Info • Lactarius sanguifluus B21 v1.0


[August 2018] (August 2018) The Lactarius sanguifluus 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 sanguifluus B21 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 86.24
Sequencing read coverage depth 150.25x
# of contigs 986
# of scaffolds 986
# of scaffolds >= 2Kbp 898
Scaffold N50 89
Scaffold L50 (Mbp) 0.24
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.90, 1.66, 1.25

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 106907 95859 89.7%
Ests est.fasta 222310080 218192572 98.1%

Gene Models FilteredModels1
length (bp) of: average median
gene 1699 1439
transcript 1367 1142
exon 242 154
intron 73 58
protein length (aa) 400 317
exons per gene 5.66 4
# of gene models 17481

Genome Reference(s)


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.