Info • Laccaria bicolor S238N 93.12 v1.1


(Jun 2016) The Laccaria bicolor S238N 93.12 genome was sequenced using PacBio, assembled using Falcon, and annotated using the JGI Annotation Pipeline. The transcriptome was sequenced using Illumina and assembled using Trinity.

Laccaria bicolor S238N 93.12 is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. 412 of the 614 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 Laccaria bicolor S238N 93.12 v1.1 release are below.
Genome Assembly
Genome Assembly size (Mbp) 96.43
Sequencing read coverage depth
# of contigs 1034
# of scaffolds 1034
# of scaffolds >= 2Kbp 1028
Scaffold N50 109
Scaffold L50 (Mbp) 0.24
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.47, 1.41, 1.05

ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 124840611 122511749 98.1%
Other JGI_RNA_contigs 101217 87795 86.7%

Gene Models FilteredModels1
length (bp) of: average median
gene 1456 1153
transcript 1137 882
exon 220 140
intron 78 56
protein length (aa) 341 251
exons per gene 5.17 4
# of gene models 25412


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.