Phylogenetic and Evolutionary Studies of Grapevine Pinot Gris Virus Isolates from Canada

Minh Vu; Bhadra Murthy Vemulapati; Wendy McFadden-Smith; Mamadou L Fall; José Ramón Úrbez-Torres; Debra L Moreau; Sudarsana Poojari

doi:10.3390/v15030735

Phylogenetic and Evolutionary Studies of Grapevine Pinot Gris Virus Isolates from Canada

Viruses. 2023 Mar 12;15(3):735. doi: 10.3390/v15030735.

Authors

Minh Vu¹, Bhadra Murthy Vemulapati¹, Wendy McFadden-Smith², Mamadou L Fall³, José Ramón Úrbez-Torres⁴, Debra L Moreau⁵, Sudarsana Poojari¹

Affiliations

¹ Cool Climate Oenology and Viticulture Institute, Brock University, St. Catharines, ON L2S 3A1, Canada.
² Ontario Ministry of Agriculture, Food and Rural Affairs, Vineland Station, Lincoln, ON L0R 2E0, Canada.
³ Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 7B5, Canada.
⁴ Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada.
⁵ Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS B4N 1J5, Canada.

Abstract

This study investigated the phylogenetic relationship of grapevine Pinot gris virus (GPGV) isolates from Canada with GPGV isolates reported worldwide. Full-length genomes of 25 GPGV isolates representing the main four grape-growing regions in Canada (British Columbia, Ontario, Nova Scotia and Quebec) were sequenced and compared to genomes of 43 GPGV isolates representing eight countries and three continents. Phylogenetic analysis based on full genome sequences revealed an unambiguous separation of North American GPGV isolates with isolates from Europe and Asia. Within the North American clade, GPGV isolates from the USA segregated into a distinct subclade, whereas the relationships amongst GPGV isolates from different regions of Canada were not clearly defined. The phylogenetic analysis of the overlapping regions of MP and CP genes involving 169 isolates from 14 countries resulted in two distinctive clades, which were seemingly independent of their country of origin. Clade 1 included the majority of asymptomatic isolates (81% asymptomatic), whereas clade 2 was predominantly formed of symptomatic isolates (78% symptomatic). This research is the first study focused on the genetic variability and origin of GPGV in Canada.

Keywords: data mining; grapevine; high-throughput sequencing; phylogenetic analysis; virus evolution.

Publication types

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

MeSH terms

Flexiviridae* / genetics
Genome, Viral
Ontario
Phylogeny
Vitis*

Grants and funding

This research was supported by Genome British Columbia and Genome Canada through the project (code 189GRP), entitled “CLEan plAnt extractioN sEquencing Diagnostics (CLEANSED) for Clean Grapevines in Canada” and “by matching funds from the British Columbia Wine Grape Council, Ontario Grape and Wine Research Inc., Canadian Grapevine Certification Network and Agriculture and Agri-Food Canada (AAFC) through the Growing Forward Canadian Agriculture Partnerships (CAP) Program and by AAFC Genomic Research and Development Initiative program”.