Characterization of a novel genomovirus in the phytopathogenic fungus Botrytis cinerea

Highlights: • A novel genomovirus, Botrytis cinerea genomovirus 1 (BcGV1), was characterized in Botrytis cinerea. • BcGV1 may belong to a new genus in the family Genomoviridae. • BcGV1 was widely distributed in the Chinese B. cinerea population with an incidence of 6.7%. This study characterized a single-stranded circular DNA virus in Botrytis cinerea—namely, Botrytis cinerea genomovirus 1 (BcGV1). The genome of BcGV1 was 1710 nucleotides (nts) long, possessing two ORFs, encoding a putative replication initiation protein (Rep) and a hypothetical protein. The Rep contained seven conserved motifs. The two ORFs were separated by two intergenic regions; the large intergenic region (LIR) contained 259 nts while the small intergenic region (SIR) contained 95 nts. A nonanucleotide, TAACAGTAC, in the LIR was predicted to be associated with the initiation of viral replication. Based on the phylogenetic tree constructed by Reps, BcGV1 belongs to the family Genomoviridae, forming an independent branch, indicating that BcGV1 may belong to a new genus. BcGV1 could be detected in 6.7% of tested B. cinerea strains, suggesting that BcGV1 may be widely distributed in the Chinese B. cinerea population.