Info • Lactarius subdulcis FM v1.0


The Lactarius subdulcis FM v1.0 genome was sequenced with PacBio, assembled with HiCanu, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the Download tab.

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.

Genome Assembly
Genome Assembly size (Mbp) 110.45
Sequencing read coverage depth 18.24x
# of contigs 300
# of scaffolds 300
# of scaffolds >= 2Kbp 300
Scaffold N50 20
Scaffold L50 (Mbp) 1.43
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 5.19, 5.11, 4.26

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 103074 89430 86.8%
Ests est.fasta 166755581 165518159 99.3%

Gene Models FilteredModels2
length (bp) of: average median
gene 1886 1613
transcript 1546 1289
exon 256 155
intron 70 57
protein length (aa) 444 348
exons per gene 6.03 5
# of gene models 14533


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.