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A comprehensive analysis of chimpanzee (Pan Troglodytes)-specific AluYb8 element

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.

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Acknowledgments

This research was supported by Basic Science Research Capacity Enhancement Project through Korea Basic Science Institute (National research Facilities and Equipment Center) grant funded by the Ministry of Education (Grant No. 2019R1A6C1010033). The present research was supported by the research fund of Dankook university in 2019 for the University Innovation Support Program. This work was supported by the Korea Foundation for the Advancement of Science &Creativity (KOFAC), and funded by the Korean Government (MOE) in 2019. The authors would like to thank Cherljoon Lee, Yujun Park, Yunseok Oh, Hyunjune Park, and Seungwon Yang (Dankook University) for their assistance with the initial data collection and analysis.

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Correspondence to Kyudong Han.

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The authors declare that there is no conflict of interest regarding the publication of this paper.

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Experiments with the chimpanzee and gorilla were carried out in accordance with the guidelines and regulations approved by the Animal Experimentation Committees of Kyoto University.

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13258_2020_989_MOESM1_ESM.pptx

Supplementary Figure 1. Diagnostic nucleotide position of 11 AluYb8 elements and 29 AluYb-like elements. Blue and Yellow boxes indicate diagnostic mutation position of AluYb8 elements and 7-bp duplication regions, respectively

13258_2020_989_MOESM2_ESM.pptx

Supplementary Figure 2. Sequence alignment of CS8 in human, chimpanzee, and gorilla. Black upper case letters indicate shared flanking unique sequences. The red and blue characters indicate chimpanzee-specific AluYb8 sequences and deleted counterpart sequences in the human and gorilla, respectively

Supplementary Table 1. Summary of 40 chimpanzee AluYb8 elements

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Kim, S., Kim, D.H., Imai, H. et al. A comprehensive analysis of chimpanzee (Pan Troglodytes)-specific AluYb8 element. Genes Genom 42, 1207–1213 (2020). https://doi.org/10.1007/s13258-020-00989-7

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Keywords

  • Alu elements
  • AluYb8
  • Chimpanzee-specific
  • Retrotransposons