Info • Armillaria luteobubalina HWK02 v1.0

Status

[June 2018] The Armillaria luteobubalina HWK02 genome was sequenced with PacBio, assembled with Falcon (v 1.8.8), and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

This A. luteobubalina 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 Armillaria luteobubalina v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 97.11
Sequencing read coverage depth 47.28x
# of contigs 439
# of scaffolds 439
# of scaffolds >= 2Kbp 435
Scaffold N50 28
Scaffold L50 (Mbp) 0.84
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 3.69, 3.51, 2.98


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 87576 83165 95.0%
Ests est.fasta 139354726 138726453 99.5%


Gene Models FilteredModels1
length (bp) of: average median
gene 1676 1465
transcript 1341 1163
exon 216 136
intron 66 55
description:
protein length (aa) 392 326
exons per gene 6.21 5
# of gene models 20318


Collaborators

Jonathan Plett, Western Sydney University, Australia

Joseph Spatafora, Oregon State University, USA

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.