遗传 ›› 2021, Vol. 43 ›› Issue (11): 1023-1037.doi: 10.16288/j.yczz.21-214

• 综述 • 上一篇    下一篇

泛基因组:高质量参考基因组的新标准

边培培(), 张禹, 姜雨()   

  1. 西北农林科技大学动物科技学院,杨凌 712100
  • 收稿日期:2021-08-26 修回日期:2021-10-28 出版日期:2021-11-20 发布日期:2021-10-28
  • 通讯作者: 姜雨 E-mail:bppisc@163.com;yu.jiang@nwafu.edu.cn
  • 作者简介:边培培,在读博士研究生,专业方向:动物遗传。E-mail: bppisc@163.com
  • 基金资助:
    国家自然科学基金项目资助编号(31822052)

Pan-genome: setting a new standard for high-quality reference genomes

Bian Peipei(), Zhang Yu, Jiang Yu()   

  1. College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
  • Received:2021-08-26 Revised:2021-10-28 Online:2021-11-20 Published:2021-10-28
  • Contact: Jiang Yu E-mail:bppisc@163.com;yu.jiang@nwafu.edu.cn
  • Supported by:
    Supported by the National Natural Science Foundation of China No(31822052)

摘要:

随着三代测序组装的高质量参考基因组的陆续发布,以及大规模重测序和群体遗传学分析的广泛进行,研究人员发现来自单一个体的参考基因组远不能涵盖整个物种的所有遗传序列,大量缺失序列导致群体遗传变异图谱不完整,而构建来自多个个体的泛基因组能很好地解决这一缺陷,其研究内容包括负责基本生物学功能及该物种主要表型特征的核心基因组以及与物种的遗传多样性和个体独特性相关的可变基因组。根据核心和可变基因组所占比例的不同,泛基因组存在开放型和闭合型两种类型。本文主要综述了细菌、真菌和动植物的泛基因组学研究进展,讨论了其在各生物类群中的特征,其中哺乳动物泛基因组是相对闭合的,而目前已知的微生物、被子植物和部分低等动物的泛基因组倾向于开放,通过泛基因组的构建可以完善现有参考基因组并获取整个物种的完整变异信息,将有助于深入研究遗传多样性和表型变异产生的分子机制。

关键词: 泛基因组, 存在/缺失变异, 核心基因组, 可变基因组

Abstract:

With the release of high-quality reference genomes assembled by long reads from the third-generation sequencing technology, as well as extensive re-sequencing and population genetic analysis, researchers found that a single reference genome does not represent the diversity within a species. The missing sequences on the reference genome result in an incomplete population genetic polymorphism map. The emergence of pan-genome can well repair the deficiency of single reference genome, which include core genome (responsible for basic biological functions and the main phenotypic characteristics within a species) and the variable genome (related to the genetic diversity or biological characteristics). According to the core and variable genome proportion, the types of pan-genomes can be either open or closed. Here, we review the current exploring of pan-genome for a range of species, to discuss the characteristics of pan-genome in various biological groups. The pan-genome of mammals are more likely closed, while the pan-genomes of microbes, angiosperms, and some invertebrates are likely non-closed. It is possible to complete the reference genome and obtain complete variation information through the pan-genomic study, which will contribute to the study of molecular mechanism for genetic diversity and phenotypic evolution.

Key words: pan-genome, presence and absence variations, core genome, variable genome