Badnavirus sequence diversity reveals one previously uncharacterized virus associated with air yam ( Dioscorea bulbifera L.) in Brazil

Dioscorea bulbifera L., commonly known as air yam, is an edible crop belonging to the botanical family Dioscoreaceae , and it has increasingly attracted attention due to its socioeconomical relevance. To molecularly characterize the species diversity of badnaviruses associated with D. bulbifera in Brazil, plant samples ( n = 60) were collected from different growing regions. Partial sequences of the reverse transcriptase (RT) and ribonuclease H (RNase H) domains were obtained from 26 PCR-positive samples. Based on pairwise nucleotide sequence comparisons, the RT-RNase H sequences (~ 580 bp in length) reported here belong to the badnaviral species dioscorea bacilliform AL virus (DBALV, n = 2), dioscorea bacilliform SN virus (DBSNV, n = 8), and dioscorea bacilliform TR virus (DBTRV, n = 2), and the endogenous pararetrovirus dioscorea rotundata endogenous virus eDBV12 ( n = 5). Furthermore, a putative novel badnavirus tentatively named Dioscorea bacilliform BL virus ( n = 9) was partially characterized, sharing the highest nucleotide identity (75.7–79.9%) with eDBV12. The Bayesian phylogenetic tree reconstructed based on partial RT-RNase H nucleotide sequences showed the newly characterized isolates were clustered in three different clades, with dioscorea bacilliform BL virus (DBBLV) being more closely related to eDBV12 and forming a sister group with DBALV isolates. Together, these results reinforce the high badnaviral species diversity usually observed associated with Dioscorea spp. and constitute the first report of DBTRV in D. bulbifera .