Abstract
Platy-1 elements are Platyrrhine-specific, short interspersed elements originally discovered in the Callithrix jacchus (common marmoset) genome. To date, only the marmoset genome has been analyzed for Platy-1 repeat content. Here, we report full-length Platy-1 insertions in other New World monkey (NWM) genomes (Saimiri boliviensis, squirrel monkey; Cebus imitator, capuchin monkey; and Aotus nancymaae, owl monkey) and analyze the amplification dynamics of lineage-specific Platy-1 insertions. A relatively small number of full-length and lineage-specific Platy-1 elements were found in the squirrel, capuchin, and owl monkey genomes compared with the marmoset genome. In addition, only a few older Platy-1 subfamilies were recovered in this study, with no Platy-1 subfamilies younger than Platy-1-6. By contrast, 62 Platy-1 subfamilies were discovered in the marmoset genome. All of the lineage-specific insertions found in the squirrel and capuchin monkeys were fixed present. However, ∼15% of the lineage-specific Platy-1 loci in Aotus were polymorphic for insertion presence/absence. In addition, two new Platy-1 subfamilies were identified in the owl monkey genome with low nucleotide divergences compared with their respective consensus sequences, suggesting minimal ongoing retrotransposition in the Aotus genus and no current activity in the Saimiri, Cebus, and Sapajus genera. These comparative analyses highlight the finding that the high number of Platy-1 elements discovered in the marmoset genome is an exception among NWM analyzed thus far, rather than the rule. Future studies are needed to expand upon our knowledge of Platy-1 amplification in other NWM genomes.
Highlights
Transposable elements (TEs) are discrete pieces of DNA that are able to move from one genomic location to another
With 145 loci, the owl monkey genome had the largest number of lineage-specific insertions of the three New World monkey (NWM) genomes investigated
This study expanded upon the research reported by Konkel et al (2016) by recovering Platy-1 insertions unique to other NWM genomes and analyzing the amplification dynamics of these insertions
Summary
Transposable elements (TEs) are discrete pieces of DNA that are able to move from one genomic location to another These elements can be broadly categorized based on their movement mechanism, either “cut-and-paste” or “copyand-paste.”. (Hellen and Brookfield 2013) The latter category includes retrotransposable elements that move via an RNA intermediate (Batzer and Deininger 2002; Konkel et al 2010). The high copy number Alu elements are $300 base pairs (bp) long with a dimeric structure, separated by a middle A-rich region These elements are derived from the 7SL RNA, a component of the signal recognition particle (Batzer and Deininger 2002; Konkel et al 2010). These elements are mobilized via a retrotransposition mechanism called targetprimed reverse transcription (TPRT)
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