Genetic Diversity, Evolutionary Dynamics, and Ongoing Spread of Pedilanthus Leaf Curl Virus

Area of Science:

• Plant virology
• Molecular evolution
• Bioinformatics

Background:

• Pedilanthus leaf curl virus (PeLCV), a monopartite begomovirus, has rapidly spread across Pakistan and India affecting numerous plant species.
• Viral evolution is characterized by rapid mutation rates, leading to significant genetic diversity that influences ecological and evolutionary behaviors.

Purpose of the Study:

• To computationally map sequence variation dynamics, genetic heterogeneity, regional diversity, phylogeny, and recombination events within the PeLCV genome.
• To understand the evolutionary trajectory and diversification patterns of PeLCV.

Main Methods:

• Phylogenetic analysis of 52 full-length PeLCV genome sequences.
• Network analysis to determine evolutionary relationships and clades.
• Inference of recombination events and demographic selection.

Main Results:

• Phylogenetic and network analyses revealed 7 major clades with regional but not host-specific delineation.
• The origin of PeLCV was traced to Multan, Pakistan, in 1977, with subsequent spread to India and other regions of Pakistan.
• High levels of inter- and intra-species recombination were detected throughout the genome.
• The PeLCV population exhibits high genetic diversity (π = 0.073%), a high nucleotide substitution rate (1.54 × 10^-3), and significant recombination.

Conclusions:

• PeLCV demonstrates rapid expansion and high genetic diversity, distinguishing it from other begomoviruses.
• Factors like high recombination rates and demographic selection contribute to PeLCV's divergence and potential adaptation to new hosts.
• The study provides insights into the emergence and evolutionary dynamics of PeLCV.