Discovery of a novel retrotransposon family in the Callithrix jacchus genome. M. K. Konkel1, B. Ullmer2, J. A. Walker1, R. Hubley3, E. L. Arceneaux1, S. Sanampudi1, C. C. Fontenot1, A. F. A. Smit3, M. A. Batzer1, The Common Marmoset Genome Sequencing and Analysis Consortium 1) Department of Biological Sciences, Louisiana State University, Baton Rouge, LA; 2) School of Electrical Engineering and Computer Science, Center for Computation and Technology (CCT), Louisiana State University, Baton Rouge, LA; 3) Computational Biology, Institute for Systems Biology, Seattle, WA.
The genome of the common marmoset (Callithrix jacchus) represents the first sequenced and analyzed New World monkey (NWM, platyrrhine) genome. C. jacchus is also a common animal model for studying human disease, including neuroscience and infectious diseases. In its draft genome assembly [calJac3.2], we identified a novel mobile element, dubbed Platy-1. Based on our comparative analyses, we determined that Platy-1 elements are unique to NWMs. A full-length Platy-1 element is just over 100 bp in length and does not appear to contain coding sequence. Platy-1 elements exhibit facets such as termination in an Adenosine tail of varying length, target site duplications, and an endonuclease cleavage site characteristic of non-LTR retrotransposons. The combination of these features strongly suggests that Platy-1 elements are inserted in the genome by the enzymatic machinery of L1 through a mechanism called target-primed reverse transcription. Based on our whole genome analysis, we determine that the C. jacchus draft assembly contains more than 2000 Platy-1 elements. Our Platy-1 subfamily reconstruction revealed the presence of older subfamilies that most likely were active early in NWM evolution and have ceased activity, as well as subfamilies of more recent origin. Further supported by our phylogenetic analyses, we conclude that the founder Platy-1 element arose prior to the radiation of NWMs. We determine that Platy-1 has propagated throughout the evolution of NWMs in the lineage leading to C. jacchus. Furthermore, the identification of Platy-1 elements identical to their respective consensus sequence and polymorphic within common marmoset populations indicates ongoing retrotransposition activity until at least very recently. While the overall repeat content of the common marmoset genome is comparable to other primate genomes, the finding of a novel retrotransposon family specific to NWMs illustrates that each primate lineage evolves uniquely. Furthermore, a better understanding of the composition of the C. jacchus genome will support advances in biomedical science.
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