千穗谷TALE转录因子家族的生物信息学分析

doi:10.11733/j.issn.1007-0435.2023.03.007

草地学报 ›› 2023, Vol. 31 ›› Issue (3): 676-687.DOI: 10.11733/j.issn.1007-0435.2023.03.007

千穗谷TALE转录因子家族的生物信息学分析

周敏^1,2, 周涛^1,2, 徐倩^1,2, 卢蕊^1,2, 刘明稀^1,2, 胡龙兴^1,2

1. 湖南农业大学农学院草业科学系, 湖南长沙 410128;
2. 湖南省草地研究中心, 湖南长沙 410128

收稿日期:2022-08-22 修回日期:2022-10-08 出版日期:2023-03-15 发布日期:2023-04-01
通讯作者: 胡龙兴,E-mail:grass@hunau.edu.cn;刘明稀,E-mail:Lmx75@hunau.edu.cn
作者简介:周敏(1998-),女,汉族,湖南浏阳人,硕士研究生,主要从事牧草遗传转化与种质创新研究,E-mail:1622748675@qq.com
基金资助:
山东省重点研发计划（农业良种工程）（2022LZGC018），中国科学院战略性先导科技专项（A类）（No.XDA26050201）和湖南省教厅项目（21A0126）资助

Bioinformatics Analysis of the TALE Transcription Factor Family in Amaranthus hypochondriacus

ZHOU Min^1,2, ZHOU Tao^1,2, XU Qian^1,2, LU Rui^1,2, LIU Ming-xi^1,2, HU Long-xing^1,2

1. Department of Pratacultural Science, College of Agronomy, Hunan Agricultural University, Changsha, Hunan Province 410128, China;
2. Hunan Grassland Research Center, Changsha, Hunan Province 410128, China

Received:2022-08-22 Revised:2022-10-08 Online:2023-03-15 Published:2023-04-01

摘要/Abstract

摘要： TALE转录因子广泛存在于植物中，对植物的生长发育和对外界环境的响应发挥着重要作用。本研究在千穗谷（Amaranthus hypochondriacus）基因组中共鉴定出11个TALE基因。系统发育分析将千穗谷TALE家族蛋白分为BELL和KNOX两个亚家族，同一亚家族中的AhTALEs基因具有相似的基因结构，编码蛋白也具有类似的结构域。蛋白二级结构和三级结构分析都表明AhTALEs蛋白由螺旋-角-螺旋的结构构成。此外，对千穗谷与其他物种的TALE基因共线性关系、组织表达特性和AhTALEs基因启动子区的顺式作用元件分析发现，不同AhTALEs亚家族在各组织中的表达模式不同，并且发现启动子区包含大量非生物胁迫和激素响应元件，这为AhTALE家族的进化分析提供了依据。qRT-PCR分析发现AhTALEs基因在低温和干旱胁迫下的表达水平有不同程度的变化，表明AhTALEs基因能够响应低温和干旱胁迫应答。本研究为开展千穗谷中TALE转录因子在非生物胁迫中的生物学功能研究提供了重要参考。

关键词: 千穗谷, TALE, 基因家族, 低温, 干旱

Abstract: TALE transcription factors widely present in plants and play an important role in plant growth and organ development and response to the environment. In this study, 11 TALE genes were identified in the genome of Amaranthus hypochondriacus. By the phylogenetic analysis, the AhTALEs family was divided into BELL and KNOX subfamilies. The AhTALEs genes have a similar genetic structure in the same subfamily, and the encoding protein also has similar domains. The secondary structure and tertiary structure analysis of the AhTALEs family protein showed that it was composed of helical-angular-helical structure. In addition, the syntenic relations of the four species were analyzed, which provided the basis for the evolution of the AhTALE family. Analysis of tissue expression characteristics showed that the expression patterns of different AhTALE subfamilies were different in different tissues. Analysis of cis-acting elements in the promoter region of AhTALEs gene revealed a large number of elements in response to abiotic stresses and hormones existed. Subsequently, the qRT-PCR analysis showed that the expression level of AhTALEs gene changed in different degrees under low temperature and drought stress, indicating that AhTALEs gene could take a response to low temperature and drought stress. This study provided an important reference for the biological function of TALE transcription factor in A. hypochondriacus in response to abiotic stresses.

Key words: Amaranthus hypochondriacus, TALE, Gene family, Low temperature, Drought

中图分类号:

S344.13

周敏, 周涛, 徐倩, 卢蕊, 刘明稀, 胡龙兴. 千穗谷TALE转录因子家族的生物信息学分析[J]. 草地学报, 2023, 31(3): 676-687.

ZHOU Min, ZHOU Tao, XU Qian, LU Rui, LIU Ming-xi, HU Long-xing. Bioinformatics Analysis of the TALE Transcription Factor Family in Amaranthus hypochondriacus[J]. Acta Agrestia Sinica, 2023, 31(3): 676-687.

0
/ / 推荐

导出引用管理器 EndNote|Ris|BibTeX

链接本文: https://manu40.magtech.com.cn/Jweb_cdxb/CN/10.11733/j.issn.1007-0435.2023.03.007

https://manu40.magtech.com.cn/Jweb_cdxb/CN/Y2023/V31/I3/676

参考文献

[1] BERTOLINO E, REIMUND B, WIINIC D, et al. A novel homeobox protein which recognizes a TGT core and functionally interferes with a retinoid-responsive motif[J]. Journal of Biological Chemistry, 1995, 270(52):31178-31188
[2] BRYAN R, GLASER D, SHAPIRO L. Genetic regulatory hierarchy in Caulobacter development[J]. Advances in Genetics, 1990, 27:1-31
[3] MCGINNIS W, KRUMLAUF R. Homeobox genes and axial patterning[J]. Cell, 1992, 68(2):283-302
[4] SCOTT M P. A rational nomenclature for vertebrate homeobox (HOX) genes[J]. Nucleic Acids Research, 1993, 21(8):1687-1688
[5] HAN Y, ZHANG L, YAN L, et al. Genome-wide analysis of TALE superfamily in Triticum aestivum reveals TaKNOX11-A is involved in abiotic stress response[J]. BMC Genomics, 2022, 3(1):1-21
[6] WANG L, YANG X, GAO Y, et al. Genome-wide identification and characterization of TALE superfamily genes in soybean (Glycine max L.)[J]. International Journal of Molecular Sciences, 2021, 22(8):4117
[7] WANG J, ZHAO P, CHENG B,et al. Identification of TALE transcription factor family and expression patterns related to fruit chloroplast development in tomato (Solanum lycopersicum L.)[J]. International Journal of Molecular Sciences, 2022, 23(9):4507
[8] 韩潇. 不同生长速率欧美杨形成层基因表达分析及杨树BELL基因功能研究[D]. 北京:北京林业大学, 2017:71-72
[9] 赵伟, 李锡香, 王海平, 等. 萝卜TALE转录因子家族的鉴定与分析[J]. 生物工程学报, 2022, 38(1):343-358
[10] BILLETER M, QIAN Y Q, OTTING G, et al. Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex[J]. Journal of Molecular Biology, 1993, 234(4):1084-1097
[11] BVRGLIN T R. Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals[J]. Nucleic Acids Research, 1997, 25(21):4173-4180
[12] HAY A, TSIANTIS M. KNOX genes:versatile regulators of plant development and diversity[J]. Development, 2010, 137(19):3153-3165
[13] CHEN H, ROSIN F M, PRAT S, et al. Interacting transcription factors from the three-amino acid loop extension superclass regulate tuber formation[J]. Plant Physiology, 2003, 132(3):1391-1404
[14] 马强. 棉花TALE超家族转录因子的鉴定分析及GhBLH7-D06的功能验证[D]. 武汉:华中农业大学, 2019:14-15
[15] BRAMBILLA V, BATTAGLIA R, COLOMBO M, et al. Genetic and molecular interactions between BELL1 and MADS box factors support ovule development in Arabidopsis[J]. The Plant Cell, 2007, 19(8):2544-2556
[16] KUMAR R, KUSHALAPPA K, GODT D, et al. The Arabidopsis BEL1-LIKE HOMEODOMAIN proteins SAW1 and SAW2 act redundantly to regulate KNOX expression spatially in leaf margins[J]. The Plant Cell, 2007, 19(9):2719-2735
[17] TSUDA K, ABRAHAM-JUAREZ M J, MAENO A, et al. KNOTTED1 cofactors, BLH12 and BLH14, regulate internode patterning and vein anastomosis in maize[J]. The Plant Cell, 2017, 29(5):1105-1118
[18] YAN F, GAO Y, P ANG X, et al. BEL1-LIKE HOMEODOMAIN4 regulates chlorophyll accumulation, chloroplast development, and cell wall metabolism in tomato fruit[J]. Journal of Experimental Botany, 2020, 71(18):5549-5561
[19] HIRANO K, KONDO M, AYA K, et al. Identification of transcription factors involved in rice secondary cell wall formation[J]. Plant and Cell Physiology, 2013, 54(11):1791-1802
[20] WANG S, YAMAGUCHI M, GRIENENBERGER E, et al. The Class II KNOX genes KNAT3 and KNAT7 work cooperatively to influence deposition of secondary cell walls that provide mechanical support to Arabidopsis stems[J]. The Plant Journal, 2020, 101(2):293-309
[21] FURUMIZU C, A LVAREZ J P, S AKAKIBARA K, et al. Antagonistic roles for KNOX1 and KNOX2 genes in patterning the land plant body plan following an ancient gene duplication[J]. PLoS Genetics, 2015, 11(2):e1004980
[22] TRUERNIT E, HASELOFF J. A role for KNAT class II genes in root development[J]. Plant Signaling & Behavior, 2007, 2(1):10-12
[23] RUPP H M, FRANK M, WERNER T, et al. Increased steady state mRNA levels of the STM and KNAT1 homeobox genes in cytokinin overproducing Arabidopsis thaliana indicate a role for cytokinins in the shoot apical meristem[J]. The Plant Journal, 1999, 18(5):557-563
[24] CHAUDHURY A M, LETHAM S, CRAIG S, et al. amp1-a mutant with high cytokinin levels and altered embryonic pattern, faster vegetative growth, constitutive photomorphogenesis and precocious flowering[J]. The Plant Journal, 1993, 4(6):907-916
[25] CONWAY L J, POETHIG R S. Mutations of Arabidopsis thaliana that transform leaves into cotyledons[J]. Proceedings of the National Academy of Sciences, 1997, 94(19):10209-10214
[26] NADAKUDUTI S S, HOLDSWORTH W L, KLEIN C L, et al. KNOX genes influence a gradient of fruit chloroplast development through regulation of GOLDEN 2-LIKE expression in tomato[J]. The Plant Journal, 2014, 78(6):1022-1033
[27] DI GIACOMO E, LAFFONT C, SCIARRA F, et al. KNAT 3/4/5-like class 2 KNOX transcription factors are involved in Medicago truncatula symbiotic nodule organ development[J]. New Phytologist, 2017, 213(2):822-837
[28] MA Q, WANG N, HAO P, et al. Genome-wide identification and characterization of TALE superfamily genes in cotton reveals their functions in regulating secondary cell wall biosynthesis[J]. BMC Plant Biology, 2019, 19(1):1-20
[29] TAO Y, CHEN M, SHU Y, et al. Identification and functional characterization of a novel BEL1-LIKE homeobox transcription factor GmBLH4 in soybean[J]. Plant Cell, Tissue and Organ Culture (PCTOC), 2018, 134(2):331-344
[30] 王中林. 籽粒苋的利用价值及高效种植技术[J]. 科学种养, 2018(11):22-24
[31] 王建丽, 刘杰淋, 朱瑞芬, 等. 28份籽粒苋种质资源的主要农艺性状遗传多样性分析[J]. 草地学报, 2020, 28(4):1050-1059
[32] 周涛, 彭辉, 喻望晨, 等. 千穗谷TCP基因家族生物信息学分析[J]. 草地学报, 2022, 30(4):867-878
[33] 杨辉. 籽粒苋的特性和种植技术[J]. 现代畜牧科技, 2021(10):63-64
[34] 孙鸿良. 高产优质耐旱一年生粮饲兼用作物——籽粒苋[M]. 北京:台海出版社, 2002:33
[35] LIGHTFOOT D J, JARVIS D E, RAMARAJ T, et al. Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution[J]. BMC Biology, 2017, 15(1):1-15
[36] 李波, 刘畅, 李红, 等. 外源氯化钙对‘龙牧807’苜蓿幼苗干旱缓解效应分析[J]. 草地学报, 2020, 28(4):990-997
[37] LI X B, FAN X P, WANG X L, et al. The cotton ACTIN₁gene is functionally expressed in fibers and participates in fiber elongation[J]. The Plant Cell, 2005, 17(3):859-875
[38] HAMANT O, PAUTOT V. Plant development:a TALE story[J]. Comptes Rendus Biologies, 2010, 333(4):371-381
[39] 张中荣, 吉雪花, 张海英, 等. 辣椒TALE转录因子的生物信息学分析[J]. 分子植物育种, 2020, 18(5):1401-1408
[40] WILLIAM ROY S, GILBERT W. The evolution of spliceosomal introns:patterns, puzzles and progress[J]. Nature Reviews Genetics, 2006, 7(3):211-221
[41] MICHELMORE R W, MEYERS B C. Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process[J]. Genome Research, 1998, 8(11):1113-1130.
[42] WANG Y, ZHAO Y, YAN M, et al. Genome-wide identification and expression analysis of TALE gene family in Pomegranate (Punica granatum L.)[J]. Agronomy, 2020, 10(6):829
[43] 孙韵雅, 陈佳, 王悦, 等. 根际促生菌促生机理及其增强植物抗逆性研究进展[J]. 草地学报, 2020, 28(5):1203-1215
[44] GONG Z, XIONG L, SHI H, et al. Plant abiotic stress response and nutrient use efficiency[J]. Science China Life Sciences, 2020, 63(5):635-674
[45] ZHAO K, ZHANG X, CHENG Z, et al. Comprehensive analysis of the three-amino-acid-loop-extension gene family and its tissue-differential expression in response to salt stress in poplar[J]. Plant Physiology and Biochemistry, 2019, 136:1-12
[46] ALI H, LIU Y, AZAM S M, et al. Genome wide identification and expression profiles of TALE genes in pineapple (Ananas comosus L)[J]. Tropical Plant Biology, 2019, 12(4):304-317

千穗谷TALE转录因子家族的生物信息学分析

Bioinformatics Analysis of the TALE Transcription Factor Family in Amaranthus hypochondriacus

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

本文评价

[1]	刘行行, 种培芳. 胡杨AHL基因家族生物信息学分析及逆境胁迫下的表达特征[J]. 草地学报, 2023, 31(3): 741-750.
[2]	吴学蕤, 赵庆霞, 蔡银美, 张成富, 李官亮. 干旱-复水对构树叶片水势和气孔开闭的影响[J]. 草地学报, 2023, 31(3): 769-776.
[3]	师微柠, 苏世平, 李毅, 张龚, 席杰. 干旱生境下外源脯氨酸对红砂气孔形态的影响[J]. 草地学报, 2023, 31(3): 777-784.
[4]	马小兰, 周华坤, 张正芳, 李珍珍, 徐梦真, 黄奥伟, 王文颖, 殷恒霞. 外源IAA对干旱胁迫下红豆草种子萌发及幼苗生长的影响[J]. 草地学报, 2023, 31(3): 796-803.
[5]	李震, 戴玲玲, 邓海玲, 郭海滨, 强胜, 宋小玲. 碧护缓解低温对草坪草萌发及苗期胁迫的作用[J]. 草地学报, 2023, 31(3): 804-812.
[6]	柴继宽, 赵桂琴, 琚泽亮. 添加不同乳酸菌对燕麦低温青贮发酵的影响[J]. 草地学报, 2023, 31(3): 923-928.
[7]	侯燕红, 生小燕, 韩博, 姜华, 何承刚. 干旱和高温胁迫下紫花苜蓿PEPC酶活性变化及其基因序列分析[J]. 草地学报, 2023, 31(2): 330-336.
[8]	李春艳, 钟华, 杜利霞, 侯向阳. 白羊草BiMYB52基因的克隆及转基因拟南芥抗旱性表达分析[J]. 草地学报, 2023, 31(1): 29-39.
[9]	赵文武, 赵鑫, 谢文辉, 赵丽丽, 陈可可, 王普昶. 干旱胁迫下白刺花幼苗根系生长和生理特性的响应[J]. 草地学报, 2023, 31(1): 120-129.
[10]	刘淑兰, 李进, 马永慧, 巫利梅, 李莹, 朱丽春. 独脚金内酯对干旱胁迫下黑果枸杞种子萌发和幼苗生理变化的影响[J]. 草地学报, 2023, 31(1): 130-139.
[11]	张慎彤, 高浩, 张金鹏, 任智慧, 姜惠娜, 其美拉姆, 普布卓玛, 付娟娟. 西藏野生垂穗披碱草EnCBL10基因的克隆与功能研究[J]. 草地学报, 2022, 30(9): 2315-2324.
[12]	邹瑾, 王晓佳, 曹兵, 李运毛, 冯学瑞, 刘佳欣. 花棒种子萌发对NaCl及聚乙二醇胁迫的响应[J]. 草地学报, 2022, 30(8): 2002-2008.
[13]	史佳梅, 许冬梅, 刘万龙, 白博文, 郭艳菊, 马晓静. 沙化草地土壤有机碳及碳库管理指数的分异特征研究[J]. 草地学报, 2022, 30(7): 1630-1640.
[14]	唐军, 丁西朋, 陈志坚, 马向丽, 毕玉芬, 郭凤根. 木豆响应低温胁迫差异表达基因分析[J]. 草地学报, 2022, 30(7): 1701-1711.
[15]	杜雨, 刘筠, 胡晓桐, 贾西贝, 柳迪, 马彦军. 黑果枸杞GRF转录因子家族鉴定与生物信息学分析[J]. 草地学报, 2022, 30(6): 1403-1412.