Determination of genetic structure and endosymbionts in populations of cotton mealybug [Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae)] collected from different hosts in Antalya, Aydın and Denizli provinces using the ddRAD method

This study investigated the genetic variation and population-level structural characteristics of Phenacoccus solenopsis Tinsley, 1898 (Hemiptera: Pseudococcidae), an invasive and economically significant pest species, using specimens collected from Antalya, Aydın, and Denizli provinces. The primary objective of this study was to elucidate the genetic diversity and population STRUCTURE of this species through the application of double-digest Restriction-site Associated DNA (ddRAD) sequencing technology. Additionally, the presence and potential effects of endosymbiotic bacteria associated with the same individual specimens were evaluated. As part of the field investigation, a total of 125 individuals were collected from 25 different locations. Total nucleic acid isolation was performed in the laboratory using the CTAB protocol. Following next-generation sequencing (NGS) analyses, 40,165 high quality and reliable single nucleotide polymorphism (SNP) data points were obtained. These data were subsequently used in population genetic analyses, including STRUCTURE and Principal Coordinates Analysis (PCoA). STRUCTURE results, visualized using the STRUCTURE Selector web platform, revealed the presence of four distinct genetic subpopulations. A high level of genetic variation was observed, particularly among individuals collected from Denizli and Antalya provines. This differentiation was supported by Fst analysis, with an average Fst; value of 0.2832. Comparisons of individuals from different host plants showed no significant genetic divergence observed based on host. Analyses of Hardy-Weinberg equilibrium, heterozygosity rates, and sequencing coverage assessment confirmed the high reliability of the dataset. Furthermore, a phylogenetic tree was constructed based on the UPGMA method using MEGA 12 software. Endosymbiont analysis revealed that all individuals harbored Candidatus Tremblaya phenacola, the primary symbiont species in all specimens. Despite theendosymbiont load was differing on individuals, there was no regional or host plant-specific differentiation.