Characterization of cotton virus A, a novel and distinct member of the genusCaulimoviruswith endogenous viral elements inGossypiumspp

Abstract The complete genome sequence of cotton virus A, a new virus infecting cotton ( Gossypium spp.), was determined using high-throughput sequencing, PCR and rolling circle amplification. The 7,482-nt genome is a circular dsDNA molecule that codes for six open reading frames similar to other members of the Caulimovirus genus (family Caulimoviridae ) but presenting key genome organization differences. P3, P5 and P6 are presumed movement, coat, and reverse transcriptase proteins, respectively. P1, P2 and P4 showed no homology to virus proteins. Endogenous viral elements were found in G. hirsutum and G. tomentosum , but not in G. barbadense, G. arboreum, or G. herbaceum.