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.

参考文献 37

[1]	樊希彬, 李丹, 左晓晴, 薛金燕 (2016). 气候条件对烟草生长的影响分析. 黑龙江农业科学 ( 4), 27-30.
[2]	王玲, 郭长奎, 任丁, 马红 (2017). 水稻非生物胁迫响应基因OsMIP1的表达与进化分析. 植物学报 52, 43-53.
[3]	Borden KLB (2000). RING domains: master builders of molecular scaffolds? J Mol Biol 295, 1103-1112. DOI URL PMID
[4]	Chen CJ, Chen H, Zhang Y, Thomas HR, Frank MH, He YH, Xia R (2020). TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant 13, 1194-1202. DOI URL PMID
[5]	Crocco CD, Botto JF (2013). BBX proteins in green plants: insights into their evolution, structure, feature and functional diversification. Gene 531, 44-52. DOI URL PMID
[6]	Cutler SR, Rodriguez PL, Finkelstein RR, Abrams SR (2010). Abscisic acid: emergence of a core signaling network. Annu Rev Plant Biol 61, 651-679. URL PMID
[7]	Datta S, Hettiarachchi GHCM, Deng XW, Holm M (2006). Arabidopsis CONSTANS-LIKE3 is a positive regulator of red light signaling and root growth. Plant Cell 18, 70-84. URL PMID
[8]	Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE, Soltis PS, Wendel JF (2008). Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet 42, 443-461. DOI URL PMID
[9]	Flagel LE, Wendel JF (2010). Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation. New Phytol 186, 184-193. DOI URL PMID
[10]	Griffiths S, Dunford RP, Coupland G, Laurie DA (2003). The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis. Plant Physiol 131, 1855-1867. DOI URL PMID
[11]	Holm M, Hardtke CS, Gaudet R, Deng XW (2001). Identification of a structural motif that confers specific interaction with the WD40 repeat domain of Arabidopsis COP1. EMBO J 20, 118-127.
[12]	Hu TH, Wei QZ, Wang WH, Hu HJ, Mao WH, Zhu QM, Bao CL (2018). Genome-wide identification and characterization of CONSTANS-like gene family in radish (Raphanus sativus). PLoS One 13, e0204137. URL PMID
[13]	Jin JJ, Zhang H, Zhang JF, Liu PP, Chen X, Li ZF, Xu YL, Lu P, Cao PJ (2017). Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum. BMC Genomics 18, 496. DOI URL PMID
[14]	Khanna R, Kronmiller B, Maszle DR, Coupland G, Holm M, Mizuno T, Wu SH (2009). The Arabidopsis B-box zinc finger family. Plant Cell 21, 3416-3420. DOI URL PMID
[15]	Leitch IJ, Hanson L, Lim KY, Kovarik A, Chase MW, Clarkson JJ, Leitch AR (2008). The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae). Ann Bot 101, 805-814. DOI URL PMID
[16]	Li AL, Liu DC, Wu J, Zhao XB, Hao M, Geng SF, Yan J, Jiang XX, Zhang LQ, Wu JY, Yin LY, Zhang RZ, Wu L, Zheng YL, Mao L (2014). mRNA and small RNA transcriptomes reveal insights into dynamic homoeolog regulation of allopolyploid heterosis in nascent hexaploid wheat. Plant Cell 26, 1878-1900.
[17]	Liao Y, Smyth GK, Shi W (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930. URL PMID
[18]	Liu H, Dong SY, Sun DY, Liu W, Gu FW, Liu YZ, Guo T, Wang H, Wang JF, Chen ZQ (2016a). CONSTANS-Like 9 (OsCOL9) interacts with receptor for activated C-Kinase 1 (OsRACK1) to regulate blast resistance through salicylic acid and ethylene signaling pathways. PLoS One 11, e0166249. URL PMID
[19]	Liu JH, Shen JQ, Xu Y, Li XH, Xiao JH, Xiong LZ (2016b). Ghd2, a CONSTANS-like gene, confers drought sensitivity through regulation of senescence in rice. J Exp Bot 67, 5785-5798. DOI URL PMID
[20]	Liu ZL, Adams KL (2007). Expression partitioning between genes duplicated by polyploidy under abiotic stress and during organ development. Curr Biol 17, 1669-1674.
[21]	Love MI, Huber W, Anders S (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550. URL PMID
[22]	Min JH, Chung JS, Lee KH, Kim CS (2015). The CONSTANS-like 4 transcription factor, AtCOL4, positively regulates abiotic stress tolerance through an abscisic acid-dependent manner in Arabidopsis. J Integr Plant Biol 57, 313-324. DOI URL PMID
[23]	Miura K, Furumoto T (2013). Cold signaling and cold response in plants. Int J Mol Sci 14, 5312-5337. DOI URL PMID
[24]	Putterill J, Robson F, Lee K, Simon R, Coupland G (1995). The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80, 847-857. DOI URL PMID
[25]	Qin WQ, Yu Y, Jin YY, Wang XD, Liu J, Xi JP, Li Z, Li HQ, Zhao G, Hu W, Chen CJ, Li FQ, Yang ZE (2018). Genome-wide analysis elucidates the role of CONSTANS- like genes in stress responses of cotton. Int J Mol Sci 19, 2658.
[26]	Saidi Y, Finka A, Goloubinoff P (2011). Heat perception and signaling in plants: a tortuous path to thermotolerance. New Phytol 190, 556-565.
[27]	Sauter M (2013). Root responses to flooding. Curr Opin Plant Biol 16, 282-286.
[28]	Sierro N, Battey JND, Ouadi S, Bakaher N, Bovet L, Willig A, Goepfert S, Peitsch MC, Ivanov NV (2014). The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun 5, 3833. DOI URL PMID
[29]	Singh D, Laxmi A (2015). Transcriptional regulation of drought response: a tortuous network of transcriptional factors. Front Plant Sci 6, 895. DOI URL PMID
[30]	Skalická K, Lim KY, Matyasek R, Matzke M, Leitch AR, Kovarik A (2005). Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco. New Phytol 166, 291-303. URL PMID
[31]	Song YH, Song NY, Shin SY, Kim HJ, Yun DJ, Lim CO, Lee SY, Kang KY, Hong JC (2008). Isolation of CONSTANS as a TGA4/OBF4 interacting protein. Mol Cells 25, 559-565. URL PMID
[32]	Suárez-López P, Wheatley K, Robson F, Onouchi H, Valverde F, Coupland G (2001). CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature 410, 1116-1120. DOI URL PMID
[33]	Tang XL, Mu XM, Shao HB, Wang HY, Brestic M (2015). Global plant-responding mechanisms to salt stress: physiological and molecular levels and implications in biotechnology. Crit Rev Biotechnol 35, 425-437. DOI URL PMID
[34]	Yamori W, Evans JR, Von Caemmerer S (2010). Effects of growth and measurement light intensities on temperature dependence of CO₂ assimilation rate in tobacco leaves. Plant Cell Environ 33, 332-343. DOI URL PMID
[35]	Yoo MJ, Szadkowski E, Wendel JF (2013). Homoeolog expression bias and expression level dominance in allopolyploid cotton. Heredity 110, 171-180. DOI URL PMID
[36]	Zhang TZ, Hu Y, Jiang WK, Fang L, Guan XY, Chen JD, Zhang JB, Saski CA, Scheffler BE, Stelly DM, Hulse- Kemp AM, Wan Q, Liu BL, Liu CX, Wang S, Pan MQ, Wang YK, Wang DW, Ye WX, Chang LJ, Zhang WP, Song QX, Kirkbride RC, Chen XY, Dennis E, Llewellyn DJ, Peterson DG, Thaxton P, Jones DC, Wang Q, Xu XY, Zhang H, Wu HT, Zhou L, Mei GF, Chen SQ, Tian Y, Xiang D, Li XH, Ding J, Zuo QY, Tao LN, Liu YC, Li J, Lin Y, Hui YY, Cao ZS, Cai CP, Zhu XF, Jiang Z, Zhou BL, Guo WZ, Li RQ, Chen ZJ (2015). Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol 33, 531-537. DOI URL PMID
[37]	Zhang ZL, Ji RH, Li HY, Zhao T, Liu J, Lin CT, Liu B (2014). CONSTANS-LIKE 7 (COL7) is involved in phytochrome B (phyB)-mediated light-quality regulation of auxin homeostasis. Mol Plant 7, 1429-1440. DOI URL PMID

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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