Contrasting Rates of LINE-1 Amplification among New World Primates of the Atelidae Family

Abstract

LINE-1 (L1) retrotransposons constitute the dominant category of transposons in mammalian genomes. L1 elements are active in the vast majority of mammals, and only a few cases of L1 extinction have been documented. The only possible case of extinction in primates was suggested for South American spider monkeys. However, these previous studies were based on a single species. We revisited this question with a larger phylogenetic sample, covering all 4 genera of Atelidae and 3 species of spider monkeys. We used an enrichment method to clone recently inserted L1 elements and performed an evolutionary analysis of the sequences. We were able to identify young L1 elements in all taxa, suggesting that L1 is probably still active in all Atelidae examined. However, we also detected considerable variations in the proportion of recent elements indicating that the rate of L1 amplification varies among Atelidae by a 3-fold factor. The extent of L1 amplification in Atelidae remains overall lower than in other New World monkeys. Multiple factors can affect the amplification of L1, such as the demography of the host and the control of transposition. These factors are discussed in the context of host life history.

Centromeric enrichment of LINE-1 retrotransposon in two species of South American monkeys Alouatta belzebul and Ateles nancymaae (Platyrrhini, Primates)

“…This result is in agreement with sequence data analysis that showed active LINE on Cebidae species (Boissinot et al 2004) and, more recently, also in Atelidae (Sookdeo et al 2018). At the beginning, from an analysis of just Ateles paniscus (Boissinot et al 2004), the extinction of LINE 1 in Atelidae was proposed, but a larger phylogenetic sampling permitted researchers to show their presence (Sookdeo et al 2018).…”

“…In mammals and primates, LINE-1 were studied through different approaches including the use of restriction enzymes (Seuanez et al, 1989) or whole genome screening in simians (Ohshima et al 2003). In humans and anthropoids, LINE-1 sequence comparisons have been made (Ovchinnikov et al 2001, Mathews et al 2003 showing that LINE-1 amplification may change rapidly during primate evolution giving different families with variable forms Among New World monkeys, high LINE activity has also been shown in the Saimiri and Saguinus lineages (Callitrichini), and reduced activity has been found in the Ateles lineage (Boissinot et al 2004, Sookdeo et al 2018. So far, however, the distribution of these repetitive sequences through FISH with LINE-1 probes has been studied in few platyrrhine species, belonging to the Callithricini subfamily of the Cebidae family (Serfaty et al 2017, Ceraulo et al 2021b.…”

Factors Regulating the Activity of LINE1 Retrotransposons

“…In most species of New and Old World primates, the L1 remains active. Only in New World South American spider monkeys the absence of L1 activity was found [87,88]. The evolutionary history of the Old World primates began approximately 21-25 myrs and is associated with the distribution of L1PA6-L1PA5 elements [83,[89][90][91].…”

Massive LINE‐1 retrotransposon enrichment in tamarins of the Cebidae family (Platyrrhini, Primates) and its significance for genome evolution

“…Other studies suggest that rates of LINE-1 amplification differ substantially between the Homo and Pan lineages, indicating that LINE-1 amplification may have changed rapidly during primate evolution (Mathews et al, 2003). LINE activity has also been shown in Saimiri, Saguinus (Callitrichinae, Platyrrhini), and Ateles lineages (Boissinot et al, 2004;Sookdeo et al, 2018).…”