Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation

IF 44.7 1区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Science Pub Date : 2024-10-17 DOI:10.1126/science.adn0609

Feyza Yilmaz, Charikleia Karageorgiou, Kwondo Kim, Petar Pajic, Kendra Scheer, Human Genome Structural Variation Consortium, Christine R. Beck, Ann-Marie Torregrossa, Charles Lee, Omer Gokcumen

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Abstract

Previous studies suggested that the copy number of the human salivary amylase gene, AMY1, correlates with starch-rich diets. However, evolutionary analyses are hampered by the absence of accurate, sequence-resolved haplotype variation maps. We identified 30 structurally distinct haplotypes at nucleotide resolution among 98 present-day humans, revealing that the coding sequences of AMY1 copies are evolving under negative selection. Genomic analyses of these haplotypes in archaic hominins and ancient human genomes suggest that a common three-copy haplotype, dating as far back as 800,000 years ago, has seeded rapidly evolving rearrangements through recurrent nonallelic homologous recombination. Additionally, haplotypes with more than three AMY1 copies have significantly increased in frequency among European farmers over the past 4000 years, potentially as an adaptive response to increased starch digestion.

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人类淀粉酶基因座的重建揭示了现代变异的古老重复。

以前的研究表明，人类唾液淀粉酶基因 AMY1 的拷贝数与富含淀粉的饮食有关。然而，由于缺乏准确的、序列解析的单倍型变异图，进化分析受到了阻碍。我们在 98 个现今人类中发现了 30 个结构不同、核苷酸分辨率不同的单倍型，揭示了 AMY1 基因拷贝的编码序列是在负选择下进化的。在古人类和古人类基因组中对这些单倍型进行的基因组分析表明，一种常见的三拷贝单倍型最早可追溯到 800 KYA，它通过反复发生的非等位同源重组为快速进化的重排提供了种子。此外，在过去的4000年中，欧洲农民中具有三个以上AMY1拷贝的单倍型频率显著增加，这可能是对淀粉消化增加的一种适应性反应。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Science 综合性期刊-综合性期刊

CiteScore

61.10

自引率

0.90%

发文量

审稿时长

2.1 months

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