Preliminary identification and phylogenetic relationships of begomoviruses associated with Capsicum spp. in the Yucatan peninsula, Mexico

Abstract

Pepper plants with viral symptoms were collected in the Yucatan Peninsula, Mexico (YPM) with the objective to characterize the partial identity and the genetic and phylogenetic relationship of the begomoviruses infecting different pepper species, including <em>Capsicum chinense</em>, various <em>C. annuum</em> landraces, <em>C. frutescens</em>, <em>C. a</em>. var. <em>aviculare</em>, as well as some weeds. The leaf samples were collected during two severe whitefly infestation seasons. Total genomic DNA from the sampled plants was extracted and a fragment of the begomoviruses was amplified using universal primers. Amplicons obtained were sequenced and sequences were used for genetic and phylogenetic analysis. Our results demonstrate that 90.1 % of the total sampled plants (151) were infected with begomoviruses. The data identified Pepper golden mosaic virus (PepGMV) as the most frequent species found within cultivated, semi-cultivated, and wild-analyzed samples. In addition, sequence analysis indicates the presence of <em>Euphorbia mosaic virus-Yucatán Peninsula</em> (EuMV-YP) infecting a Habanero chili plant, as well as the predominance of PepGMV in different weed plant species. Genetic variation based on nucleotide distance analysis from partial DNA-A begomovirus sequences indicated that the PepGMV isolates were closely related among them sharing 95 to 99% nucleotide sequence identity. Data showed that begomovirus that infected the sampled plants included the partially identified species of PepGMV, <em>Pepper huasteco yellow vein virus</em> (PHYVV), <em>Tomato severe leaf curl virus</em> (ToSLCV), <em>Tomato yellow leaf curl virus</em> (TYLCV) and EuMV-YP.