Info • Lactarius hatsudake 109 v1.0

Status

[August 2018] (August 2018) The Lactarius hatsudake genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity. The mitochondrial genome was assembled separately and is available on the Download page.

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.

Summary statistics for the Lactarius hatsudake 109 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 95.49
Sequencing read coverage depth 195.32x
# of contigs 815
# of scaffolds 815
# of scaffolds >= 2Kbp 788
Scaffold N50 86
Scaffold L50 (Mbp) 0.26
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.84, 1.73, 1.51


ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 117324 105983 90.3%
Ests est.fasta 246253718 239695979 97.3%


Gene Models FilteredModels1
length (bp) of: average median
gene 1724 1467
transcript 1394 1168
exon 241 154
intron 71 57
description:
protein length (aa) 406 321
exons per gene 5.79 5
# of gene models 16831


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.