title: 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.
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA;
authors.forename: Miriam K
authors.initials: MK
authors.lastname: Konkel
authors.affiliation: School of Electrical Engineering and Computer Science, Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, USA;
authors.forename: Brygg
authors.initials: B
authors.lastname: Ullmer
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA;
authors.forename: Erika L
authors.initials: EL
authors.lastname: Arceneaux
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA;
authors.forename: Sreeja
authors.initials: S
authors.lastname: Sanampudi
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA;
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Brantley
authors.affiliation: Institute for Systems Biology, Seattle, Washington 98109-5263, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Hubley
authors.affiliation: Institute for Systems Biology, Seattle, Washington 98109-5263, USA.
authors.forename: Arian F A
authors.initials: AF
authors.lastname: Smit
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA;
authors.forename: Mark A
authors.initials: MA
authors.lastname: Batzer
mesh_terms: D020087:Alu Elements; D000818:Animals; D002144:Callithrix / Q000235:genetics*; D019143:Evolution, Molecular; D010802:Phylogeny; D018626:Retroelements
chemical_list: D018626:Retroelements