Abstract
BACKGROUND: LTR-retrotransposons are widely distributed among the eukaryote tree of life and have extensive impacts on genome evolution. Among the three canonical superfamilies, the Copia superfamily demonstrates the lowest abundances and repartitions among metazoans. To better understand their dynamics, we have conducted the first large-scale study of LTR-retrotransposon diversity in metazoans and we report on the diversity and distribution of the Copia elements. RESULTS: We have identified over than 2,300 Copia elements from 263 metazoan genomes. The sequences were annotated at the clade level based on the classification of their RT/RNaseH domain. Our results confirmed that Copia are scarce in metazoans. However, we observed a great variation in Copia abundance between taxa. Surprisingly, some genomes, had a record number of copies, especially in Squamata. In contrast, terrestrial Deuterostomia display a clear loss of Copia diversity leading to their disappearance in some taxa. Additionally, we identified 18 new clades, tripling the number of previously defined clades. By studying more than 50 widespread taxa, we believe that most metazoan Copia clades have now been identified. The most striking result is that environment appears to be related to Copia distribution. We defined two sets of clades characterizing marine or terrestrial taxa. This two-sided pattern could be partially explained by horizontal transfers within both environments. CONCLUSIONS: This research enhances our understanding of transposable element evolution and emphasizes the influence of sharing the same ecological contexts on genomic diversity, and highlights the importance of annotating them at the clade level to characterize their evolutionary dynamics.