泛基因组：高质量参考基因组的新标准

doi:10.16288/j.yczz.21-214

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

泛基因组：高质量参考基因组的新标准

边培培(), 张禹, 姜雨()

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

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

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/Abstract

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

边培培, 张禹, 姜雨. 泛基因组：高质量参考基因组的新标准[J]. 遗传, 2021, 43(11): 1023-1037.

Peipei Bian, Yu Zhang, Yu Jiang. Pan-genome: setting a new standard for high-quality reference genomes[J]. Hereditas(Beijing), 2021, 43(11): 1023-1037.

图/表 5

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表2

泛基因组代表性研究"

年份	物种	基因组大小	个体数目	构建策略	主要新进展	参考文献
2005	无乳链球菌 (Streptococcus agalactiae)	～2 Mb	8	基于多个从头组装的基因组的比较	泛基因组概念的引入	[1]
2007	N/A	N/A	N/A	N/A	综述文章,第一次在植物中应用泛基因组这个术语	[45]
2010	人(Homo sapiens)	～3.2 Gb	3	基于多个从头组装的基因组的比较	估计一个完整的泛基因组可能包含19~ 40 Mb在当前参考基因组中不存在的新序列,鉴定了额外86个新基因	[5]
2014	大豆(Glycine soya)	～0.9 Gb	7	基于多个从头组装的基因组的比较	第一个植物泛基因组文章,测序和重新组装了野生大豆个体的基因组,将注释基因聚类到基因家族,核心基因簇的比例为49%	[46]
2014	玉米(Zea mays)	～2.4 Gb	503	基于多个从头组装的转录组的比较	获得了约8600个有代表性的在参考基因组中不存在的转录本,其中的16.4%在所有品系中表达,82.7%在部分品系中表达	[50]
2016	甘蓝(Brassica oleracea )	～650 Mb	10	reads映射到参考基因组;unmapping reads的组装;通过新组装的contigs更新旧序列来产生新的参考序列。(将从每个基因组获得的reads映射到不断增长的泛基因组)	核心基因簇比例占泛基因组总数的81%,近20%的基因受到存在/缺失变异的影响	[53]
2018	水稻(Oryza sativa)	～400 Mb	3010	对个体测序数据进行组装,通过从与参考基因组unaligned的contigs中移除冗余序列来构建具有代表性的非参考序列,结合参考基因组构建泛基因组	鉴定了超过10,000个新的全长蛋白编码基因和大量的存在-缺失变异,核心基因簇比例占泛基因组总数的54%~62%	[10]
2019	人(Homo sapiens)	～3.2Gb	910	reads映射到参考基因组,组装unmapping的reads,保留新组装的长度大于1 kb的非参考序列的contigs用于构建泛基因组	利用非洲血统的人类群体基因组构建泛基因组,获取了参考基因组中296 Mb不存在的序列	[20]
	番茄(Solanum lycopersicum)	～810Mb	725	对个体测序数据进行组装,通过从与参考基因组unaligned的contigs中移除冗余序列来构建具有代表性的非参考序列,结合参考基因组构建泛基因组	鉴定出一个约 4 kb 与风味相关的基因TomLoxC的启动子的存在缺失变异,表明泛基因组研究可以帮助物种恢复驯化或者改良过程中丢失的理想性状	[4]
	猪(Sus scrofa)	～2.7 Gb	12	基于从头组装的基因组之间的相互比较	第一个家养动物的线性泛基因组,获得了额外的72.5 Mb序列	[3]
	山羊(Capra hircus)	～2.9 Gb	10	基于从头比较来自近缘物种的基因组	第一个跨物种比对的泛基因组,从参考基因组中寻找缺失序列的有效且可靠的策略,获得了38.3 Mb 序列	[70]
2020	大豆 (Glycine soja和 Glycine max)	～1 Gb	29	基于从头组装的基因组之间的相互比较,图结构泛基因组	鉴定了大的结构变异和基因融合事件,将结构变异与基因表达和农艺性状联系起来	[30]
	牛(Bos taurus)	～2.6 Gb	300	集成了线性参考基因组坐标和预先选择的变异(<50 bp),图结构泛基因组	第一个家养动物的图结构泛基因组,在人类以外的大基因组动物上对图结构泛基因组的首个尝试	[32]
	贻贝 (Mytilus galloprovincialis)	～1.28 Gb	16	测序reads被映射到贻贝参考基因组上,收集未映射的reads从头组装。新组装的contigs被添加到参考基因组中,构建了一个贻贝泛基因组(将从每个基因组获得的reads映射到不断增长的泛基因组)。	开放型的动物泛基因组,高比例的可变基因组(45%),展示了动物泛基因组的潜能	[71]
2021	水稻(Oryza sativa和Oryza glaberrima)	～400 Mb	33	基于从头组装的基因组之间的相互比较,图结构泛基因组	共鉴定了171,072个SVs和25,549个gCNVs,可以用于全基因组关联研究	[31]
2021	牛(Bos taurus)	～2.6 Gb	6	基于从头组装的基因组之间的相互比较,图结构泛基因组	70 Mb的非参考基因组等位序列,提供了一个构建图结构泛基因组的框架,适合于多种物种	[19]

表2

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泛基因组：高质量参考基因组的新标准

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

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构建方法	基于重测序unmapping 序列的迭代组装	基于多个从头组装基因组的比较
(1)计算资源需求	低	高
(2)测序深度要求	低	高
(3)研究个体规模	大	小
(4)结构变异检测能力	低	高
(5)存在缺失变异检测能力	高	较低