Info • Porosterum spadiceum BS34 v1.0

Status

[March 2022] The Porosterum spadiceum BS34 v1.0 genome was sequenced with PacBio, assembled with Flye, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

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) 85.20
Sequencing read coverage depth 30.86x
# of contigs 309
# of scaffolds 309
# of scaffolds >= 2Kbp 307
Scaffold N50 49
Scaffold L50 (Mbp) 0.57
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.28, 1.24, 1.22


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 65096 63767 98.0%
Ests est.fasta 158628146 157756665 99.5%


Gene Models FilteredModels1
length (bp) of: average median
gene 1917 1641
transcript 1578 1346
exon 258 159
intron 68 56
description:
protein length (aa) 456 369
exons per gene 6.12 5
# of gene models 16879


Collaborators

Funding

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.