Ancient segmentally duplicated LCORL retrocopies in equids

LINE-1 is an active transposable element encoding proteins capable of inserting host gene retrocopies, resulting in retro-copy number variants (retroCNVs) between individuals. Here, we performed retroCNV discovery using 86 equids and identified 437 retrocopy insertions. Only 5 retroCNVs were shared between horses and other equids, indicating that the majority of retroCNVs inserted after the species diverged. A large number (17-35 copies) of segmentally duplicated Ligand Dependent Nuclear Receptor Corepressor Like (LCORL) retrocopies were present in all equids but absent from other extant perissodactyls. The majority of LCORL transcripts in horses and donkeys originate from the retrocopies. The initial LCORL retrotransposition occurred 18 million years ago (17-19 95% CI), which is coincident with the increase in body size, reduction in digit number, and changes in dentition that characterized equid evolution. Evolutionary conservation of the LCORL retrocopy segmental amplification in the Equidae family, high expression levels and the ancient timeline for LCORL retrotransposition support a functional role for this structural variant.

Automated summary

LINE-1 is an active transposable element that inserts host gene retrocopies, resulting in retrocopy number variants (retroCNVs). We discovered 437 retrocopy insertions in 86 equids, with only 5 retroCNVs shared between horses and other equids. A large number of segmentally duplicated LCORL retrocopies were found in all equids but absent in other perissodactyls, and the majority of LCORL transcripts in horses and donkeys originated from these retrocopies. The initial LCORL retrotransposition occurred 18 million years ago, coinciding with equid evolution characterized by body size increase, digit number reduction, and dentition changes. Evolutionary conservation, high expression levels, and ancient timeline support a functional role for the LCORL retrocopy.