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

DIVERSIFICATION INTO THE GENUS Badnavirus: PHYLOGENY AND POPULATION GENETIC VARIABILITY

“…The high levels of nucleotide diversity for the partial RT/RNaseH region in some badnavirus species (BSUAV, BSULV, BSUMV, PYMoV, SPBVB, SCBIMV and DBALV) are comparable to values observed for RNA viruses (Guimarães et al, 2015). However, this variability is lower when compared to less conserved regions [ORFs I, II and intergenic region (IGR)], with IGR showing the highest values of genetic diversity (0.468) followed by ORFII 0.367; Sharma et al, 2015).…”

“…Badnaviruses have been reported infecting economically important crops worldwide (Eni et al, 2008;James et al, 2011;Johnson et al, 2012;Kouakou et al, 2012;Deeshma and Bhat, 2015;Silva et al, 2015), causing great losses in cacao (Kouakou et al, 2012) and banana (Dahal et al, 2000;Daniells et al, 2001). They comprise a highly diversified group, and recent studies have shown that badnavirus populations exhibit high levels of genetic variability (Muller et al, 2011;Karuppaiah et al, 2013;Guimarães et al, 2015;Silva et al, 2015). Nucleotide sequence comparisons of the partial RT/RNaseH domains (579pb) and a threshold of ≥80% identity have largely been used for species demarcation in the genus Badnavirus (Muller et al, 2011;Geering and Hull, 2012;Guimarães et al, 2015;Silva et al, 2015), with universal primers described by Yang et al, (2003) being very efficient to amplify this genomic region.…”

“…They comprise a highly diversified group, and recent studies have shown that badnavirus populations exhibit high levels of genetic variability (Muller et al, 2011;Karuppaiah et al, 2013;Guimarães et al, 2015;Silva et al, 2015). Nucleotide sequence comparisons of the partial RT/RNaseH domains (579pb) and a threshold of ≥80% identity have largely been used for species demarcation in the genus Badnavirus (Muller et al, 2011;Geering and Hull, 2012;Guimarães et al, 2015;Silva et al, 2015), with universal primers described by Yang et al, (2003) being very efficient to amplify this genomic region. However, the existence of closely related badnavirus species which share more than 80% nucleotide identity in that region suggests this criterion needs to be revised (Harper et al, 2005;Muller et al, 2011;Karuppaiah et al, 2013;Silva et al, 2015).…”

“…A total of 299 RT/RNaseH partial sequences were obtained for 11 distinct badnavirus species, and the nucleotide diversity of each dataset/population was calculated (Table 3). Additionally, 96 Dioscorea bacilliform AL virus (DBALV) partial sequences from Guimarães et al (2015) were added. High values of per-site nucleotide diversity were observed for Banana streak UA virus (BSUAV), Banana streak UL virus (BSULV), Banana streak UM virus (BSUMV), Piper yellow mottle virus (PYMoV), SPBV and SCBIMV, suggesting high genetic variability for the partial RT/RNaseH region in different badnavirus species/populations ( Table 3).…”

“…Badnaviruses have also been reported as integrated sequences into their host genomes, commonly referred to as endogenous pararetroviruses (EPRVs;Hohn et al, 2008;Staginnus et al, 2009), and it is known some EPRVs are able to 'scape' from the host genome and establish a systemic infection (episomal forms; Dallot et al, 2001;Lheureux et al, 2003;Côte et al, 2010). Besides this high species diversity, badnavirus populations also show high levels of molecular variability (Geering et al, 2000;Geijskes et al, 2002;Harper et al, 2005;Govind et al, 2014;Guimarães et al, 2015;Silva et al, 2015). The lack of a proofreading activity of the badnavirus reverse transcriptase (Svarovskaia et al, 2003) and the occurrence of recombination events (Govind et al, 2014) may directly affect the high genetic variability observed in this viral group.…”