Contrasted patterns of evolution of the LINE-1 retrotransposon in perissodactyls: the history of a LINE-1 extinction

Stéphane Boissinot,Akash Sookdeo,Crystal M Hepp

doi:10.1186/s13100-018-0117-4

Stéphane Boissinot, Akash Sookdeo + Show 1 more

Open Access

https://doi.org/10.1186/s13100-018-0117-4

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Abstract

BackgroundLINE-1 (L1) is the dominant autonomously replicating non-LTR retrotransposon in mammals. Although our knowledge of L1 evolution across the tree of life has considerably improved in recent years, what we know of L1 evolution in mammals is biased and comes mostly from studies in primates (mostly human) and rodents (mostly mouse). It is unclear if patterns of evolution that are shared between those two groups apply to other mammalian orders. Here we performed a detailed study on the evolution of L1 in perissodactyls by making use of the complete genome of the domestic horse and of the white rhinoceros. This mammalian order offers an excellent model to study the extinction of L1 since the rhinoceros is one of the few mammalian species to have lost active L1.ResultsWe found that multiple L1 lineages, carrying different 5’UTRs, have been simultaneously active during the evolution of perissodactyls. We also found that L1 has continuously amplified and diversified in horse. In rhinoceros, L1 was very prolific early on. Two successful families were simultaneously active until ~20my ago but became extinct suddenly at exactly the same time.ConclusionsThe general pattern of L1 evolution in perissodactyls is very similar to what was previously described in mouse and human, suggesting some commonalities in the way mammalian genomes interact with L1. We confirmed the extinction of L1 in rhinoceros and we discuss several possible mechanisms.

Highlights

Long Interspersed Nuclear Element 1 (LINE-1) (L1) is the dominant autonomously replicating non-LTR retrotransposon in mammals
We found that L1 has diversified and persisted in the horse genome but became extinct in the rhinoceros lineages, the last active L1 families in this genome did not show sign of decreased activity until their relatively sudden extinction
We found that several lineages of L1 families have evolved in horse but that these lineages coexisted only when they harbored different 5’untranslated regions (UTR), suggesting that similar mechanisms are limiting L1 diversity in perissodactyls, rodents and primates

Summary

Introduction

LINE-1 (L1) is the dominant autonomously replicating non-LTR retrotransposon in mammals. Most of what we know about L1 evolution in mammals comes from the detailed analysis of two orders, primates and rodents, both belonging to the euarchontoglires super-order [5, 7, 9, 12, 13, 19,20,21, 23, 42,43,44,45,46] In these two groups L1 generally evolves as a single lineage of family, so that only the most recently evolved family is active [4, 5, 47]. With the availability of numerous mammalian genomes, a comprehensive study of L1 evolution in other mammalian orders is warranted [2]

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