烟草Trihelix转录因子家族鉴定及表达分析

doi:10.3969/j.issn.1009-7791.2022.01.001

亚热带植物科学 ›› 2022, Vol. 51 ›› Issue (1): 1-12.DOI: 10.3969/j.issn.1009-7791.2022.01.001

• 植物生理生化与分子生物学 • 下一篇

烟草Trihelix转录因子家族鉴定及表达分析

李栋成1，李魁印2，韦兴启3，段丽丽1，莫泽君1，刘仁祥1*

(1. 贵州大学烟草学院／贵州省烟草品质研究重点实验室，贵州贵阳 550025；2. 安顺学院农学院，贵州安顺 561000；3. 黔南州烟草公司长顺县分公司，贵州长顺 550700)

收稿日期:2022-01-02 接受日期:2022-01-25 发布日期:2022-05-17
通讯作者: 刘仁祥

Identification and Expression Analysis of Trihelix Transcription Factor Family in Tobacco

LI Dong-cheng1, LI Kui-yin2, WEI Xing-qi3, DUAN Li-li1, MO Ze-jun1, LIU Ren-xiang1*

(1. Tobacco College of Guizhou University / Key Laboratory of Tobacco Quality Research of Guizhou Province, Guiyang 550025, Guizhou China; 2. Agricultural College of Anshun College, Anshun 561000, Guizhou China; 3. Changshun County Branch of Qiannan Tobacco Company, Changshun 550700, Guizhou China)

Received:2022-01-02 Accepted:2022-01-25 Published:2022-05-17
Contact: LIU Ren-xiang

摘要/Abstract

摘要： 运用生物信息学分析方法，通过对烟草(Nicotiana tabacum)全基因组数据中的Trihelix家族基因的理化性质、染色体分布、染色体共线性、基序组成、基因结构、顺式作用元件及其低温处理下的表达进行完整的鉴定分析，初步解析烟草Trihelix家族成员的结构与功能。从普通烟草中鉴定出32个Trihelix基因，分为GT-1、GT-2、GTγ、SH4、SIP1等5个亚家族；32个NtTH基因有着10种分布不均匀的基序，且有不同的基因结构，但在同一个亚家族内有相似性；烟草与番茄(Lycopersicon esculentum)、拟南芥(Arabidopsis thaliana)、水稻(Oryza sativa)存在同源的Trihelix基因，普通烟草Trihelix家族自身也存在共线性基因；鉴定出13种不同类型的顺式元件，主要与非生物胁迫、激素和生长发育有关，其中ABRE和MeJA是最多的两个顺式元件，表明NtTH基因的功能主要与非生物胁迫和生长发育响应调控有关；烟草NtTH3和NtTH16等11个基因在对低温胁迫的响应方面有着重要作用。本研究挖掘到与烟草抗冷有关的基因，为烟草抗冷性遗传改良提供了理论依据。

Abstract: Tobacco is a kind of temperature-loving economic crop. Screening and utilization of cold-resistant genes plays an important role in the growth and development, yield and quality of tobacco. In this study, bioinformatics analysis was used to identify and analyze the physical and chemical properties, chromosome distribution, chromosome collinearity, motif composition, gene structure, cis-acting elements and expression of Trihelix family genes in tobacco genome data, and the structure and function of tobacco Trihelix family members were preliminarily analyzed. Thirty-two Trihelix genes were identified from common tobacco, which were divided into 5 subfamilies: GT-1, GT-2, GTγ, SH4 and SIP1. Thirty-two NtTH genes had 10 different motifs and different gene structures, but were similar in the same subfamily. There were homologous Trihelix genes in tobacco, tomato, Arabidopsis and rice, and there were collinear genes in the Trihelix family of common tobacco. Thirteen different types of cis elements were identified, which were mainly related to abiotic stress, hormone and growth and development. ABRE and MeJA were the two most cis elements, indicating that the function of NtTH gene was mainly related to abiotic stress and the regulation of growth and development response. Among them, 11 genes, such as tobacco NtTH3 and NtTH16, played an important role in response to low temperature stress. In this study, the genes related to cold resistance of tobacco were found, which provided a theoretical basis for the genetic improvement of cold resistance and stress resistance of tobacco.

李栋成，李魁印，韦兴启，段丽丽，莫泽君，刘仁祥. 烟草Trihelix转录因子家族鉴定及表达分析[J]. 亚热带植物科学, 2022, 51(1): 1-12.

LI Dong-cheng, LI Kui-yin, WEI Xing-qi, DUAN Li-li, MO Ze-jun, LIU Ren-xiang. Identification and Expression Analysis of Trihelix Transcription Factor Family in Tobacco[J]. Subtropical Plant Science, 2022, 51(1): 1-12.

参考文献

[1] 纪剑辉, 周颖君, 吴贺贺, 杨立明. 水稻Trihelix转录因子家族全基因组分析及功能预测[J]. 遗传, 2015, 37(12): 1228–1241.
[2] Ma Z, Liu M, Sun W, Huang L, Wu Q, Bu T, Li C, Chen H. Genome–wide identification and expression analysis of the trihelix transcription factor family in tartary buckwheat (Fagopyrum tataricum)[J]. BMC Plant Biology, 2019, 19(1): 344.
[3] Kaplan-Levy R N, Brewer P B, Quon T, Smyth D R. The trihelix family of transcription factors––light, stress and development[J]. Trends in Plant Science, 2012, 17(3): 163–171.
[4] Lampugnani E R, Kilinc A, Smyth D R. PETAL LOSS is a boundary gene that inhibits growth between developing sepals in Arabidopsis thaliana[J]. Plant Journal, 2012, 71(5): 724–735.
[5] Du H, Huang M, Liu L. The genome wide analysis of GT transcription factors that respond to drought and waterlogging stresses in maize[J]. Euphytica, 2016, 208(1): 113–122.
[6] Xi J, Qiu Y, Du L, Poovaiah B W. Plant-specific trihelix transcription factor AtGT2L interacts with calcium/calmodulin and responds to cold and salt stresses[J]. Plant Science, 2012, 185–186: 274–280.
[7] Yu C, Song L, Song J, Ouyang Bo, Guo L, Shang L, Wang T, Li H, Zhang J, Ye Z. ShCIGT, a Trihelix family gene, mediates cold and drought tolerance by interacting with SnRK1 in tomato[J]. Plant Science, 2018, 270: 140–149.
[8] Qin Y, Ma X, Yu G, Wang Q, Wang L, Kong L, Kim W, Wang H W. Evolutionary history of trihelix family and their functional diversification[J]. DNA Research, 2014, 21(5): 499–510.
[9] 周轲. 转BcICE1基因烟草抗逆性研究[D]. 兰州: 西北师范大学硕士学位论文, 2017.
[10] 李晓旭, 郭存, 蒲文宣, 刘万峰, 张银霞, 孙楠, 何鑫玺, 刘成, 许良涛, 高军平. 普通烟草WOX转录因子家族的全基因组鉴定及分析[J]. 中国烟草学报, 2021, 27(1): 90–100.
[11] Russo E T, Laio A, Punta M. Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation[J]. BMC Bioinformatics, 2021, 22(1): 121.
[12] Letunic I, Doerks T, Bork P. SMART 7: recent updates to the protein domain annotation resource[J]. Nucleic Acids Research, 2012, 40: D302–D305.
[13] Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios I, Stockinger H. ExPASy: SIB bioinformatics resource portal[J]. Nucleic Acids Research, 2012, 40(Web Server issue): W597–W603.
[14] Softberry, Inc. Softberry Releases 80 Free Bioinformatics Programs for Immediate Download by Academic Users[R]. Biotech Business Week, 2013.
[15] Chen C, Chen H, Zhang Y, Thomas H R, Frank M H, He Y, Xia R. TBtools: An integrative toolkit developed for interactive analyses of big biological data[J]. Molecular Plant, 2020, 13(8): 1194–1202.
[16] Li X, Guo C, Ahmad S, Wang Q, Yu J, Liu C, Guo Y. Systematic analysis of MYB family genes in potato and their multiple roles in development and stress responses[J]. Biomolecules, 2019, 9(8): 317.
[17] Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Molecular Biology and Evolution, 2016, 33(7): 1870–1874.
[18] He Z, Zhang H, Gao S, Lercher M J, Chen W H, Hu S. Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees[J]. Nucleic Acids Research, 2016, 44(W1): W236–W241.
[19] Chanhee K, Lorna H, Yuhan F, Dietmar K. Predicting hyperosmolality-inducible transcription factors using MEME tools[J]. The FASEB Journal, 2021, 35(S1): 4656.
[20] Higo K, Ugawa Y, Iwamoto M, Korenaga T. Plant cis–acting regulatory DNA elements (PLACE) database: 1999[J]. Nucleic Acids Research, 1999, 27(1): 297–300.
[21] Magwanga R O, Kirungu J N, Lu P, Yang X, Dong Q, Cai X, Xu Y, Wang X, Zhou Z, Hou Y, Nyunja R, Agong S G, Hua J, Zhang B, Wang K, Liu F. Genome wide identification of the trihelix transcription factors and overexpression of Gh_A05G2067 (GT-2), a novel gene contributing to increased drought and salt stresses tolerance in cotton[J]. Physiologia Plantarum, 2019, 167(3): 447–464.
[22] Cannon S B, Mitra A, Baumgarten A, Young N D, May G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana[J]. BMC Plant Biology, 2004, 4: 10.
[23] Tang H, Bowers J E, Wang X, Ming R, Alam M, Paterson A H. Synteny and collinearity in plant genomes[J]. Science, 2008, 320(5875): 486–488.
[24] Liu W, Zhang Y, Li W, Lin Y, Wang C, Xu R, Zhang L. Genome-wide characterization and expression analysis of soybean trihelix gene family[J]. PeerJ, 2020, 8: e8753.
[25] O'Brien M, Kaplan-Levy R N, Quon T, Sappl P G, Smyth D R. PETAL LOSS, a trihelix transcription factor that represses growth in Arabidopsis thaliana, binds the energy-sensing SnRK1 kinase AKIN10[J]. Journal of Experimental Botany, 2015, 66(9): 2475–2485.
[26] Tzafrir I, Pena-Muralla R, Dickerman A, Berg M, Rogers R, Hutchens S, Sweeney TC, Mcelver J, Aux G, Patton D, Meinke D. Identification of genes required for embryo development in Arabidopsis[J]. Plant Physiology, 2004, 135(3): 1206–1220.
[27] Song J, Shen W Y, Shaheen S, Li Y Y, Liu Z R, Wang Z, Pang H B, Ahmed Z, Genome wide identification and analysis of the trihelix transcription factors in sunflower[J]. Biologia Plantarum, 2021, 65: 80–87.
[28] Fujita Y, Fujita M, Satoh R, Maruyama K, Parvez M M, Seki M, Hiratsu K, Ohme-Takagi M, Shinozaki K, Yamaguchi-Shinozaki K. AREB1 is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis[J]. Plant Cell, 2005, 17(12): 3470–3488.
[29] White A J, Dunn M A, Katebrown, Hughes M A. Comparative analysis of genomic sequence and expression of a lipid transfer protein gene family in winter barley[J]. Journal of Experimental Botany, 1994, 45(12): 1885–1892.
[30] Li J, Zhang M, Sun J, Mao X, Wang J, Wang J, Liu H, Zheng H, Zhen Z, Zhao H, Zou D. Genome-wide characterization and identification of trihelix transcription factor and expression profiling in response to abiotic stresses in rice (Oryza sativa L.)[J]. International Journal of Molecular Sciences, 2019, 20(2): 251.

编辑推荐

Metrics

闽ICP备11008787号-5　

烟草Trihelix转录因子家族鉴定及表达分析

Identification and Expression Analysis of Trihelix Transcription Factor Family in Tobacco

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 0

编辑推荐

Metrics