Info • Inosperma lanatodiscum 2018PMI007 v1.0

Status

[April 2023] The Inosperma lanatodiscum 2018PMI007 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.

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) 123.81
Sequencing read coverage depth 63.01x
# of contigs 1501
# of scaffolds 1501
# of scaffolds >= 2Kbp 1498
Scaffold N50 256
Scaffold L50 (Mbp) 0.14
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.69, 0.69, 0.66


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 101769 83985 82.5%
Ests est.fasta 170514981 169006868 99.1%


Gene Models FilteredModels1
length (bp) of: average median
gene 1749 1440
transcript 1433 1176
exon 263 162
intron 73 56
description:
protein length (aa) 430 337
exons per gene 5.44 4
# of gene models 23215


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.