Abundance of Poleroviruses within Tasmanian Pea Crops and Surrounding Weeds, and the Genetic Diversity of TuYV Isolates Found

Muhammad Umar; Robert S Tegg; Tahir Farooq; Tamilarasan Thangavel; Calum R Wilson

doi:10.3390/v14081690

Abundance of Poleroviruses within Tasmanian Pea Crops and Surrounding Weeds, and the Genetic Diversity of TuYV Isolates Found

Viruses. 2022 Jul 30;14(8):1690. doi: 10.3390/v14081690.

Authors

Muhammad Umar¹, Robert S Tegg¹, Tahir Farooq², Tamilarasan Thangavel^{1

3}, Calum R Wilson¹

Affiliations

¹ New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, 13 St. Johns Avenue, New Town, Hobart, TAS 7008, Australia.
² Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
³ Department of Agriculture and Fisheries (Queensland), Bundaberg Research Facility, 49 Ashfield Road, Bundaberg, QLD 4670, Australia.

Abstract

The genus Polerovirus contains positive-sense, single-stranded RNA plant viruses that cause significant disease in many agricultural crops, including vegetable legumes. This study aimed to identify and determine the abundance of Polerovirus species present within Tasmanian pea crops and surrounding weeds that may act as virus reservoirs. We further sought to examine the genetic diversity of TuYV, the most commonly occurring polerovirus identified. Pea and weed samples were collected during 2019-2020 between October and January from thirty-four sites across three different regions (far northwest, north, and midlands) of Tasmania and tested by RT-PCR assay, with selected samples subject to next-generation sequencing. Results revealed that the presence of polerovirus infection and the prevalence of TuYV in both weeds and pea crops varied across the three Tasmanian cropping regions, with TuYV infection levels in pea crops ranging between 0 and 27.5% of tested plants. Overall, two species members from each genus, Polerovirus and Potyvirus, one member from each of Luteovirus, Potexvirus, and Carlavirus, and an unclassified virus from the family Partitiviridae were also found as a result of NGS data analysis. Analysis of gene sequences of the P0 and P3 genes of Tasmanian TuYV isolates revealed substantial genetic diversity within the collection, with a few isolates appearing more closely aligned with BrYV isolates. Questions remain around the differentiation of TuYV and BrYV species. Phylogenetic inconsistency in the P0 and P3 ORFs supports the concept that recombination may have played a role in TuYV evolution in Tasmania. Results of the evolutionary analysis showed that the selection pressure was higher in the P0 gene than in the P3 gene, and the majority of the codons for each gene are evolving under purifying selection. Future full genome-based analyses of the genetic variations will expand our understanding of the evolutionary patterns existing among TuYV populations in Tasmania.

Keywords: NGS; Turnip yellows virus; genome diversity; legumes; phylogenetic analysis; polerovirus; recombination; vegetables.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Crops, Agricultural
Genetic Variation
Luteoviridae*
Phylogeny
Pisum sativum
Plant Diseases
Plant Weeds

Grants and funding

This research was funded by Hort Innovation, using the Vegetable Industry research and development levy and contributions from the Australian Government (project VG16086: Area-wide management of vegetable diseases: virus and bacteria). Hort Innovation is the grower-owned, not-for-profit research and development corporation for Australian horticulture.