Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses

Abstract

Yams (Dioscorea spp.) host a diverse range of badnaviruses (genus Badnavirus, family Caulimoviridae). The first complete genome sequence of Dioscorea bacilliform RT virus 3 (DBRTV3), which belongs to the monophyletic species group K5, is described. This virus is most closely related to Dioscorea bacilliform SN virus (DBSNV, group K4) based on a comparison of genome sequences. Recombination analysis identified a unique recombination event in DBRTV3, with DBSNV likely to be the major parent and Dioscorea bacilliform AL virus (DBALV) the minor parent, providing the first evidence for recombination in yam badnaviruses. This has important implications for yam breeding programmes globally.Electronic supplementary materialThe online version of this article (doi:10.1007/s00705-017-3605-9) contains supplementary material, which is available to authorized users.

A Complex of Badnavirus Species Infecting Cacao Reveals Mixed Infections, Extensive Genomic Variability, and Interspecific Recombination

“…Additional, unique intraspecies recombination events were detected in the CSSGQV and CSSCEV isolates, also having breakpoints in the IR and ORF3, respectively. Recombination has been reported among yam-, banana-and sugarcane-infecting badnaviruses, with similar genomic locations of recombination breakpoints [73,74]. Together, the results demonstrate that recombination is an important evolutionary mechanism among cacao-infecting badnaviruses, with hotspots of recombination occurring in the IR and ORF2/C-terminal of ORF3.…”

Molecular Viral Diagnosis and Sanitation of Yam Genetic Resources: Implications for Safe Yam Germplasm Exchange

“…These efforts led to the characterization of several novel viruses and/or the sequencing of the complete genomes belonging to genera Ampelovirus , Aureusvirus , Badnavirus , Carlavirus , Comovirus , Cucumovirus , Fabavirus , Macluravirus , Potexvirus and Potyvirus . Thus, within the last five years alone, the complete genomes of 13 novel yam viral species were sequenced: one potyvirus, Dioscorea mosaic virus (DMV, [ 5 ]); six badnaviruses, Dioscorea bacilliform AL virus 2 (DBALV2, [ 6 ]), Dioscorea bacilliform ES virus (DBESV, [ 6 ]), Dioscorea bacilliform RT virus 1 (DBRTV1, [ 7 ]), Dioscorea bacilliform RT virus 2 (DBRTV2, [ 7 ]), Dioscorea bacilliform RT virus 3 (DBRTV3, [ 8 ]) and Dioscorea bacilliform TR virus (DBTRV, [ 9 ]); one sadwavirus, Dioscorea mosaic associated virus (DMaV, [ 10 ]); two macluraviruses, Yam chlorotic mosaic virus (YCMV, [ 11 ]) and Yam chlorotic necrosis virus (YCNV, [ 12 ]); two ampeloviruses, Air potato ampelovirus 1 (AiPoV1, [ 5 ]) and yam asymptomatic virus 1 (YaV1, [ 13 ]) and one virus belonging to the family Betaflexiviridae , yam virus Y (YVY, [ 14 ]).…”

Characterization and genetic diversity of Dioscorea bacilliform viruses present in a Pacific yam germplasm collection

“…An additional putative species, namely Dioscorea bacilliform RT virus 3 (DBRTV3) has also been described (Bömer et al . , ), with additional PCR‐based studies suggesting the existence of at least another eight putative yam‐associated badnavirus species worldwide (Kenyon et al . , ; Bousalem et al .…”

“…Although infection of yams with DBVs has been associated with leaf symptoms such as veinal chlorosis, necrosis, puckering, and crinkling, symptomless infections can also occur (Phillips et al, 1999;Lebot, 2009;Seal et al, 2014;Bömer et al, 2016 (Adams and Carstens, 2012;Sukal et al, 2017;Adams et al, 2018). An additional putative species, namely Dioscorea bacilliform RT virus 3 (DBRTV3) has also been described (Bömer et al, 2018), with additional PCR-based studies suggesting the existence of at least another eight putative yam-associated badnavirus species worldwide (Kenyon et al, 2008;Bousalem et al, 2009;Bömer et al, 2016).…”