Comparison of three annotation methods for characterizing transposable elements in the Spodoptera frugiperda genome.
[Objectives] To find the best method to annotate and characterize Transposable elements (TEs), an important component of insect genomes that vary widely in content, families and transposition activity, among insect taxa, in the Spodoptera frugiperda genome. [Methods] Three annotation methods were used to identify S. frugiperda TEs; Repbase- and ArTEdb- based, homologous prediction and RepeatModeler based de novo annotation. [Results] The ArTEdb and de novo methods predicted TE percentages of 21.48% and 27.26%, respectively. LINEs were the most dominant TEs, both in terms of copy number and density. TEs divergence rates peaked at around 10%, indicating that the majority of TEs have appeared in the S. frugiperda genome recently. TEs with divergence rates <10% were mainly LINEs and DNA transposons. In addition, several superfamilies were abundant in S. frugiperda that are rare or lacking in other Lepidopteran species. Of the three annotation methods, Repbase had the lowest sensitivity and identified the least number of TEs. ArTEdb identified abundant TEs, and had good sensitivity to DNA elements but failed to further classify TEs into superfamilies. The de novo method not only identified the most TEs but also successfully classified these into different superfamilies. It also identified new superfamilies currently not included in the Lepidopteran repbase database. [Conclusion] We successfully characterized TE content and composition in S. frugiperda and found that the de novo method was superior to the Repbase and ArTEdb methods in terms of both identifying and categorizing TEs. These findings improve our understanding of the TEs of S. frugiperda and should benefit further studies on the functional significance of TEs and their contribution to genomic diversity.