Info • Laxitextum bicolor CBS 258.73 v1.0

Status

[July 2018] The Laxitextum bicolor CBS 258.73 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

This L. bicolor assembly is likely partially diploid, and this is reflected in an assembly and annotation with significant separation of alleles. A significant proportion of smaller scaffolds were 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.

Summary statistics for the Laxitextum bicolor v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 40.78
Sequencing read coverage depth 421.5x
# of contigs 1042
# of scaffolds 1042
# of scaffolds >= 2Kbp 1023
Scaffold N50 73
Scaffold L50 (Mbp) 0.15
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.90, 0.66, 0.61


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 56623 51628 91.2%
Ests est.fasta 176700232 169356612 95.8%


Gene Models FilteredModels1
length (bp) of: average median
gene 1845 1585
transcript 1500 1275
exon 241 152
intron 68 57
description:
protein length (aa) 435 354
exons per gene 6.23 5
# of gene models 11418


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.