Evolutionary Genomics of Bemisia tabaci and Characterization of its Endosymbiont Metacommunities using nextRAD Sequencing

The sweetpotato whitefly Bemisia tabaci harbours a wide range of cryptic species that have been placed in phylogenetically distinct clades based on partial mitochondrial DNA cytochrome oxidase I (mtCOI) gene sequence characterisation. Four cryptic species i.e. MEAM1, MEAM2, MED and ‘Indian Ocean’ are currently placed within the invasive clade of the global Bemisia phylogeny. Here, we applied a genome-wide single nucleotide polymorphism (SNP) analysis using a Nextera-tagmented, reductively amplified DNA protocol (nextRAD) to: 1) investigate the phylogenomics of the Bemisia cryptic invasive species complex; 2) infer their demographic history, and 3) investigate the endobacterial composition in each of these species. We provide a short overview of the nextRAD genome-wide scan analysis pipeline and its application to understanding the evolutionary genomics of this global agricultural insect pest. nextRAD is a PCR-based protocol that mimics RAD-sequencing without using restriction enzymes. We obtained >3,000 shared SNPs from 83 individuals with relatively low DNA quality and concentration. We identified reads mapping to primary and secondary endosymbionts such as Candidatus Portiera aleyrodidarum and Cand. Hamiltonella defensa, which, may have implications to host fitness and adaptations across different agricultural landscapes. Using the nextRAD genome-wide SNP identification method, we were able to demonstrate a clear and high-resolution phylogeny for delimitating i B. tabaci species boundaries within the invasive clade, ascertain levels of endobacterial abundances in each cryptic species, and infer global invasion pathway for  B. tabaci species. We discuss our findings and potential implications with respect to global agricultural biosecurity in the age of insect pest population genomics.