Plant Virology and Next Generation Sequencing: Experiences with a Potyvirus

Abstract

Next generation sequencing is quickly emerging as the go-to tool for plant virologists when sequencing whole virus genomes, and undertaking plant metagenomic studies for new virus discoveries. This study aims to compare the genomic and biological properties of Bean yellow mosaic virus (BYMV) (genus Potyvirus), isolates from Lupinus angustifolius plants with black pod syndrome (BPS), systemic necrosis or non-necrotic symptoms, and from two other plant species. When one Clover yellow vein virus (ClYVV) (genus Potyvirus) and 22 BYMV isolates were sequenced on the Illumina HiSeq2000, one new ClYVV and 23 new BYMV sequences were obtained. When the 23 new BYMV genomes were compared with 17 other BYMV genomes available on Genbank, phylogenetic analysis provided strong support for existence of nine phylogenetic groupings. Biological studies involving seven isolates of BYMV and one of ClYVV gave no symptoms or reactions that could be used to distinguish BYMV isolates from L. angustifolius plants with black pod syndrome from other isolates. Here, we propose that the current system of nomenclature based on biological properties be replaced by numbered groups (I–IX). This is because use of whole genomes revealed that the previous phylogenetic grouping system based on partial sequences of virus genomes and original isolation hosts was unsustainable. This study also demonstrated that, where next generation sequencing is used to obtain complete plant virus genomes, consideration needs to be given to issues regarding sample preparation, adequate levels of coverage across a genome and methods of assembly. It also provided important lessons that will be helpful to other plant virologists using next generation sequencing in the future.

A proposal to rationalize within-species plant virus nomenclature: benefits and implications of inaction

“…Before we recommended it for three other viruses [12,19,20,23], this same nomenclature system was already in use with potato virus X [21] and hardenbergia mosaic virus [28]. There are other alternatives, such as using a mixture of Latinised numerals and alphabet letters (as with zucchini yellow mosaic virus [5]), alphabet letters alone, or standard numerals.…”

“…The phylogenetic group names selected corresponded to original isolation hosts, resulting in the names 'broad bean', 'lupin', 'pea', 'canna' and 'monocot' for the specialist groups, and 'general' for the original 'generalist' group [29]. However, when a comprehensive phylogenetic study of complete genomes was done, it became clear that these host-dependent names were unjustified as new isolates were found to occur in members of host plant species, genera or families other than the ones originally used to name the group [19]. Recombination was found to have played an important role in the evolutionary history of the virus, and assumptions about host adaptation and geographical origins of sequenced isolates in relation to crop Fig.…”

“…The names used became unsustainable following an increase in numbers of complete genome sequences, presence within specialist groups of isolates from different host species from those after which the group was originally named and findings that recombination splits the former ''general'' group into separate groups. Use of Latinized numerals to name groups overcame all such issues (modified from reference [19]) Rationalization of within-species plant virus names 2053 domestication centres proved incorrect [20]. Use of Latinised numerals for phylogenetic groups resolved all the inconsistencies (Fig.…”

“…An important contributory factor is the rapid increase in numbers of complete genome sequences becoming available and changing the landscape of phylogenetic analyses [19]. Using complete genome sequences gives much more information and allows recombination to be taken into account in interpretation of phylogenetic trees.…”

“…Using complete genome sequences gives much more information and allows recombination to be taken into account in interpretation of phylogenetic trees. In contrast, employing partial genome sequences for phylogenetic analysis can produce misleading phylogenetic trees, which, when recombination occurs, often result in incorrect deductions about the positioning of isolates in within-species phylogenetic groups [18][19][20]29]. Other factors increasingly impacting on the sequences that make up within-species phylogenetic groups include emergence of known and novel viruses in new hosts or world regions driven by (i) new encounters between wild and crop plants at interfaces between wild and managed vegetation, (ii) rapidly expanding world trade in plants and plant products moving viruses and vectors around the world, (iii) agricultural intensification, extensification and diversification underway to feed the burgeoning world population, (iv) encroaching urbanization as population centers expand, and (v) climate change causing plant viruses to adapt, shift hosts and change their geographical distributions [1,3,4,7,[10][11][12][13][14]24].…”