Abstract
Transposable elements (TEs) are ubiquitous in arthropods. However, analyses of large-scale and long-term coevolution between TEs and host genomes remain scarce in arthropods. Here, we choose 14 representative Arthropoda species from eight orders spanning more than 500 million years of evolution. By developing an unbiased TE annotation pipeline, we obtained 87 to 2266 TE reference sequences in a species, which is a considerable improvement compared to the reference TEs previously annotated in Repbase. We find that TE loads are diversified among species and were previously underestimated. The highly species- and time-specific expansions and contractions, and intraspecific sequence diversification are the leading driver of long terminal repeat (LTR) dynamics in Lepidoptera. Terminal inverted repeats (TIRs) proliferated substantially in five species with large genomes. A phylogenetic comparison reveals that the loads of multiple TE subfamilies are positively correlated with genome sizes. We also identified a few horizontally transferred TE candidates across nine species. In addition, we set up the Arthropod Transposable Elements database (ArTEdb) to provide TE references and annotations. Collectively, our results provide high-quality TE references and uncover that TE loads and expansion histories vary greatly among arthropods, which implies that TEs are an important driving force shaping the evolution of genomes through gain and loss.
Highlights
Transposable elements (TEs) are DNA sequences that can jump in host genomes [1]
We found that frequent gains and losses, sequence diversification, and horizontal transfer of TEs (HTTs) jointly contributed to TE load diversity in arthropods
Repbase [23] provides TE annotations for many arthropods, high-quality TE references are available for only a small subset of the 14 species investigated in this study (Table 1)
Summary
Transposable elements (TEs) are DNA sequences that can jump in host genomes [1]. TEs are widespread in eukaryotic organisms and occupy more than 45% of the human genome [2]. As TE translocation might cause genomic instabilities or waste energy of the host organisms, TEs used to be regarded as “junk DNA” [4]. The genomes of many arthropods have been sequenced in the past decades, which suggests the contents of TEs are highly variable in Arthropoda [5,6,7,8,9,10,11,12,13,14,15,16,17,18]. As the number of genes does not differ significantly between these two species [9,17], the 65-fold genome size variation might be mainly due to the rapid evolution of TEs
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