We will have a brief downtime on Tuesday May 28 between 8:45 and 9:30 am PDT due to network equipment maintenance.
Info • Armillaria mellea ELDO17 v1.0


[June 2019] The Armillaria mellea ELDO17 v1.0 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available in the downloads section.

The genome is likely diploid, 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 Armillaria mellea v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 70.86
Sequencing read coverage depth 125.27x
# of contigs 474
# of scaffolds 474
# of scaffolds >= 2Kbp 473
Scaffold N50 8
Scaffold L50 (Mbp) 2.54
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 8.68, 5.01, 4.85

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 69673 66903 96.0%
Ests est.fasta 136964463 135437583 98.9%

Gene Models FilteredModels1
length (bp) of: average median
gene 1728 1504
transcript 1393 1209
exon 215 135
intron 63 54
protein length (aa) 403 336
exons per gene 6.49 5
# of gene models 15646


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.