Genetic Diversity of a Natural Population of Apple stem pitting virus Isolated from Apple in Korea

Abstract

Apple stem pitting virus (ASPV), of the Foveavirus genus in the family Betaflexiviridae, is one of the most common viruses of apple and pear trees. To examine variability of the coat protein (CP) gene from ASPV, eight isolates originating from 251 apple trees, which were collected from 22 apple orchards located in intensive apple growing areas of the North Gyeongsang and North Jeolla Provinces in Korea, were sequenced and compared. The nucleotide sequence identity of the CP gene of eight ASPV isolates ranged from 77.0 to 97.0%, while the amino acid sequence identity ranged from 87.7 to 98.5%. The N-terminal region of the viral CP gene was highly variable, whereas the C-terminal region was conserved. Genetic algorithm recombination detection (GARD) and single breakpoint recombination (SBP) analyses identified base substitutions between eight ASPV isolates at positions 54 and 57 and position 771, respectively. GABranch analysis was used to determine whether the eight isolates evolved due to positive selection. All values in the GABranch analysis showed a ratio of substitution rates at non-synonymous and synonymous sites (dNS/dS) below 1, suggestive of strong negative selection forces during ASPV CP history. Although negative selection dominated CP evolution in the eight ASPV isolates, SLAC and FEL tests identified four possible positive selection sites at codons 10, 22, 102, and 158. This is the first study of the ASPV genome in Korea.

Evolving by deleting: patterns of molecular evolution of Apple stem pitting virus isolates from Poland

“…It has been shown that all five genes encoded by ASPV had large genetic variability, especially in the CP-encoding ORF5. The CP gene is one of the most commonly used markers for evolutionary analyses of viruses in the Betaflexiviridae family [11][12][13] as well as for other plant viruses [14][15][16][17][18]. Previous studies about the genetic diversity of ASPV isolates have shown that the nucleotide identity among CP sequences was high, though with a certain degree of discrepancy among studies: between 81.7-99.3 % [4], 64.…”

Population genetic analysis of potato virus X based on the CP gene sequence

“…Here, population genetic analysis of PVX isolates from different countries was done based on the CP sequences because conserved nature of the CP gene makes it a suitable candidate for such studies. The CP gene in plant viruses is commonly used for investigation on genetic variation and molecular evolution [10,27,41,43] and was therefore selected for this study.…”

Distribution and genetic diversity of three apple viruses in Belarus

“…Эти вирусы распространены как в соседних с Беларусью странах (Poniedziałek et al, 2001;PaduchCichal et al, 2005;Gospodaryk et al, 2008;Pūpola et al, 2011;Сироткин, 2012;Stankienė et al, 2012;Yoon et al, 2014), так и в географически удаленных от нее (German мест, где они были выделены, и таким образом проследить направление их распространения. С одной стороны, бело-русский изолят ACLSV оказался близок трем изолятам из граничащей с ней Литвы (см.…”

“…Исследования, проведенные в разных странах, свидетельствуют о доминировании от-рицательной селекции в эволюции вирусов, поражающих яблоню. Однако отдельные нуклеотиды или регионы ге-номов вирусов могут находиться под влиянием положи-тельной селекции (Komorowska et al, 2011;Liebenberg et al, 2012;Liu et al, 2014;Yoon et al, 2014). Возможно, такое селективное давление обусловлено участием одного вирусного белка в множестве процессов.…”