Info • Paragyrodon sphaerosporus FC442 v2.0


[May 2023] The nuclear genome was sequenced with PacBio, assembled with Flye, 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.

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) 41.91
Sequencing read coverage depth 165.32x
# of contigs 416
# of scaffolds 416
# of scaffolds >= 2Kbp 414
Scaffold N50 14
Scaffold L50 (Mbp) 0.77
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 3.49, 3.03, 2.82

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 107456 96460 89.8%
Ests est.fasta 110229306 109139783 99.0%

Gene Models FilteredModels1
length (bp) of: average median
gene 1901 1609
transcript 1529 1284
exon 237 146
intron 70 57
protein length (aa) 447 358
exons per gene 6.46 5
# of gene models 11162


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.