title: Complete genome sequences of new divergent potato virus X isolates and discrimination between strains in a mixed infection using small RNAs sequencing approach.
abstract: Potato virus X (PVX; genus Potexvirus, family Alphaflexiviridae, order Tymovirales) is one of the most widespread and intensively studied viruses of potato. However, little is known about its diversity in its likely center of radiation, the Andean region of South America. To fill this gap, the strategy of Illumina deep sequencing of small RNAs was used to obtain complete or near complete genome sequence of PVX from 5 symptomatically infected greenhouse and 3 field samples (Solanum tuberosum) from Peru. PVX sequences determined in this study were assigned into three different phylogenetic groups of isolates. Notably, a complete genome sequence of a representative of a new PVX phylogenetic lineage was obtained, which shows a high level of sequence dissimilarity to other completely sequenced isolates (∼17%). The new PVX genotype was detected in greenhouse and field samples. One of the field samples was infected with the mixture of two PVX strains, which were efficiently discriminated using small RNA sequencing approach. The study confirms the utility of small RNAs deep sequencing for successful viral strain differentiation and discovery of new viral strains and indicates a high diversity of PVX in the Andean region of South America, a pattern which may be expected also for other potato pathogens.
authors: Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
authors: Denis
authors: D
authors: Kutnjak
authors: International Potato Center (CIP), Lima, Peru.
authors: Rocio
authors: R
authors: Silvestre
authors: International Potato Center (CIP), Lima, Peru.
authors: Wilmer
authors: W
authors: Cuellar
authors: International Potato Center (CIP), Lima, Peru.
authors: Wilmer
authors: W
authors: Perez
authors: International Potato Center (CIP), Lima, Peru.
authors: Giovanna
authors: G
authors: Müller
authors: Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
authors: Maja
authors: M
authors: Ravnikar
authors: International Potato Center (CIP), Lima, Peru. Electronic address: j.kreuze@cgiar.org.
authors: Jan
authors: J
authors: Kreuze
mesh_terms: D060085:Coinfection / Q000821:virology; D019143:Evolution, Molecular; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D017863:Potexvirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D012367:RNA, Viral / Q000235:genetics*; D017423:Sequence Analysis, RNA; D011198:Solanum tuberosum / Q000821:virology
chemical_list: D012367:RNA, Viral
keywords: Andes; Next generation sequencing; Phylogeny; Potato virus X; Small RNAs