Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

Yukinori Okada, Yukihide Momozawa, Saori Sakaue, Masahiro Kanai, Kazuyoshi Ishigaki, Masato Akiyama, Toshihiro Kishikawa, Yasumichi Arai, Takashi Sasaki, Kenjiro Kosaki, Makoto Suematsu, Koichi Matsuda, Kazuhiko Yamamoto, Michiaki Kubo, Nobuyoshi Hirose, Yoichiro Kamatani

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Understanding natural selection is crucial to unveiling evolution of modern humans. Here, we report natural selection signatures in the Japanese population using 2234 high-depth whole-genome sequence (WGS) data (25.9×). Using rare singletons, we identify signals of very recent selection for the past 2000-3000 years in multiple loci (ADH cluster, MHC region, BRAP-ALDH2, SERHL2). In large-scale genome-wide association study (GWAS) dataset (n = 171,176), variants with selection signatures show enrichment in heterogeneity of derived allele frequency spectra among the geographic regions of Japan, highlighted by two major regional clusters (Hondo and Ryukyu). While the selection signatures do not show enrichment in archaic hominin-derived genome sequences, they overlap with the SNPs associated with the modern human traits. The strongest overlaps are observed for the alcohol or nutrition metabolism-related traits. Our study illustrates the value of high-depth WGS to understand evolution and their relationship with disease risk.

Original languageEnglish
Article number1631
JournalNature Communications
Volume9
Issue number1
DOIs
Publication statusPublished - 01-12-2018

Fingerprint

sequencing
genome
Genes
Genetic Selection
signatures
Genome
Genome-Wide Association Study
Hominidae
Gene Frequency
Single Nucleotide Polymorphism
Japan
nutrition
Nutrition
Alcohols
Metabolism
metabolism
loci
alcohols
Population

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Okada, Y., Momozawa, Y., Sakaue, S., Kanai, M., Ishigaki, K., Akiyama, M., ... Kamatani, Y. (2018). Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese. Nature Communications, 9(1), [1631]. https://doi.org/10.1038/s41467-018-03274-0
Okada, Yukinori ; Momozawa, Yukihide ; Sakaue, Saori ; Kanai, Masahiro ; Ishigaki, Kazuyoshi ; Akiyama, Masato ; Kishikawa, Toshihiro ; Arai, Yasumichi ; Sasaki, Takashi ; Kosaki, Kenjiro ; Suematsu, Makoto ; Matsuda, Koichi ; Yamamoto, Kazuhiko ; Kubo, Michiaki ; Hirose, Nobuyoshi ; Kamatani, Yoichiro. / Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese. In: Nature Communications. 2018 ; Vol. 9, No. 1.
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Okada, Y, Momozawa, Y, Sakaue, S, Kanai, M, Ishigaki, K, Akiyama, M, Kishikawa, T, Arai, Y, Sasaki, T, Kosaki, K, Suematsu, M, Matsuda, K, Yamamoto, K, Kubo, M, Hirose, N & Kamatani, Y 2018, 'Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese', Nature Communications, vol. 9, no. 1, 1631. https://doi.org/10.1038/s41467-018-03274-0

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese. / Okada, Yukinori; Momozawa, Yukihide; Sakaue, Saori; Kanai, Masahiro; Ishigaki, Kazuyoshi; Akiyama, Masato; Kishikawa, Toshihiro; Arai, Yasumichi; Sasaki, Takashi; Kosaki, Kenjiro; Suematsu, Makoto; Matsuda, Koichi; Yamamoto, Kazuhiko; Kubo, Michiaki; Hirose, Nobuyoshi; Kamatani, Yoichiro.

In: Nature Communications, Vol. 9, No. 1, 1631, 01.12.2018.

Research output: Contribution to journalArticle

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AU - Okada, Yukinori

AU - Momozawa, Yukihide

AU - Sakaue, Saori

AU - Kanai, Masahiro

AU - Ishigaki, Kazuyoshi

AU - Akiyama, Masato

AU - Kishikawa, Toshihiro

AU - Arai, Yasumichi

AU - Sasaki, Takashi

AU - Kosaki, Kenjiro

AU - Suematsu, Makoto

AU - Matsuda, Koichi

AU - Yamamoto, Kazuhiko

AU - Kubo, Michiaki

AU - Hirose, Nobuyoshi

AU - Kamatani, Yoichiro

PY - 2018/12/1

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N2 - Understanding natural selection is crucial to unveiling evolution of modern humans. Here, we report natural selection signatures in the Japanese population using 2234 high-depth whole-genome sequence (WGS) data (25.9×). Using rare singletons, we identify signals of very recent selection for the past 2000-3000 years in multiple loci (ADH cluster, MHC region, BRAP-ALDH2, SERHL2). In large-scale genome-wide association study (GWAS) dataset (n = 171,176), variants with selection signatures show enrichment in heterogeneity of derived allele frequency spectra among the geographic regions of Japan, highlighted by two major regional clusters (Hondo and Ryukyu). While the selection signatures do not show enrichment in archaic hominin-derived genome sequences, they overlap with the SNPs associated with the modern human traits. The strongest overlaps are observed for the alcohol or nutrition metabolism-related traits. Our study illustrates the value of high-depth WGS to understand evolution and their relationship with disease risk.

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