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

Abstract

Yam is an important food staple in many Pacific Island countries, but its production is limited by several factors including virus infection. The presence of viruses also hinders the exploitation of the crop by restricting the international dissemination of yam germplasm due to quarantine concerns. In this study, a total of 224 yam accessions present in the Pacific germplasm collection at SPC‐CePaCT, Fiji, were tested for the presence of badnaviruses using a combination of rolling circle amplification (RCA) and sequencing. Of these, 35 tested positive for either Dioscorea bacilliform AL virus (DBALV) or Dioscorea bacilliform AL virus 2 (DBALV2). DBALV was only detected in samples from Vanuatu and Tonga, while DBALV2 was restricted to Papua New Guinean samples. Ten complete genome sequences of DBALV and DBALV2 were obtained and pairwise comparison of the partial reverse transcriptase/ribonuclease H (RT/RNase H)‐coding sequence revealed identities ranging from 89% to 100% and 92% to 100%, respectively. The results suggest that DBALV and DBALV2 are the prevalent badnavirus species infecting yams in the Pacific region.

Detection and diversity of viruses infecting African yam (Dioscorea rotundata) in a collection and F1 progenies in Côte d'Ivoire shed light to plant‐to‐plant viral transmission

“…Whilst it was first detected in D. alata, it is now known to infect other yam species, such as D. bulbifera, D. nummularia, D. rotundata, and D. trifida (Kenyon et al, 2008;Sukal et al, 2020;Umber et al, 2017). Three of the badnaviral sequences obtained in this study clustered with Group 5 (DBV5), of which the complete genome of the corresponding species, named Dioscorea bacilliform RT virus 3 (DBRTV3), has been recently sequenced in Nigeria from D. rotundata (Bömer et al, 2018).…”

“…rotundata , and D . trifida (Kenyon et al, 2008 ; Sukal et al, 2020 ; Umber et al, 2017 ). Three of the badnaviral sequences obtained in this study clustered with Group 5 (DBV5), of which the complete genome of the corresponding species, named Dioscorea bacilliform RT virus 3 (DBRTV3), has been recently sequenced in Nigeria from D .…”

Viruses of Yams (Dioscorea spp.): Current Gaps in Knowledge and Future Research Directions to Improve Disease Management

“…While serological and classical molecular diagnostics are target-specific, HTS circumvents this limitation by generating sequences from both known and unknown pathogens, which removes the need for prior knowledge of target sequences [84,85]. The use of HTS has led to the discovery and molecular characterization of numerous new yam viruses in the genera Ampelovirus, Badnavirus, Macluravirus, Potyvirus, and Sadwavirus (Table 1; [5,28,29,36,54,58,86]). HTS has proved very versatile and well suited for filling knowledge gaps around the diversity of yam viruses, but it requires an informed choice of samples and a sequencing platform.…”

A Review of Viruses Infecting Yam (Dioscorea spp.)

“…The genus Badnavirus is a group of plant pararetroviruses that have been reported to infect a wide range of economically important plants, such as aroids, banana, black pepper, citrus, cocoa, gooseberry, grape, ornamental spiraea, red raspberry, sugarcane, sweet potato and yam of the tropical and temperate regions of Africa, Asia, Europe, Oceania and the Americas [76,77]. The Badnavirus genome comprises a single circular dsDNA ca.…”