Coinfection of cotton plants with cotton leafroll dwarf virus‐atypical and a novel cotton begomovirus

Abstract

Cotton is a commercial crop of global importance whose versatile fibre is widelyused in the textile industry. Cotton is vulnerable to infectious pathogens, includingviruses, that are a major threat to cotton production. Cotton blue disease is causedby cotton leafroll dwarf virus (CLRDV), a polerovirus transmitted by aphids. This virus is controlled by sowing cotton varieties resistant to CLRDV, although, in recentyears an atypical variant (CLRDV-at), that breaks the resistance, has been identified.An outbreak of a disease occurred in cotton fields of the province of Chaco, in thenorth-west of Argentina, in the 2014–2015 growing season. NuOpal cotton plants (avariety resistant to CLRDV and susceptible to CLRDV-at) showed mosaic symptomsand had virus-transmitting insect vectors, such as aphids and whiteflies (Bemisiatabaci). The symptoms were common for virus infections but different from thosecaused by CLRDV or CLRDV-at. According to a reverse transcription-PCR analysiswith polerovirus primers and sequencing, the plants contained CLRDV-at. Toidentify the complete virome of these plants, we performed a massive RNA-baseddeep sequencing assay using Illumina technology. As a result, a new begomovirusthat infects cotton in Argentina was identified. Structural and functional annotationindicated that its sequences corresponded to complete DNA components A and B of anovel New World bipartite begomovirus. Genetic distance and evolutionary analysessupport that the detected sequences correspond to a new virus, which we propose toname cotton mosaic virus (CoMV). In addition, we report the first begomovirus andpolerovirus coinfection in cotton.