Genetic variability of badnavirus isolates infecting yam (Dioscorea spp.) in northeastern Brazil

Diseases caused by viruses of the genus Badnavirus are responsible for great losses in yam crops in northeastern Brazil. Knowledge of pathogen variability can provide important information about its evolutionary potential and may allow for development of better strategies for disease management. The analysis of 425 leaf samples of yam obtained in 2010 in three states of northeastern Brazil revealed a high incidence (93.3%) of badnaviruses. To evaluate the variability of yam-infecting badnaviruses, a 579-nucleotide fragment corresponding to the reverse transcriptase (RT)/RNaseH coding region was PCR-amplified and directly sequenced. Phylogenetic analysis of nucleotide sequences revealed that the isolates can be divided into two groups. The first group is highly related to Dioscorea bacilliform AL virus (DBALV), while the other set of sequences formed a highly divergent clade within the genus Badnavirus. The DBALV isolates have 70-98% nucleotide sequence identity with each other. DBALV was detected in all areas assessed and in the two most cultivated species of yam in the northeast (D. alata and D. cayanensis). The other group shares 47-58% nucleotide sequence identity with the DBALV isolates and 78-95% amongst themselves, and was found only in D. alata in the state of Paraiba.