Yams (Dioscorea spp.) from the South Pacific Islands contain many novel badnaviruses: implications for international movement of yam germplasm

Abstract

Yam (Dioscorea spp.) samples (n = 690) from seven South Pacific Islands were screened for badnavirus infection by ELISA using two antisera to African badnaviruses. Positive readings were obtained for 26.4-34.6% of samples representing both known (D. bulbifera, D. nummularia and D. pentaphylla) and unreported host species (D. alata, D. esculenta, D. rotundata and D. trifida) in this region. Total DNAs were extracted from 25 ELISA-positive plants and 4 ELISA-negative controls and subjected to PCR amplification with badnavirus-specific primers targeting the reverse transcriptase (RT)-RNaseH genes. All 29 samples yielded the expected size PCR-product for badnaviruses, which were cloned and sequenced. Phylogenetic analyses of the resulting 45 partial (500-527 bp) RT-RNaseH sequences revealed 11 new sequence groups with <79% nucleotide identity to each other or any EMBL sequence. Three sequences (two groups) were highly divergent to the other nine new South Pacific yam badnavirus groups (47.9-57.2% identity) and probably represent either new Caulimoviridae genera or endogenous pararetrovirus sequences. Some sequence groups appeared specific to particular Dioscorea host species. Four 99.9% identical RT-RNaseH sequences possessing nine amino acid deletions from D. esculenta from three islands represent a putative integrated sequence group. The distribution of sequence groups across the islands indicates that badnaviruses have spread extensively between islands and continents through infected germplasm.

The Response of White Yam (Dioscorea rotundata Poir) Tuber Portions to Positive Selection for Quality Seed Yam Production

“…In their study they found out that out of 300 D.rotundata leaf samples collected, 184 (61.3%) tested positive for YMV. This finding buttresses previous report of YMV as one of the most important yam viruses occurring in very high incidence and it is also widely distributed in yam fields throughout the world [14,15]. The high incidence of YMV observed in this study can be attributed to unselected farmers planting material that have accumulated viruses and diseases over several cycles of vegetative propagation and the exchange of yam germplasm between field and screen house plants accounts for YMV incidence in the screen house plants.…”

Molecular analysis of gooseberry vein banding associated virus

“…Their infection can lead to development of flecks, freckles, streaks, chlorosis or yellowing along veins, or there may be no visible symptoms whatsoever. In the past decade, badnaviruses have been the subject of increased attention since the discovery of their endogenous sequences in various plant genomes (Geering et al, 2005(Geering et al, , 2011Gayral et al, 2008;Kenyon et al, 2008;Bousalem et al, 2009;James et al, 2011) and risk of their putative spread through infected germplasm and/or activation by an abiotic stress during propagation (Dallot et al, 2001).…”

“…Mostly the RT/RNase H coding sequence is used for detecting badnaviruses and evaluating differences. Comparison of this sequences in yams (Dioscorea) revealed a very high degree of variability between isolates and resulted in identifying many novel badnaviruses (Kenyon et al, 2008;Bousalem et al, 2009), as the recent species demarcation criteria in the badnavirus genus suppose more than 20% nucleotide (nt) differences in this region (Geering and Hull 2012). Seven phylogenetic groups have been characterized according to the 529 nt long RT/RNase H segment among 35 sugarcane bacilliform virus (SCBV) isolates, and three additional SCBV viruses were proposed using the 20% nt difference threshold (Muller et al, 2011).…”

Rolling Circle Amplification to Screen Yam Germplasm for Badnavirus Infections and to Amplify and Characterise Novel Badnavirus Genomes

“…germplasm in the 1970s (Harrison and Roberts, 1973), several hundred partial badnavirus reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences have been characterised (Kenyon et al, 2008;Bousalem et al, 2009), but only a few complete Dioscorea bacilliform virus (DBV) genome sequences have been reported (Phillips et al, 1999;Seal and Muller, 2007;Bömer et al, 2016 andSukal et al, 2017;Umber et al, 2017). We have optimised a workflow involving total nucleic acid extractions and rolling circle amplification (RCA) combined with restriction enzyme analysis for the detection and amplification of DBVs present in yam germplasm.…”