10.5061/DRYAD.D81073K
Dale, Angela L.
University of British Columbia
Feau, Nicolas
University of British Columbia
Everhart, Sydney E.
University of Nebraska - Lincoln
Dhillon, Braham
University of British Columbia
Wong, Barbara
University of British Columbia
Sheppard, Julie
University of British Columbia
Bilodeau, Guillaume J.
Canadian Food Inspection Agency
Brar, Avneet
Canadian Food Inspection Agency
Tabima, Javier F.
Oregon State University
Shen, Danyu
Nanjing Agricultural University
Brasier, Clive M.
Forest Research
Tyler, Brett M.
Oregon State University
Grünwald, Niklaus J.
Oregon State University
Hamelin, Richard C.
University of British Columbia
Data from: Mitotic recombination and rapid genome evolution in the
invasive forest pathogen Phytophthora ramorumm
Dryad
dataset
2019
Phytophthora ramorum
2019-03-04T21:22:18Z
2019-03-04T21:22:18Z
en
https://doi.org/10.1128/mbio.02452-18
126575 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Invasive alien species often have reduced genetic diversity and must adapt
to new environments. Given the success of many invasions, this is
sometimes called the genetic paradox of invasion. Phytophthora ramorum is
invasive, limited to asexual reproduction within four lineages, and
presumed clonal. NA1 is responsible for sudden oak death in the USA, NA1,
NA2 and EU1 are responsible for ramorum blight in the USA and Canada and
EU1 and EU2 are responsible for sudden larch death and blight in Europe.
We sequenced 107 genomes to determine how this pathogen can overcome the
invasion paradox. Mitotic recombination (MR) associated with transposons
and low gene density has generated runs of homozygosity (ROH) affecting
2698 genes, resulting in novel genotypic diversity within the lineages.
One ROH enriched in putative pathogenicity genes was fixed in NA1. An
independent ROH affected the same scaffold in EU1 suggesting an MR hotspot
and selection target. EU1 individuals with and without the ROH may differ
in aggressiveness. Non-core regions (not shared by all lineages) had
signatures of accelerated evolution and were enriched in putative
pathogenicity genes and transposons. There was a striking pattern of gene
loss, including all effectors, in the non-core EU2 genome. Positive
selection was observed in 8.0% of RxLR and 18.8% of Crinkler effector
genes compared with 0.9% of the core eukaryotic gene set. We conclude that
the P. ramorum lineages are diverging via a rapidly evolving non-core
genome and the invasive asexual lineages are not clonal, but display
genotypic diversity caused by MR.
Dryad_S1Metadata (Location Year Host) and Illumina sequencing statistics
for the 107 Phytophthora ramorum isolates resequenced in this
studyDryad_S2Quality control of Illumina sequencing and SNP filtering of
Phytophthora ramorum.Dryad_S3Assembly statistics (size, size of longest
scaffold, # of scaffolds and N50) and completeness (BUSCO coverage) for
eight de novo assemblies generated for Phytophthora ramorum with
AbyssDryad_S4Nucleotide and gene content of the de novo assemblies
obtained for the four Phytophthora ramorum lineages
Europe
North America