Info • Serendipita sp. 411 v1.0


[June 2021] The Serendipita sp. 411 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 Download 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) 38.49
Sequencing read coverage depth 615.35x
# of contigs 225
# of scaffolds 225
# of scaffolds >= 2Kbp 225
Scaffold N50 7
Scaffold L50 (Mbp) 2.03
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 3.39, 3.25, 2.89

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 65104 59594 91.5%
Ests est.fasta 222480593 220377374 99.1%

Gene Models FilteredModels1
length (bp) of: average median
gene 1985 1693
transcript 1636 1390
exon 261 154
intron 68 56
protein length (aa) 478 394
exons per gene 6.26 5
# of gene models 10821


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.