The family Caulimoviridae comprises virus species that replicate by reverse transcription, and is composed by seven genera. Viruses classified within the genus Badnavirus are pathogens in economically important crops worldwide, and previous studies suggest a high genetic diversity in badnaviruses infecting cultivated hosts. To assess the genetic diversity of sugarcane-infecting badnaviruses, samples were obtained from a germplasm collection in Brazil in 2013. A total of 300 samples were collected, and PCR-analysis showed a badnavirus incidence level of 36 %. Partial sequences comprising the RT/RNaseH genomic region were obtained for 37 isolates. Sequence analysis showed the presence of at least six badnavirus species, with one being novel. The phylogenetic analysis showed that some sugarcane isolates are closely related to badnaviruses infecting banana (Musa spp.). KeywordsCaulimoviridae . Saccharum spp . Sugarcane bacilliform viruses The family Caulimoviridae comprises virus species that replicate by reverse transcription, and is composed of seven genera: Badnavirus, Caulimovirus, Cavemovirus, Petuvirus, Solendovirus, Soymovirus and Tungrovirus (Geering and Hull 2012). Viruses classified within the genus Badnavirus have bacilliform morphology, with particles measuring ca. 130×30 nm and containing a double-stranded DNA genome of 7.2-9.2 kb (Geering and Hull 2012). The demarcation of badnavirus species is based on host range, vector specificities and the determination of the nucleotide sequence of the RT/ RNaseH genomic region. The International Committee on Taxonomy of Viruses (ICTV) has established a species demarcation threshold of ≥80 % nucleotide identity for the RT/ RNaseH region (Geering and Hull 2012). Badnaviruses are transmitted in a semi-persistent manner by mealybugs (Geering and Hull 2012) and can infect a wide range of economically important crops including sugarcane (Saccharum spp.; Lockhart and Autrey 1988), banana (Musa spp.; Geering et al. 2000), yams (Dioscorea spp.; Phillips et al. 1999) and pineapple (Ananas comosus; Gambley et al. 2008).
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