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Elucidating the genetic diversity of Phthorimaea operculella granulovirus (PhopGV)

GND
1059093758
Affiliation
Institute for Biological Control, Federal Research Centre for Cultivated Plants, Julius Kühn Institute, Heinrichstraße 243, 64287 Darmstadt, Germany.
Larem, Andreas;
Affiliation
Institute for Biological Control, Federal Research Centre for Cultivated Plants, Julius Kühn Institute, Heinrichstraße 243, 64287 Darmstadt, Germany.
Ben-Tiba, Saoussen;
GND
1059101742
Affiliation
Institute for Biological Control, Federal Research Centre for Cultivated Plants, Julius Kühn Institute, Heinrichstraße 243, 64287 Darmstadt, Germany.
Wennmann, Jörg T.;
GND
1059093367
Affiliation
Institute for Biological Control, Federal Research Centre for Cultivated Plants, Julius Kühn Institute, Heinrichstraße 243, 64287 Darmstadt, Germany.
Gueli Alletti, Gianpiero;
GND
17274184X
Affiliation
Institute for Biological Control, Federal Research Centre for Cultivated Plants, Julius Kühn Institute, Heinrichstraße 243, 64287 Darmstadt, Germany.
Jehle, Johannes A.

Twelve complete genome sequences of Phthorimaea operculella granulovirus (PhopGV) isolates from four different continents (Africa, South America, Asia and Europe) were analysed after Illumina next-generation sequencing (NGS). The isolates have a circular double-stranded DNA genome that is 118 355 to 119 177 bp in length and all of them encode 130 open reading frames (ORFs). Analysis of single-nucleotide polymorphisms (SNPs) revealed a unique set of SNP positions for every tested isolate. The genome sequences of the investigated PhopGV isolates were classified into a new system of four (1-4) groups according to the presence of group-specific SNPs as well as insertions and deletions. These genome groups correlated with phylogenetic lineages inferred from minimum-evolution trees of the whole-genome consensus nucleotide sequences. All members of group 3 originated from the Mediterranean area, whereas the geographical origin and the group assignment did not correlate for isolates belonging to genome groups 1, 2 or 4. The high degree of coverage facilitated the determination of variant nucleotide frequencies. We conclude that the geographical isolates of PhopGV are genetically highly similar. On the other hand, they were rarely genetically homogenous and in most cases appeared to be mixtures of multiple genotypes.

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