Info • Leucoagaricus gongylophorus AS2 v1.0


[September 2018] The Leucoagaricus gongylophorus AS2 genome was sequenced with PacBio, assembled with Falcon (v1.8.8), and annotated using the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available on the Download page.

L. gongylophorus AS2 is known to be polykaryotic, 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 repertoire 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 Leucoagaricus gongylophorus AS2 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 181.80
Sequencing read coverage depth 71.61x
# of contigs 1833
# of scaffolds 1833
# of scaffolds >= 2Kbp 1795
Scaffold N50 284
Scaffold L50 (Mbp) 0.19
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.91, 0.81, 0.81

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 96399 90014 93.4%
Ests est.fasta 144874902 144169018 99.5%

Gene Models FilteredModels2
length (bp) of: average median
gene 1779 1518
transcript 1431 1209
exon 221 137
intron 65 55
protein length (aa) 422 342
exons per gene 6.49 5
# of gene models 13095



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.