Tissue culture and next-generation sequencing: A combined approach for detecting yam (Dioscorea spp.) viruses

Moritz Bömer; Ajith I Rathnayake; Paul Visendi; Steven O Sewe; Juan Paolo A Sicat; Gonçalo Silva; P Lava Kumar; Susan E Seal

doi:10.1016/j.pmpp.2018.06.003

Tissue culture and next-generation sequencing: A combined approach for detecting yam (Dioscorea spp.) viruses

Physiol Mol Plant Pathol. 2019 Jan:105:54-66. doi: 10.1016/j.pmpp.2018.06.003.

Authors

Moritz Bömer¹, Ajith I Rathnayake¹, Paul Visendi¹, Steven O Sewe¹, Juan Paolo A Sicat¹, Gonçalo Silva¹, P Lava Kumar², Susan E Seal¹

Affiliations

¹ Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK.
² International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria.

Abstract

In vitro culture offers many advantages for yam germplasm conservation, propagation and international distribution. However, low virus titres in the generated tissues pose a challenge for reliable virus detection, which makes it difficult to ensure that planting material is virus-free. In this study, we evaluated next-generation sequencing (NGS) for virus detection following yam propagation using a robust tissue culture methodology. We detected and assembled the genomes of novel isolates of already characterised viral species of the genera Badnavirus and Potyvirus, confirming the utility of NGS in diagnosing yam viruses and contributing towards the safe distribution of germplasm.

Keywords: Badnavirus; Cucumber mosaic virus, CMV; Dioscorea bacilliform virus, DBV; Dioscorea spp.; In vitro culture; RNA-Seq; Yam mild mosaic virus, YMMV; Yam mosaic virus; Yam mosaic virus, YMV; endogenous pararetroviruses, EPRV.