Identification and evolution of the silkworm helitrons and their contribution to transcripts

In this study, we developed a structure-based approach to identify Helitrons in four lepidopterans and systematically analysed Helitrons in the silkworm genome. We found that the content of Helitrons varied greatly among genomes. The silkworm genome harboured 67,555 Helitron-related sequences that could be classified into 21 families and accounted for ≈ 4.23% of the genome. Thirteen of the families were new. Three families were putatively autonomous and included the replication initiator motif and helicase domain. The silkworm Helitrons were widely and randomly distributed in the genome. Most Helitron families radiated within the past 2 million years and experienced a single burst of expansion. These Helitron families captured 3724 gene fragments and contributed to at least 1.4% of the silkworm full-length cDNAs, suggesting important roles of Helitrons in the evolution of the silkworm genes. In addition, we found that some new Helitrons were generated by combinations of other Helitrons. Overall, the results presented in this study provided insights into the generation and evolution of Helitron transposons and their contribution to transcripts.