十字花科植物PEBP基因家族的分子进化

doi:10.17520/biods.2021545

生物多样性 ›› 2022, Vol. 30 ›› Issue (6): 21545. DOI: 10.17520/biods.2021545

• 研究报告: 遗传多样性 • 上一篇下一篇

十字花科植物PEBP基因家族的分子进化

李永光¹^,², 任辉¹, 张英杰¹, 李瑞宁², 艾昊², 黄先忠²^,³^,^*()

1.石河子大学生命科学学院, 新疆石河子 832003
2.安徽科技学院农学院, 安徽凤阳 233100
3.石河子大学生命科学学院植物基因组学实验室, 新疆石河子 832003

收稿日期:2021-12-30 接受日期:2022-03-10 出版日期:2022-06-20 发布日期:2022-03-11
通讯作者: 黄先忠
作者简介:* E-mail: huangxz@ahstu.edu.cn
基金资助:
国家自然科学基金(U1303302);安徽科技学院学科带头人引进人才启动经费(NXYJ202001);安徽省2021年高校拔尖人才项目

Analysis of the molecular evolution of the PEBP gene family in cruciferous plants

Yongguang Li¹^,², Hui Ren¹, Yingjie Zhang¹, Ruining Li², Hao Ai², Xianzhong Huang²^,³^,^*()

1. College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003
2. College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui 233100
3. Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003

Received:2021-12-30 Accepted:2022-03-10 Online:2022-06-20 Published:2022-03-11
Contact: Xianzhong Huang

摘要/Abstract

摘要：

近年来植物基因组测序物种数量的指数增长, 为我们对植物环境适应性状的遗传和变异的全面理解提供了保障。磷脂酰乙醇胺结合蛋白(phosphatidylethanolamine-binding protein, PEBP)在植物的开花转变和株型建立中起着重要作用, 一直是植物生物学研究关注的热点领域之一。然而对该家族并没有利用新近测序的基因组数据进行比较基因组分析, 制约了对其在分子水平上的进化研究。为了确定PEBP基因家族的分子进化机制, 本研究利用生物信息学方法开展了7种十字花科植物拟南芥(Arabidopsis thaliana)、琴叶拟南芥(A. lyrata)、小鼠耳芥(A. pumila)、亚麻荠(Camelina sativa)、甘蓝(Brassica oleracea)、白菜(B. rapa)和油菜(B. napus)的PEBP基因家族成员的全基因组鉴定、结构特征和比较进化分析。从7个物种中共鉴定出91个PEBP基因, 系统进化分析表明它们分属5个亚家族: MFT、FT/TSF、TFL1、CEN和BFT。基因结构分析发现甘蓝、白菜和油菜的CEN基因内含子明显比其余4个物种的内含子长。蛋白结构域分析表明MFT比其他4个亚家族成员少了一个motif 2, TFL1比其他亚家族多了motif 8。选择压力分析发现7个物种PEBP同源基因均受到较强的纯化选择, 其中TFL1亚家族受到的纯化选择最弱。共线性分析表明十字花科植物PEBP基因家族随古代多倍体事件发生不同程度的扩张, TSF在甘蓝、白菜和油菜中丢失。非生物胁迫下, 在拟南芥中过量表达小鼠耳芥的一个MFT基因, 转基因拟南芥种子的萌发率明显低于野生型, 暗示MFT基因在调控种子萌发上的功能保守。本研究为深入研究十字花科植物PEBP基因的进化特征和生物学功能奠定了基础。

关键词: 短命植物, 小鼠耳芥, MFT, 基因扩增, 萌发率

Abstract

Aims: In recent years, the exponential growth of genomic data across diverse plant species provides unprecedented comprehensive understanding of the inheritance and variation of plant environment adaptation traits. The phosphatidylethanolamine-binding protein (PEBP) plays crucial roles in flowering transition and architectural establishment of plants, a topic of extreme interest in plant biology research. However, comparative genome analysis of the PEBP gene family has not been performed using newly sequenced genome data, which restricts the study of its evolution at the molecular level. To explore its molecular evolution mechanism, we performed comparative genomics analysis of PEBP gene family in Cruciferae plants in this study.
Methods: We utilized the methods of genome-wide identification, characterization, and evolution analysis of PEBP genes from seven Cruciferae plants: Arabidopsis thaliana, A. lyrata, A. pumila, Camelina sativa, Brassica oleracea, B. rapa, and B. napus.
Results: Our results indicated that 91 PEBP genes were identified from seven plant species, and phylogenetic analysis suggested that they were categorized into five subfamilies: MFT, FT/TSF, TFL1, CEN, and BFT. Gene structure analysis indicated that the introns of CEN genes in B. oleracea, B. rapa and B. napus were significantly longer than those in the other four species. Protein domain analysis demonstrated that MFT lacks motif 2 and TFL1 has one more motif 8 than the other four subfamilies. Selection pressure analysis revealed that the PEBP genes form seven plant species were subject to strong purification selection, of which, the TFL1 subfamily was the weakest in purification selection. Collinearity analysis indicated that the PEBP genes in Cruciferous expanded in varying degrees with the ancient polyploid events, and all genes except CEN were partially lost after expansion. In addition, when overexpression of the A. pumila MFT gene in A. thaliana, the germination rates of transgenic seeds were significantly lower than that in wild type under abiotic stresses, suggesting that the functions of MFT were conserved in the regulation of seed germination.
Conclusion: This study lays the foundation for the research of the evolutionary characterizations and biological functions of PEBP genes in cruciferous plants.

Key words: ephemeral plant, Arabidopsis pumila, MFT, gene amplification, germination rate

李永光, 任辉, 张英杰, 李瑞宁, 艾昊, 黄先忠 (2022) 十字花科植物PEBP基因家族的分子进化. 生物多样性, 30, 21545. DOI: 10.17520/biods.2021545.

Yongguang Li, Hui Ren, Yingjie Zhang, Ruining Li, Hao Ai, Xianzhong Huang (2022) Analysis of the molecular evolution of the PEBP gene family in cruciferous plants. Biodiversity Science, 30, 21545. DOI: 10.17520/biods.2021545.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2021545

https://www.biodiversity-science.net/CN/Y2022/V30/I6/21545

图/表 5

图1 拟南芥、琴叶拟南芥、小鼠耳芥、亚麻荠、甘蓝、白菜和油菜PEBP基因家族的基因结构及motif分布。A: 7个物种PEBP系统进化树; B: PEBP基因的外显子-内含子分布; C: PEBP蛋白保守基序分布特征。CDS: 蛋白质编码序列区域; UTR: 非编译区域; aa: 氨基酸。

Fig. 1 Motif distributions and exon-intron structures of the PEBP family members in Arabidopsis thaliana, A. lyrata, A. pumila, Camelina sativa, Brassica oleracea, B. rapa, and B. napus. A, PEBP phylogenetic tree of seven species; B, Exon-intron distribution of PEBP genes; C, Distribution characteristics of the conserved motifs of PEBP proteins; CDS, Coding sequence; UTR, Untranslated region; aa, Amino acid.

图2 物种内PEBP共线性基因对的选择压力统计。At: 拟南芥; Al: 琴叶拟南芥; Ap: 小鼠耳芥; Cs: 亚麻荠; Bo: 甘蓝; Br: 白菜; Bn: 油菜。

Fig. 2 Statistics of selection pressures on the PEBP collinearity genes within species. At, Arabidopsis thaliana; Al, A. lyrata; Ap, A. pumila; Cs, Camelina sativa; Bo, Brassica oleracea; Br, B. rapa; Bn, B. napus.

图3 拟南芥与甘蓝、白菜和油菜PEBP基因的共线性关系。圆柱分别代表拟南芥、甘蓝、白菜和油菜的5、9、10和21条染色体, 黑线表示物种间PEBP共线性关系。灰线表示基因组共线性关系。三角形代表TSF基因的位置。

Fig. 3 Syntenic relationships of PEBP genes in Arabidopsis thaliana, Brassica oleracea, B. rapa, and B. napus. The cylinder represents 5, 9, 10 and 21 chromosomes of A. thaliana, B. oleracea, B. rapa, and B. napus, respectively. The black line represents a common linear relationship of the PEBP gene, and the gray line represents a genomic linear relationship. The triangle represents the location of the TSF gene.

表1 十字花科植物PEBP家族基因的复制类型

Table 1 Types of replication of PEBP gene family in Cruciferae plants

物种 Species	PEBP基因数量 No. of PEBP gene	不同复制类型PEBP基因数量(百分比) No. of PEBP genes from different origins (percentage)
物种 Species	PEBP基因数量 No. of PEBP gene	单例型 Singleton	分散型 Dispersed	近端型 Proximal	串联重复 Tandem	全基因组复制或片段复制 WGD/S
拟南芥 Arabidopsis thaliana	6	0	1 (16.6)	0	0	5 (83.3)
琴叶拟南芥 Arabidopsis lyrata	7	0	7 (100)	0	0	0
小鼠耳芥 Arabidopsis pumila	11	0	1 (9.1)	0	0	10 (90.9)
亚麻芥 Camelina sativa	17	0	1 (5.9)	0	0	16 (94.1)
甘蓝 Brassica oleracea	11	0	1 (9.1)	0	0	10 (90.9)
白菜 Brassica rapa	14	0	3 (21.4)	1 (7.1)	0	10 (71.4)
油菜 Brassica napus	25	0	6 (24)	0	0	19 (76)

图4 35S:ApMFT转基因拟南芥在1/2 MS、ABA、GA3、NaCl、PEG6000处理下种子萌发率。WT: 野生型; #3和#9: 35S:ApMFT转基因株系; *差异显著(P < 0.05), **差异极显著(P < 0.01)。

Fig. 4 The germination rate of 35S:GhMFT1 transgenic Arabidopsis thaliana seeds treated with GA, ABA, NaCl and PEG6000. WT, Wild type; #3, #9: 35S:ApMFT transgenic lines, * Significant differences at P < 0.05; ** Significant differences at P < 0.01.

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十字花科植物PEBP基因家族的分子进化

Analysis of the molecular evolution of the PEBP gene family in cruciferous plants

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