不同食性雁形目鸟类线粒体基因组的适应性进化分析

doi:10.19586/j.2095-2341.2023.0054

生物技术进展 ›› 2023, Vol. 13 ›› Issue (5): 748-754.DOI: 10.19586/j.2095-2341.2023.0054

不同食性雁形目鸟类线粒体基因组的适应性进化分析

张卫平¹^,²(), 邱冰滢¹^,², 张东升¹^,²()

^1.上海海洋大学水产与生命学院，水产科学国家级实验教学示范中心，上海 201306
^2.上海海洋大学水产与生命学院，环境DNA技术与水生态健康评估工程中心，上海 201306

收稿日期:2023-04-17 接受日期:2023-05-17 出版日期:2023-09-25 发布日期:2023-10-10
通讯作者: 张东升
作者简介:张卫平 E-mail: 1211587144@qq.com；
基金资助:
国家重点研发计划项目(2022YFC2601301)

Adaptive Evolution Analysis of Mitochondrial Genomes in Anseriform Birds with Various Feeding Habits

Weiping ZHANG¹^,²(), Bingying QIU¹^,², Dongsheng ZHANG¹^,²()

^1.National Demonstration Center for Experimental Fisheries Science Education，College of Fisheries and Life Science，Shanghai Ocean University，Shanghai 201306，China
^2.Environmental DNA Technology and Water Ecological Health Assessment Engineering Center，College of Fisheries and Life Science，Shanghai Ocean University，Shanghai 201306，China

Received:2023-04-17 Accepted:2023-05-17 Online:2023-09-25 Published:2023-10-10
Contact: Dongsheng ZHANG

摘要/Abstract

摘要：

以往的研究表明，动物的食性与能量代谢及生存适应密切相关。能量代谢主要发生在线粒体中，线粒体编码的13个蛋白质亚基是氧化磷酸化复合体的重要组成部分。雁形目鸟类的食性主要包括肉食性、杂食性和植食性3种类型。为了分析食性对鸟类基因组进化的影响，研究选取了20种雁形目鸟类，并根据食性分成3组，下载其线粒体基因组，通过适应性进化分析、放松性选择分析、多态性氨基酸位点检测以及3D结构预测分析，研究这3组鸟类的线粒体蛋白编码基因在进化上的表现。结果发现，食肉组鸟类线粒体基因组的进化速率高于食草组和杂食组鸟类，并且只有食肉组鸟类线粒体蛋白编码基因受到了放松性的选择压力作用。此外，多态性氨基酸位点检测表明，食肉组线粒体基因组编码的蛋白质中，多态性位点和有害位点数量远高于食草组和杂食组。而杂食组鸟类线粒体蛋白编码基因进化速率较低，大部分基因受到强化性选择作用，蛋白质序列中的多态性位点也较少。研究结果表明，不同食性的雁形目鸟类，其线粒体基因组编码的蛋白质受到了不同的选择压力，这为食性差异影响鸟类线粒体基因组适应性进化提供了分子依据。

关键词: 雁形目, 食性, 线粒体, 适应性进化

Abstract:

Previous studies showed that， animals' feeding habits are related to their energy metabolism and adaptation. Energy metabolism takes place in mitochondria， and 13 subunits of the oxidative phosphorylation complexes were encoded by mitochondrial genome. According to feeding habits， birds of Anteriformes could be divided into three groups， including carnivorous， herbivorous and omnivorous. To study the evolutionary effects of feeding habit on mitogenomes， we selected 20 anteriformes species and divided them into three groups. We downloaded their mitogenomes， and did adaptive analysis， relax analysis， polymorphism analysis and 3D structure prediction. Our results showed that， the carnivorous group had higher evolutionary rates than the other two groups， and only the carnivorous group had multiple genes under relaxed selection. Meanwhile， the carnivorous group had more polymorphism sites and deterious sites among their proteins sequences than the other two groups. The genes from the omnivorous group showed decreased evolutionary rates， and most of the genes were under intensification selection， furthermore， less polymorphic sites were detected in this group. The results indicated that the proteins encoded by mitochondrial genomes of anteriformes birds with different feeding habits are subject to different selective pressures. This study provides a molecular basis for the influence of dietary differences on the adaptive evolution of avian mitochondrial genomes.

Key words: anteriformes, diets, mitochondria, adaptive evolution

中图分类号:

Q951

张卫平, 邱冰滢, 张东升. 不同食性雁形目鸟类线粒体基因组的适应性进化分析[J]. 生物技术进展, 2023, 13(5): 748-754.

Weiping ZHANG, Bingying QIU, Dongsheng ZHANG. Adaptive Evolution Analysis of Mitochondrial Genomes in Anseriform Birds with Various Feeding Habits[J]. Current Biotechnology, 2023, 13(5): 748-754.

图/表 5

图1 基于拼接序列构建的雁形目鸟类系统发育树

Fig. 1 Phylogenetic tree based on the spliced data of Anseriformes birds

表1 结果中有显著放松性选择或显著强化性选择的基因

Table 1 The significant results of the relaxation and intensification

选择类型	测试支	基因	P值	K值
放松性选择	食肉组	COX2	0.027	0.74
		COX3	0.001	0.05
		CYTB	0.027	0.79
		ND1	0.004	0.80
		ND3	0.045	0.62
		ND4	0.001	0.64
	食草组	ND2	0	0
	食草组	ND6	0.002	0.07
强化性选择	食草组	ATP6	0	6.54
		COX2	0.012	14.13
		COX3	0	5.70
		ND3	0.042	22.02
	杂食组	COX1	0.017	24.93
		COX2	0.002	2.23
		CYTB	0.006	41.17
		ND2	0.034	4.06
		ND3	0.028	44.75

图2 食肉组、食草组、杂食组的dN、dS和ω比较注：dN—非同义替换率；dS—同义替换率；ω—进化速率。**表示两组数据间差异显著(P<0.01)

Fig. 2 Comparisons of dN, dS and ω values among the groups of carnivore birds, herbivorous birds and omnivorous birds

图3 食肉组、食草组、杂食组的氨基酸多态性和有害性的频率A：拼接序列（spliced data）的氨基酸多态性和有害性位点频率； B：13个蛋白质序列的多态性位点频率；C：13个蛋白质序列的有害性位点频率。

Fig. 3 Proportion of amino acid polymorphism sites and amino acid harmful sites in carnivore, herbivorous and omnivorous birds

图4 食肉组、食草组、杂食组中ND2的3D结构预测和氨基酸多态性、有害性位点的比例A：三组食性鸟类中ND2的3D结构；B：三组食性鸟类ND2的氨基酸多态性位点频率；C：三组食性鸟类ND2的有害性位点比例。

Fig. 4 3D structure prediction and proportion of polymorphism sites and harmful sites of ND2 in carnivore, herbivorous and omnivorous birds

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不同食性雁形目鸟类线粒体基因组的适应性进化分析

Adaptive Evolution Analysis of Mitochondrial Genomes in Anseriform Birds with Various Feeding Habits

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