Info • Flagelloscypha sp. PMI_526 v1.0


[October 2018] The nuclear 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 on the Download page.

Flagelloscypha sp. PMI_526 is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. Many of the smaller 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 Flagelloscypha sp. PMI_526 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 72.73
Sequencing read coverage depth 141.4x
# of contigs 397
# of scaffolds 397
# of scaffolds >= 2Kbp 394
Scaffold N50 18
Scaffold L50 (Mbp) 1.13
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 3.49, 3.27, 3.21

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 83340 75991 91.2%
Ests est.fasta 322685216 319110786 98.9%

Gene Models FilteredModels2
length (bp) of: average median
gene 1728 1487
transcript 1437 1242
exon 247 152
intron 62 56
protein length (aa) 415 342
exons per gene 5.82 5
# of gene models 19929


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.