Discovery of a new repeat family in the Callithrix jacchus genome

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 leng...

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Bibliographic Details
Published in:	Genome research Vol. 26; no. 5; pp. 649 - 659
Main Authors:	Konkel, Miriam K, Ullmer, Brygg, Arceneaux, Erika L, Sanampudi, Sreeja, Brantley, Sarah A, Hubley, Robert, Smit, Arian F A, Batzer, Mark A
Format:	Journal Article
Language:	English
Published:	United States Cold Spring Harbor Laboratory Press 01-05-2016
Subjects:	Alu Elements Animals Callithrix - genetics Callithrix jacchus Evolution, Molecular Phylogeny Retroelements
Online Access:	Get full text
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors contributed equally to this work.
ISSN:	1088-9051 1549-5469
DOI:	10.1101/gr.199075.115