Nuclear Orthologs Derived from Whole Genome Sequencing Indicate Cryptic Diversity in the Bemisia tabaci (Insecta: Aleyrodidae) Complex of Whiteflies

Abstract

The Bemisia tabaci complex of whiteflies contains globally important pests thought to contain cryptic species corresponding to geographically structured phylogenetic clades. Although mostly morphologically indistinguishable, differences have been shown to exist among populations in behavior, plant virus vector capacity, ability to hybridize, and DNA sequence divergence. These differences allow for certain populations to become invasive and cause great economic damage in a monoculture setting. Although high mitochondrial DNA divergences have been reported between putative conspecifics of the B. tabaci species complex, there is limited data that exists across the whole genome for this group. Using data from 2184 orthologs obtained from whole genome sequencing (Illumina), a phylogenetic analysis using maximum likelihood and coalescent methodologies was completed on ten individuals of the B. tabaci complex. In addition, automatic barcode gap discovery methods were employed, and results suggest the existence of five species. Although the divergences of the mitochondrial cytochrome oxidase I gene are high among members of this complex, nuclear divergences are much lower in comparison. Single-copy orthologs from whole genome sequencing demonstrate divergent population structures among members of the B. tabaci complex and the sequences provide an important resource to aid in future genomic studies of the group.

Genetic Diversity of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Colonizing Sweet Potato and Cassava in South Sudan

“…A study has demonstrated that NUMTs Insects 2020, 11, 58 9 of 15 were the cause for the incorrect identification of a putative Bemisia species that was given the name MEAM2 based on mtDNA COI data [87]. Another study using whole genome nuclear markers on the major clades of B. tabaci revealed the existence of fewer putative species (five so far), as opposed to the much larger number reported with mtCO1 [73]. In this study, B. tabaci Indian Ocean were collected from sweet potato and tomato, and their sequences were most closely related to Reunion 1 from Spain [88], although B. tabaci Indian Ocean has also been widely reported from sub-Saharan Africa and the surrounding islands [60,65,89].…”

“…Microsatellite markers have also been developed and used to study B. tabaci populations [69,70]. Recent advances have utilized SNP genotyping and nuclear genes [71][72][73]. The mitochodrial DNA cytochrome oxidase I (mtCOI) marker has been the most widely used marker for phylogenetic studies of B. tabaci.…”

Genetic variability, community structure, and horizontal transfer of endosymbionts among three Asia II‐Bemisia tabaci mitotypes in Pakistan

“…The whitefly B. tabaci collected in the Punjab province of Pakistan were identified as mitotypes Asia II‐1, ‐5, and ‐7 (Dinsdale et al, ), which belong to the Asia II major clade of B. tabaci (Brown et al, ; de Moya et al, ). Characterization of the endosymbiont communities associated with endemic B. tabaci , with respect to composition, distribution, and ecological microniche(s) within of the Punjab district, suggests that certain mitotype–endosymbiont communities may have been/be selectively associated with previous and current outbreaks of cotton leaf curl disease, respectively.…”

“…The whitefly B. tabaci collected in the Punjab province of Pakistan were identified as mitotypes Asia II-1, -5, and -7 (Dinsdale et al, 2010), which belong to the Asia II major clade of B. tabaci (Brown et al, 2010;de Moya et al, 2019) (Zubair et al, 2017). Based on complex multitrophic interactions involving different plant host-virome-mitotype vector combinations, the endosymbiont community is hypothesized to contribute to niche-specific adaptation of B. tabaci mitotypes in the urban-and agroecosystems, the latter pronouncedly influenced by cropping and pesticide use regimes (see references in Bedford et al, 1994;Brown & Czosnek, 2002).…”

“…The whitefly Bemisia tabaci (Gennadius) group (Brown, Frohlich, & Rosell, 1995;Gill & Brown, 2010) consists of five or more cryptic lineages (Brown, 2010;Brown et al, 1995;Lee, Park, & Lee, 2013;de Moya et al, 2019;Paredes-Montero et al, 2019), some of which contain mitotype groups that are important plant pests and/or vectors of plant viruses (Jones, 2003). For more than fifty years, whitefly-transmitted viruses in the genus Begomovirus (family Geminiviridae) have been recognized as important new or emergent pathogens in irrigated agroecosystems worldwide (Jones, 2003).…”