Grapevine virus T diversity as revealed by full-length genome sequences assembled from high-throughput sequence data

Area of Science:

• Plant Virology
• Molecular Evolution
• Bioinformatics

Background:

• Grapevine virus T (GVT) is a recently discovered virus impacting grapevines.
• Understanding GVT diversity is crucial for grapevine health management and breeding programs.

Purpose of the Study:

• To conduct the first pan-genomic analysis of grapevine virus T (GVT) diversity.
• To characterize the evolutionary dynamics and genetic variation within GVT populations.
• To assess the effectiveness of current detection methods for GVT.

Main Methods:

• Genome reconstruction using RNASeq and double-stranded RNA approaches.
• Bioinformatic analysis of publicly available grapevine transcriptome data.
• Phylogenetic analysis and assessment of nucleotide/amino acid polymorphism and selection pressures.

Main Results:

• Reconstruction of 27 GVT genomes (9 novel, 14 from data mining, 4 existing).
• High nucleotide and amino acid polymorphism in GVT, comparable to GRSPaV.
• Identification of at least seven distinct GVT phylogenetic groups.
• Evidence of conservative selection pressure and recombination in GVT evolution.
• Potential failure of existing PCR primers to detect all GVT isolates.

Conclusions:

• GVT exhibits significant genetic diversity and distinct evolutionary characteristics.
• GVT shares notable similarities with grapevine rupestris stem pitting-associated virus (GRSPaV).
• Current GVT detection primers may require re-evaluation for broad applicability.