Info • Laccaria sp. KIS6 v1.0


[January 2023] The Laccaria sp. LAT2 TL2844-KIS6 v1.0 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assemblied with Trinity, but suffered from significant contamination, leading to poor genome-mapping rates. The mitochondrial genome was assembled separately and is available in the Download tab.

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) 165.36
Sequencing read coverage depth 90.59x
# of contigs 8797
# of scaffolds 8797
# of scaffolds >= 2Kbp 8086
Scaffold N50 958
Scaffold L50 (Mbp) 0.04
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.85, 0.76, 0.71

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 178157 74067 41.6%
Ests est.fasta 95250400 80179207 84.2%

Gene Models FilteredModels1
length (bp) of: average median
gene 1617 1343
transcript 1248 1004
exon 213 137
intron 78 56
protein length (aa) 388 305
exons per gene 5.85 5
# of gene models 38625


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.