Status
(Oct 2015) The Armillaria solidipes 28-4 genome was sequenced using the Illumina platform and assembled with AllPathsLG version R49403.
Summary statistics for the Armillaria solidipes 28-4 v1.0
release are below.
Genome Assembly | |
Genome Assembly size (Mbp) | 58.01 |
Sequencing read coverage depth | 67.6x |
# of contigs | 693 |
# of scaffolds | 229 |
# of scaffolds >= 2Kbp | 198 |
Scaffold N50 | 21 |
Scaffold L50 (Mbp) | 0.72 |
# of gaps | 464 |
% of scaffold length in gaps | 3.9% |
Three largest Scaffolds (Mbp) | 3.40, 3.38, 2.25 |
ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
EstClusters | ESTclusters | 45396 | 44778 | 98.6% |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 1580 | 1354 |
transcript | 1290 | 1095 |
exon | 227 | 140 |
intron | 64 | 55 |
description: | ||
protein length (aa) | 371 | 308 |
exons per gene | 5.69 | 4 |
# of gene models | 20811 |
Collaborators
James Anderson, University of Toronto
Joseph Spatafora, Oregon State University
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Sipos G, Prasanna AN, Walter MC, O'Connor E, Bálint B, Krizsán K, Kiss B, Hess J, Varga T, Slot J, Riley R, Bóka B, Rigling D, Barry K, Lee J, Mihaltcheva S, LaButti K, Lipzen A, Waldron R, Moloney NM, Sperisen C, Kredics L, Vágvölgyi C, Patrignani A, Fitzpatrick D, Nagy I, Doyle S, Anderson JB, Grigoriev IV, Güldener U, Münsterkötter M, Nagy LG
Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria.
Nat Ecol Evol. 2017 Dec;1(12):1931-1941. doi: 10.1038/s41559-017-0347-8
Sipos G, Prasanna AN, Walter MC, O'Connor E, Bálint B, Krizsán K, Kiss B, Hess J, Varga T, Slot J, Riley R, Bóka B, Rigling D, Barry K, Lee J, Mihaltcheva S, LaButti K, Lipzen A, Waldron R, Moloney NM, Sperisen C, Kredics L, Vágvölgyi C, Patrignani A, Fitzpatrick D, Nagy I, Doyle S, Anderson JB, Grigoriev IV, Güldener U, Münsterkötter M, Nagy LG
Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria.
Nat Ecol Evol. 2017 Dec;1(12):1931-1941. doi: 10.1038/s41559-017-0347-8
Funding
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.