In silico identification of Bell pepper endornavirus from pepper transcriptomes and their phylogenetic and recombination analyses

•Eight Bell pepper endornavirus (BPEV) isolates were identified from nine different pepper transcriptomes.•Phylogenetic identified two different groups of BPEV isolates.•Recombination analysis identified two possible recombinant events in the isolate Yolo Wonder.•Single nucleotide variation profiles revealed the presence of BPEV variants within a single pepper cultivar.

Here, we identified eight Bell pepper endornavirus (BPEV) isolates from nine different pepper transcriptomes. BPEV was present with low copy numbers ranging from 0.01% to 0.18% in the host transcriptome. Phylogenetic identified two different groups of BPEV isolates. Sequence alignment of the five BPEV genomes revealed conservation of the 5′ and 3′ untranslated regions. Recombination analysis identified two possible recombinant events in the isolate Yolo Wonder. Single nucleotide variation profiles revealed the presence of BPEV variants within a single pepper cultivar. Taken together, this study provides phylogenetic and recombination analyses of the genus Endornavirus using pepper transcriptome data.