Info • Leucoagaricus gongylophorus AL2 v1.0


[March 2019] The Leucoagaricus gongylophorus AL2 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 AL2 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 AL2 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 83.26
Sequencing read coverage depth 649.39x
# of contigs 915
# of scaffolds 915
# of scaffolds >= 2Kbp 879
Scaffold N50 122
Scaffold L50 (Mbp) 0.18
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.28, 1.07, 0.83

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 115428 107300 93.0%
Ests est.fasta 137690773 134898961 98.0%

Gene Models FilteredModels2
length (bp) of: average median
gene 1697 1419
transcript 1381 1137
exon 227 142
intron 64 55
protein length (aa) 402 318
exons per gene 6.07 5
# of gene models 11694



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.