The analysis of minor taxa highlights the role of the environment and phylogeny in the distribution of the LTR-retrotransposon Copia clades.

Transposable elements, such as the Copia superfamily of the LTR-retrotransposons order, are key drivers of genome evolution, yet their diversity and distribution across metazoans remain incompletely characterized. Previous genome-based analyses identified ~25 Copia clades, the distribution of which revealed a strong dichotomy between marine and terrestrial environments, but were limited by the availability of taxonomic samples. Here, we use a complementary transcriptome-based approach to investigate Copia diversity across 315 transcriptomes, supplemented by additional database searches, substantially expanding taxonomic coverage to 12 new phyla. We identified 1285 Copia elements, most of which could be assigned to known clades based on RT/RNaseH domain analyses. Our results indicate that Copia clade diversity in metazoans is likely close to exhaustive, as no new clades were detected despite broader sampling. The previously described marine-terrestrial dichotomy is strongly conserved, with clades consistently partitioned into two environmental groups. The distribution of most taxon-specific clades remains largely restricted, although their range can be refined with increased sampling. Notably, we confirm the strong specificity of the CoCol clade in Collembola and demonstrate its presence in Diplura, suggesting a shared evolutionary origin within early-diverging Hexapoda. This contrasts with the high Copia diversity observed in other terrestrial Euarthropoda, as well as in Onychophora. Overall, this study highlights the value of transcriptomic data for refining TE diversity at clade level and provides a more comprehensive view of Copia evolution across metazoans.