烟草CONSTANS-like基因家族的鉴定与分析

doi:10.11983/CBB20147

植物学报 ›› 2021, Vol. 56 ›› Issue (1): 33-43.DOI: 10.11983/CBB20147

烟草CONSTANS-like基因家族的鉴定与分析

张雅文¹^,², 梁山¹, 徐国云³, 郭无瑕²^,⁴^,^*(), 邓书林²^,⁴^,^*()

¹华南师范大学生命科学学院, 广东省植物发育生物工程重点实验室, 广州 510631
²中国科学院华南植物园, 广东省应用植物学重点实验室, 广州 510650
³中国烟草总公司郑州烟草研究院, 郑州 450001
⁴中国科学院华南植物园, 华南农业植物分子分析与遗传改良重点实验室, 广州 510650

收稿日期:2020-08-25 接受日期:2021-01-05 出版日期:2021-01-01 发布日期:2021-01-15
通讯作者: 郭无瑕,邓书林
作者简介:*E-mail: guowx@scbg.ac.cn;
基金资助:
国家自然科学基金(32070340);郑州烟草研究院院长科技发展基金(902018CA0280)

Genome-wide Identification and Analysis of CONSTANS-like Gene Family in Nicotiana tabacum

Yawen Zhang¹^,², Shan Liang¹, Guoyun Xu³, Wuxia Guo²^,⁴^,^*(), Shulin Deng²^,⁴^,^*()

¹Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
²Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
³Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou 450001, China
⁴Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China

Received:2020-08-25 Accepted:2021-01-05 Online:2021-01-01 Published:2021-01-15
Contact: Wuxia Guo,Shulin Deng

摘要/Abstract

摘要： 烟草(Nicotiana tabacum)是基因功能分析的模式植物以及重要的经济作物之一, 适宜的生存环境对烟草的生长和繁殖至关重要。COL (CONSTANS-like)基因家族编码蛋白不仅调控植物开花, 而且在植物生物/非生物胁迫响应中发挥重要作用。该研究通过鉴定烟草COL基因家族成员, 分析其基因结构、进化关系、转录调控元件和表达模式, 探究其编码蛋白的生物学功能, 尤其是在烟草响应低温胁迫中的可能作用。结果显示, 在烟草中共鉴定出15个COL基因, 其编码的蛋白理化性质相近; 进化分析结果表明其包括3类, 每个类别的成员之间具有相似的外显子/内含子结构以及motif数量和类型; 烟草COL基因启动子区域含有大量与光、低温、干旱以及植物激素等响应相关的顺式作用元件; 基于二代高通量测序分析结果表明, 低温显著影响烟草COL基因的表达, 但对不同基因的影响存在差异, 不同COL基因的亲本(林烟草(N. sylvestris) (母本)和绒毛状烟草(N. tomentosiformis) (父本))具有表达偏好性, 且这种偏好性大部分会从6-7叶期保持到现蕾期。

关键词: 烟草, COL, 系统进化, 低温, 表达偏向

Abstract: Nicotiana tabacum (tobacco) is one of the model plants for molecular biology research as well as an important economic crop in the world. A suitable living environment is essential for the growth and reproduction of tobacco. CONSTANS-like (COL) family proteins are not only key regulators for flowering time, but also play important roles in stress response of plants. Our aim was to identify the COL family members, analyze their gene structure, evolutionary relationship, transcriptional regulatory elements and expression patterns, and explore their possible functions in response to cold stress in tobacco. We identified a total of 15 COL genes with similar physiochemical properties in tobacco. Evolutionary analysis divided all COL genes into three categories, and similar intron structure and motif distribution were observed among genes within each category. The promoter regions of tobacco COL genes contain a large number of cis-acting elements related to responses to light, low temperature, drought and phyto hormone. Gene expression analysis showed that low temperature significantly affected the expression of COL genes in tobacco, but the effects on different genes were different. Our study showed different parental (N. sylvestris (maternal) and N. tomentosiformis (paternal)) expression bias between different COL genes in tobacco, and most of the bias patterns were maintained from 6-7 leaf stage to budding stage.

Key words: Nicotiana tabacum, COL, phylogeny, low temperature, expression bias

张雅文, 梁山, 徐国云, 郭无瑕, 邓书林. 烟草CONSTANS-like基因家族的鉴定与分析. 植物学报, 2021, 56(1): 33-43.

Yawen Zhang, Shan Liang, Guoyun Xu, Wuxia Guo, Shulin Deng. Genome-wide Identification and Analysis of CONSTANS-like Gene Family in Nicotiana tabacum. Chinese Bulletin of Botany, 2021, 56(1): 33-43.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB20147

https://www.chinbullbotany.com/CN/Y2021/V56/I1/33

图/表 4

图1 5个物种COL蛋白的系统发育树从NCBI数据库下载烟草(Nitab)、拟南芥(At)、番茄(Solyc)、水稻(Os)和玉米(Zma) COL蛋白序列。采用Clustal软件进行序列比对, 采用邻接法构建系统发育树, bar表示进化距离。

Figure 1 Phylogenetic tree of COL proteins from five species COL protein sequences of Nicotiana tabacum (Nitab), Arabidopsis thaliana (At), Solanum lycopersicum (Solyc), Oryza sativa (Os), and Zea mays (Zma) were downloaded from NCBI database. The phylogenetic tree was constructed by neighbor joining method with Clustal, bar indicated evolutionary distance.

图2 烟草COL的基因结构(A)、COL蛋白的保守结构域(B)及蛋白保守基序的氨基酸序列(C) 不同颜色的矩形代表不同的蛋白保守基序以及非编码区(UTR) (绿色)和编码序列(CDS) (黄色)。比例尺分别代表基因序列长度(A)和蛋白序列长度(B), 纵坐标数字代表蛋白保守基序中相应氨基酸的频率(C)。

Figure 2 Gene structures of COL genes (A), and conserved motifs (B) and amino acid sequences (C) of conserved motifs of COL proteins in tobacco Differently colored rectangles representing different protein conserved motifs as well as untranslated region (UTR) (green) and coding sequence (CDS) (yellow). Scale bars indicating gene sequence length (A) and protein sequence length (B), respectively, and the ordinate numbers indicating the frequency of corresponding amino acid in the conserved motifs (C).

图3 烟草及其亲本COL蛋白的系统发育树从茄科基因组数据库(Solgenomics.net)下载普通烟草(Nitab) (子代)、绒毛状烟草(Nito) (父本)、林烟草(Nisy) (母本) COL蛋白序列, 采用Clustal软件进行序列比对, 并用邻接法构建系统发育树。

Figure 3 Phylogenetic tree of the COL family proteins in tobacco and its parents The COL proteins of Nicotiana tabacum (Nitab) (progeny), N. tomentosiformis (Nito) (paternal), and N. sylvestris (Nisy) (maternal) were downloaded from Solgenomics.net. The phylogenetic tree was constructed by neighbor joining method with Clustal.

图4 烟草所有COL基因(A)和5对部分同源基因(B)-(F)在低温处理下不同发育阶段叶片中的表达 FC(S): 12°C处理下6-7叶期的表达差异倍数; FC(F): 12°C处理下现蕾期的表达差异倍数; ck_S: 26°C下6-7叶期烟草; ck_F: 26°C下现蕾期烟草; cold_S: 12°C处理后6-7叶期烟草; cold_F: 12°C处理后现蕾期烟草; 黑色: 来自父本的基因; 灰色: 来自母本的基因。相对表达水平为3次生物学重复的平均值, 误差线代表标准差, 采用Student’s t-test对部分同源基因对进行差异显著性检验, * P<0.05, ** P<0.01, *** P<0.001, **** P<0.0001, ns表示无显著性差异。

Figure 4 Expression of all COL genes (A) and five homologous genes pairs (B)-(F) in tobacco leaves at different developmental stages under cold treatment FC(S): Fold change at 6-7 leaf stage under 12°C treatment; FC(F): Fold change at budding stage under 12°C treatment; ck_S: 6-7 leaf stage under 26°C; ck_F: Budding stage under 26°C; cold_S: 6-7 leaf stage under 12°C treatment; cold_F: Budding stage under 12°C treatment; Black: Orthologs from paternal plant; Gray: Orthologs from maternal plant; the relative expression level is the average of 3 biological replicates, the error bar represents standard deviation, and Student’s t-test is used for significance test, * P<0.05, ** P<0.01, *** P<0.001, **** P<0.0001, and ns means not significant.

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烟草CONSTANS-like基因家族的鉴定与分析

Genome-wide Identification and Analysis of CONSTANS-like Gene Family in Nicotiana tabacum

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