Info • Armillaria novae-zelandiae 2840 v1.0


[June 2020] The Armillaria novae-zelandiae ICMP 16352 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.

This genome is 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 novae-zelandiae 2840 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 79.33
Sequencing read coverage depth 249.53x
# of contigs 427
# of scaffolds 427
# of scaffolds >= 2Kbp 427
Scaffold N50 26
Scaffold L50 (Mbp) 0.74
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 4.21, 3.36, 3.21

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters ESTclusters 93247 90311 96.9%
Ests est.fasta 129490649 128526672 99.3%

Gene Models FilteredModels1
length (bp) of: average median
gene 1702 1483
transcript 1364 1182
exon 216 136
intron 66 55
protein length (aa) 398 332
exons per gene 6.30 5
# of gene models 18551


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.