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

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

Minh Vu  1 , Bhadra Murthy Vemulapati  1 , Wendy McFadden-Smith  2 , Mamadou L Fall  3 , José Ramón Úrbez-Torres  4 , Debra L Moreau  5 , Sudarsana Poojari  1
Affiliations

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

Minh Vu et al. Viruses. .

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.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Initial neighbor joining network for 64 full genomes (approximately 7300 bp, (A)/left) and for the 64 largest recombination-free fragments (4866 bp, (B)/right). Both trees were built using the neighbor joining network pipeline in Splittree 5.3.0, which consists of the Hamming Distances method (Hamming 1950), the Neighbor Net method (Bryant and Moulton 2004) and the Splits Network Algorithm method (Dress and Huson 2004), using all default options.
Figure 2
Figure 2
Consensus network built from three ML trees of larger recombination-free segments. The Consensus Network method (Holland and Moulton 2003) and the Splits Network algorithm method (Dress and Huson 2004) was used with default options and accepting threshold of 0.33 (Splittree 5.3.0). ML tree for the largest segment (4866 bp) is shown in Figure S2.
Figure 3
Figure 3
Maximum likelihood model for full genomes ((A)/left) and the largest recombination-free fragments 4866 bp ((B)/right) from 64 GPGV isolates. Both of these rooted bootstrap-consensus maximum likelihood trees were constructed with MEGA-X (General Time Reversal Model with discreet gamma distribution and invariant sites) and a bootstrap value of 1000, using ACLSV as an outgroup. Branches with less than 70% bootstrap consensus were collapsed. GPGV isolates collected from symptomatic grapevines are written in red.
Figure 4
Figure 4
Phylogenetic relationships between 168 GPGV isolates regarding the MP/CP interregional sequence. This rooted neighbor joining tree was constructed with MEGA-X using a bootstrap value of 1000 and using apple chlorotic leaf spot virus as the outgroup. Nodes with higher than 70% bootstrap consensus are annotated. GPGV isolates collected from symptomatic grapevines are written in red. The green-shaded area indicates clade α, and the red-shaded area indicates clade β. A circular tree was selected instead of the traditional rectangular tree due to the high number of isolates.
See this image and copyright information in PMC

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