Open AccessSequence variation of block III segment identifies three distinct lineages within Eggplant mottled dwarf virus isolates from Italy, Spain and Greece
Author(s) -
Giuseppe Parrella,
Barbara Greco
Publication year - 2016
Publication title -
acta virologica
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.412
H-Index - 33
eISSN - 1336-2305
pISSN - 0001-723X
DOI - 10.4149/av_2016_01_100
Subject(s) - biology , phylogenetic tree , nonsynonymous substitution , genetics , phylogenetics , gene , genetic variation , restriction fragment length polymorphism , polymerase chain reaction , genome
Partial polymerase (L) gene sequences of 919 nts, including the conserved segments pre-motif A and motif A of block III, of 20 Eggplant mottled dwarf virus (EMDV) isolates were generated, and trimmed sequences of 889 nts, based on the length of available sequences of other isolates, were used to determine phylogenetic relationships. Phylogenetic reconstructions revealed two divergent lineages, designated as genetic group A (Italian isolates) and group B, with the latter further divided into subgroups BI (Greek isolates) and BII (Spanish isolates). No evidence of recombination signals among sequences was detected, whereas analysis of the nonsynonymous/synonymous ratio indicated strong purifying selection, with codons under negative selection uniformly distributed along the sequences. An RT-PCR-RFLP method able to discriminate EMDV isolates of the two main genetic groups was proposed.