真核生物起源研究进展

doi:10.16288/j.yczz.20-107

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Hereditas(Beijing) ›› 2020, Vol. 42 ›› Issue (10): 929-948.doi: 10.16288/j.yczz.20-107

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Progress in elucidating the origin of eukaryotes

Zhiwei Gao¹(), Long Wang²()

^1. Kuang Yaming Honors School, Nanjing University, Nanjing210023, China
^2. State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China

Received:2020-04-18 Revised:2020-05-06 Online:2020-10-20 Published:2020-05-25
Contact: Wang Long E-mail:171240503@smail.nju.edu.cn;wanglong@nju.edu.cn
Supported by:
Supported by the National Natural Science Foundation of China No(31970236)

Abstract

Abstract:

Knowledge of the origin of eukaryotes is key to broadening our understanding of the eukaryotic genome and the relationship among internal structures within a eukaryotic cell. Since the discovery of archaea in 1977 and the proposal of three-domain tree of life by the American microbiologist Carl Woese, the intimate relationship in evolution between eukaryotes and archaea has been demonstrated by considerable experiments and analyses. From the beginning of the 21st century, with the development of phylogenetic methods and the discovery of new archaeal phyla more related to eukaryotes, increasing evidence has shown that Eukarya and Archaea should be merged into one domain, leading to a two-domain tree of life. Nowadays, the Asgard superphylum discovered via metagenomic analysis is regarded as the closest prokaryotes to eukaryotes. Nevertheless, several key questions are still under debate, such as what the ancestors of the eukaryotes were and when mitochondria emerged. Here, we review the current research progress regarding the changes of the tree of life and the detailed eukaryotic evolutionary mechanism. We show that the recent findings have greatly improved our knowledge on the origin of eukaryotes, which will pave the way for future studies.

Key words: eukaryogenesis, tree of life, archaea, three domains, two domains, endosymbiosis, mitochondria, Asgard superphylum

Zhiwei Gao, Long Wang. Progress in elucidating the origin of eukaryotes[J]. Hereditas(Beijing), 2020, 42(10): 929-948.

Figures/Tables 9

Fig. 1

Fig. 2

Table 1

Comparison among results from seven publications elucidating the relationship between eukaryotes and archaea in tree of life, published from 2003 to 2009"

文献	三域中使用的标记数目	取样种类(数目)	氨基酸位置数	方法	结果	优势	缺陷
Harris等^[33]	50	细菌(25); 泉古菌门(1); 广古菌门(7); 真核生物(3)	与所分析基因相关	单基因分析; 最大似然法; 最大简约法; 距离法	3D	选取数据范围从此前的SSU rRNA扩展到其他基因	当时的基因数据有限,单基因分析可靠性不强
Ciccarelli 等^[34]	31	细菌(150); 泉古菌门(4); 广古菌门(14); 真核生物(23)	8090	分散基因串联	3D	取样物种广泛, 增加了客观的 HGT过滤方法	先在域内对齐序列,跨域整合时可能将非同源基因对齐
Yutin等^[35]	136	与所用基因相关	与所分析基因相关	单基因分析; 最大似然法	3D	数据集丰富,分析的基因数目多	单个基因提供的系统发育信号弱
Rivera和Lake^[36]	Archaeoglobus fulgidus全基因组	细菌(2); 泉古菌门(1); 广古菌门(2); 真核生物(2)	不适用	基因组条件重建	2D; 真核生物与泉古菌门为姐妹群	使用全基因组分析	取样物种少,受HGT和基因丢失影响大
Pisani等^[37]	未提供数据	细菌(97); 泉古菌门(4); 广古菌门(17); 真核生物(17)	与所分析基因相关	超树法 (Supertree)	2D; 真核生物与广古菌门为姐妹群	综合众多数据集信息,在单基因树基础上建立二级树	过滤步骤后剩余的有效数据少,且拥有单基因分析的局限性
Cox等^[38]	45	细菌(10); 泉古菌门(3); 广古菌门(11); 真核生物(16)	5521	分散基因串联; 贝叶斯方法; 最大似然法; 最大简约法	2D; 真核生物与泉古菌门为姐妹群	除简单模型外使用了更多更复杂的模型,首例使用新模型证明了2D系统结果	复杂模型的参数估计的精确性难以保证
Foster等^[39]	41	细菌(8); 泉古菌门(8); 奇古菌门(2); 广古菌门(6); 真核生物(11)	5222	分散基因串联; 贝叶斯方法; 最大似然法; 最大简约法	2D; 真核生物是一个由泉古菌门和奇古菌门构成的群的姐妹群	同上,作者相同,选取的数据更多,使用了新发现的古细菌门类数据	复杂模型的参数估计的精确性难以保证

Table 1

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Fig. 5

Fig. 6

Fig. 7

Fig. 8

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