Characterization of yam virus X isolates from Dioscorea trifida in Brazil

Abstract

Yam virus X (YVX; Potexvirus ecsdioscoreae) is a positive-sense, flexuous RNA virus belonging to the family Alphaflexiviridae. It has been first reported from Guadeloupe, a French archipelago located in the Caribbean Sea. In this study, we investigated the virome in yam (Dioscorea spp.) plant material collected in the state of Bahia (Brazil) by high-throughput sequencing (HTS) on Illumina platform. The objective of the investigation was to explore the occurrence of YVX in yam from South America, and to study its genetic diversity compared to the only one YVX genome sequence available in the GenBank public database. An initial investigation by HTS of bulked RNA extracts (n=23, combined into 4 pools) revealed occurrence of YVX only in samples collected in the region of Valença. Subsequent screening by RT-PCR of the individual samples composing the pool uncovered infection with YVX only in Discorea trifida. Total RNA extracts from three infected plants were individually sequenced, resulting in the assembly of three complete genome sequences of YVX, showing ~84% nucleotide identity to the reference sequence from Guadeloupe. Our results contribute to expanding the pool of sequences available for YVX, supporting detection purposes and stimulating additional investigations for future studies on YVX diversity and evolution.