Discovery of a new repeat family in the Callithrix jacchus genome.

TitleDiscovery of a new repeat family in the Callithrix jacchus genome.
Publication TypeJournal Article
Year of Publication2016
AuthorsKonkel MK, Ullmer B, Arceneaux EL, Sanampudi S, Brantley SA, Hubley R, Smit AFA, Batzer MA
JournalGenome Res
Volume26
Issue5
Pagination649-59
Date Published2016 May
ISSN1549-5469
Abstract<p>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.</p>
DOI10.1101/gr.199075.115
Alternate JournalGenome Res.
PubMed ID26916108
PubMed Central IDPMC4864456
Grant ListR01 GM059290 / GM / NIGMS NIH HHS / United States