita sp. 400 v1.0


[June 2021] The Serendipita sp. 400 v1.0 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity. The mitochondrial genome was assembled separately and is available in the Downloads tab.

The genome is likely a polymorphic dikaryon, 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.

Genome Assembly
Genome Assembly size (Mbp) 38.90
Sequencing read coverage depth 770.40x
# of contigs 205
# of scaffolds 205
# of scaffolds >= 2Kbp 205
Scaffold N50 6
Scaffold L50 (Mbp) 2.71
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 5.02, 3.38, 2.98

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 62160 56638 91.1%
Ests est.fasta 204132601 201614450 98.8%

Gene Models FilteredModels1
length (bp) of: average median
gene 1985 1690
transcript 1635 1394
exon 261 153
intron 69 56
protein length (aa) 478 392
exons per gene 6.26 5
# of gene models 10802


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.