A comprehensive analysis of chimpanzee ( Pan Troglodytes )-specific Alu Yb8 element
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Genes & Genomics https://doi.org/10.1007/s13258-020-00989-7
RESEARCH ARTICLE
A comprehensive analysis of chimpanzee (Pan Troglodytes)‑specific AluYb8 element Songmi Kim1 · Dong Hee Kim2 · Hiroo Imai3 · Yong‑Moon Lee4 · Kyudong Han1,5 Received: 8 July 2020 / Accepted: 17 August 2020 © The Genetics Society of Korea 2020
Abstract Background Alu elements are most abundant retrotransposons with > 1.2 million copies in the primate genome. AluYb8 subfamily was diverged from AluY lineage, and has accumulated eight diagnostic mutations and 7-bp duplication during primate evolution. A total of 1851 AluYb copies are present in the human genome, and most of them are human-specific. On the other hand, only a few AluYb8 copies were identified in the chimpanzee genome by previous studies on AluYb8. The significantly different number of species-specific AluYb8 elements between human and chimpanzee might result from the incompletion of chimpanzee reference genome sequences at the time of the previous study. Objective AluYb8 elements could generate genomic structural variations in the chimpanzee genome. This study aimed to identify and characterize chimpanzee-specific AluYb elements using the most updated chimpanzee reference genome sequences (Jan. 2018, panTro6). Methods To identify chimpanzee-specific AluYb8, we carried out genomic comparison with non-chimpanzee primate genome using the UCSC table browser. In addition, chimpanzee-specific AluYb8 candidates were manually inspected and experimentally verified using PCR and Sanger sequencing. Results Among a total of 231 chimpanzee-specific AluYb8 candidates, 11 of the candidates are chimpanzee-specific AluYb8, and 29 elements are shared between the chimpanzee and non-chimpanzee primate genomes. Through the sequence analysis of AluYb8 and other Alu subfamilies, we were able to observe various diagnostic mutations and variable length duplications in 7-bp duplication region of AluYb8 element. In addition, we further validated two of the chimpanzee-specific AluYb8 elements (CS8 and CS20) that were not previously discovered by display PCR and Sanger sequencing. Interestingly, we identified a AluYb8 insertion-mediated deletion (CS8 locus) in the chimpanzee genome. Conclusion Our study found that AluYb8 elements are much more abundant in the human genome than chimpanzee genome, and that it could be due to the absence of hyperactive “master” AluYb8 elements in the chimpanzee genome. Keywords Alu elements · AluYb8 · Chimpanzee-specific · Retrotransposons
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13258-020-00989-7) contains supplementary material, which is available to authorized users. * Kyudong Han [email protected] 1
2
Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Republic of Korea Department of Anesthesiology and Pain Management, Dankook University Hospital, Cheonan 31116, Republic of Korea
3
Department of Cellul
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