Discovery of a new repeat family in the Callithrix jacchus genome

Abstract

We identified a novel repeat family, termed Platy-1, in the Callithrix jacchus (common marmoset) genome that arose around the time of the divergence of platyrrhines and catarrhines and established itself as a repeat family in New World monkeys (NWMs). A full-length Platy-1 element is ∼100 bp in length, making it the shortest known short interspersed element (SINE) in primates, and harbors features characteristic of non-LTR retrotransposons. We identified 2268 full-length Platy-1 elements across 62 subfamilies in the common marmoset genome. Our subfamily reconstruction and phylogenetic analyses support Platy-1 propagation throughout the evolution of NWMs in the lineage leading to C. jacchus. Platy-1 appears to have reached its amplification peak in the common ancestor of current day marmosets and has since moderately declined. However, identification of more than 200 Platy-1 elements identical to their respective consensus sequence, and the presence of polymorphic elements within common marmoset populations, suggests ongoing retrotransposition activity. Platy-1, a SINE, appears to have originated from an Alu element, and hence is likely derived from 7SL RNA. Our analyses illustrate the birth of a new repeat family and its propagation dynamics in the lineage leading to the common marmoset over the last 40 million years.

Amplification Dynamics of Platy-1 Retrotransposons in the Cebidae Platyrrhine Lineage

“…1). These genomes were analyzed for Platy-1 elements using RepeatMasker (RepeatMasker-Open-4.0) utilizing a custom library of the 62 Platy-1 subfamilies previously defined (Konkel et al. 2016) and all current Alu subfamily consensus sequences obtained from RepBase (Jurka et al.…”

“…2005). Full-length Platy-1 elements were defined as possessing a start position no less than 4 bp and an end position not shorter than two nucleotides prior to the A-tail within the consensus sequence (Konkel et al. 2016).…”

“…Recently, a new retrotransposable element was discovered in the common marmoset genome and subsequently found to be specific to the Platyrrhini parvorder. Deemed, “Platy-1,” these ∼100 bp elements have the hallmarks of movement via TPRT (Konkel et al. 2016).…”

“…2016). In addition, these elements share some structure and sequence similarity with Alu elements, a primate-specific SINE, suggesting that Platy-1 likely originated from an Alu element and is 7SL RNA derived (Konkel et al. 2016).…”

“…The purpose of this study was to characterize the Platy-1 elements found in the current genome assemblies of other Platyrrhine primates in order to determine the quantity of Platy-1 elements as well as the amplification dynamics in comparison to the common marmoset genome (Konkel et al. 2016).…”