Abstract
BackgroundWe recently discovered two composite long terminal repeat (LTR)-retrotransposon-like elements which we named DA (~300 kb) and Xiao (~30 kb), meaning big and small in Chinese respectively. Xiao and DA (three types of DA identified) were found to have been derived from several donor sites and have spread to 30 loci in the human genome, totaling to 5 Mb. Our bioinformatics analyses with the released human, chimp, rhesus macaque, orangutan, and marmoset genomic sequences indicate that DA and Xiao emerged ~25 million years (Myr) ago.ResultsTo better understand the evolution of these two complex elements, we investigated various internal junctions of DA and Xiao as well as orthologous genomic sites of the 30 DA/Xiao loci in non-human primates including great apes, lesser apes, Old World monkeys, New World monkeys, and a prosimian. We found that Xiao and type I DA first emerged in the genome between 25 and 18 Myr ago, whereas type II and Type III DAs emerged between 14 and 7 Myr ago. Xiao and DA were most active in great apes, with their amplification peaking during 25-14 and 14-7 Myr ago, respectively. Neither DA nor Xiao seem to have been active in the human and chimp genomes during last 6 Myr.ConclusionThe study has led to a more accurate age determination of the DA and Xiao elements than our previous bioinformatics analyses, and indicates that the amplification activity of the elements coincided with that of group I HERV-Es during evolution. It has also illustrated an evolutionary path with stepwise structural changes for the elements during past 25 Myr, and in doing so has shed more light on these two intriguing and complex elements that have reshaped our genome.
Highlights
We recently discovered two composite long terminal repeat (LTR)retrotransposon-like elements which we named DA (~300 kb) and Xiao (~30 kb), meaning big and small in Chinese respectively
Type II and type III DAs could be amplified only with the human, chimp, bonobo and gorilla genomic DNA but not with that of other primates. These results indicate that Xiao and type I DA first emerged in the genome between 18 and 25 million years (Myr) ago, whereas type II and type III DAs emerged between 7 and 14 Myr ago
The results indicate that the Xiao amplification peak was between 25 and 14 Myr ago, whereas the DA amplification peak was between 14 and 7 Myr ago (Fig. 4)
Summary
We recently discovered two composite long terminal repeat (LTR)retrotransposon-like elements which we named DA (~300 kb) and Xiao (~30 kb), meaning big and small in Chinese respectively. Simple DNA transposons such as insertion sequences (IS) encode a transposase and have an inverted repeat of usually 9–41 bp at each end [1,2]. DNA transposons found in bacteria such as Tn10, Tn5, and Tn9 contain a middle region (often encoding a drug resistance gene) flanked by two IS elements. Owing to these flanking IS elements, the middle region of a composite DNA transposon becomes mobile as well. While composite DNA transposons such as those in the Tn family have been known for quite some time, a composite retrotransposon with a similar architecture has yet to be discovered
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
