Computational analysis of haplotype diversity, phylogenetic variation, and population structure of Candidatus Phytoplasma aurantifolia using tuf gene sequences

Abstract

The study investigated the genetic diversity and population structure of Candidatus P. aurantifolia using tuf gene sequences sourced from GenBank™. A total of 29 sequences were analyzed based on location availability, unveiling 8 distinct haplotypes. Haplotype 5, encompassing sequences from Egypt, Australia, and Thailand, emerged as the most prevalent. Phylogenetic analysis revealed two different major clades with a significant genetic divergence within species. Notably, calculated haplotype diversity ranged from 0.0 to 0.5909, with India exhibiting the highest diversity. Moreover, haplotype diversity (Hd) was absent in several regions, including Egypt, Australia, and Burkina Faso. Furthermore, nucleotide diversity varied across regions, with Oman displaying the highest value (0.78182) and Thailand showing the lowest (0.09422). A high raggedness index value in the populations of Oman, and Thailand and a low value in India. Substantial genetic divergence in the populations between India-Egypt with limited gene flow was evident by high values of DeltaSt, GammaSt and Fst. Fu Fs values, indicative of demographic expansions or selection events, were notably high in India (34.035). Significant Tajima D values (2.035) in India further support deviations from neutral evolution. Our findings provide unprecedented insights into the population genetics and haplotype network of Candidatus P. aurantifolia, shedding light on its genetic diversity and geographic distribution in different countries. The study results will aid in the prediction of bacterium transmission and the implementation of effective quarantine measures. Moreover, the identification of regions having high genetic divergence and unique haplotypes may help in developing disease management strategies for targeted areas.