Characterization of transposable elements within the Bemisia tabaci species complex

Background: Whiteflies are agricultural pests that have caused worldwide negative impacts that have led to severe financial losses. The Bemisia tabaci whitefly species complex is the most damaging in terms of their broad crop host range and its ability to serve as vector for over 300 plant viruses. Whitefly genomes of the species complex provide valuable genomic data; however, transposable elements (TEs) within the species complex remain unexplored. This study provides the first accurate exploration of TE content within the B. tabaci species complex. Results: This study identified an average of 40.61% of the genomes of three whitefly species (MEAM1, MEDQ, and SSA-ECA) consists of TEs. Majority of the TEs identified were DNA transposons (22.85% average) while SINEs (0.14% average) were the least represented. This study also compared the TE content the three whitefly genomes with three other hemipteran genomes and found a significant difference in the presence of DNA transposons and LINEs. A total of 63 TE superfamilies were identified to be present across the three whitefly species (39 DNA transposons, six LTR, 16 LINE, and two SINE) of which 11 TE superfamilies were identified to not be present in the three other hemipteran genomes (nine DNA transposon, and two LINE). This study is the first to characterize TEs found within different B. tabaci species and has created a standardized annotation workflow that could be used to analyze future whitefly genomes. Conclusion: This study is the first to characterize the landscape of TEs within the B. tabaci species complex. The characterization of these elements within the three whitefly genomes shows that TEs occupy a significant portion of the whitefly genome, majority of which are DNA transposons. This study also identified TE superfamilies of note and provides a framework for future TE studies within the species complex.