Info • Suillus "subluteus" FC464 v1.0


[July 2019] The nuclear 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.

This is likely a polymorphic dikaryon, and this is reflected in an assembly and annotation with significant separation of alleles. 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 Suillus "subluteus" FC464 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 114.21
Sequencing read coverage depth 80.55x
# of contigs 684
# of scaffolds 684
# of scaffolds >= 2Kbp 684
Scaffold N50 67
Scaffold L50 (Mbp) 0.43
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 2.47, 2.34, 2.05

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 113908 98579 86.5%
Ests est.fasta 126245994 123904308 98.1%

Gene Models FilteredModels2
length (bp) of: average median
gene 1636 1389
transcript 1303 1083
exon 224 148
intron 71 55
protein length (aa) 389 308
exons per gene 5.82 5
# of gene models 22673


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.