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.
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
- Jon Magnuson, Pacific Northwest National Laboratory, WA, USA
- Joseph Spatafora, Oregon State University, OR, USA
Links
- 1000 Fungi project
- JGI PhyloGroup Portals: Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Russulales