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作物杂志,2021, 第2期: 35–44 doi: 10.16035/j.issn.1001-7283.2021.02.005

所属专题： 油料作物

• 遗传育种·种质资源·生物技术 • 上一篇    下一篇

花生TCP转录因子的全基因组鉴定及组织表达特性分析

王通1(), 赵孝东2, 甄萍萍3, 陈静1, 陈明娜1, 陈娜1, 潘丽娟1, 王冕1, 许静1, 禹山林1, 迟晓元1(), 张建成1()   

  1. 1山东省花生研究所/农业农村部花生生物学与遗传育种重点实验室,266100,山东青岛
    2临沂市农业科学院,276012,山东临沂
    3德州市临邑县农业农村局,251500,山东德州
  • 收稿日期:2020-07-23 修回日期:2020-10-27 出版日期:2021-04-15 发布日期:2021-04-16
  • 通讯作者: 迟晓元,张建成
  • 作者简介:王通,主要从事花生高产及抗性遗传育种研究,E-mail： wtwtp@126.com
  • 基金资助:
    国家花生产业技术体系(CARS-14);山东省自然科学基金(ZR2017YL017);青岛市应用基础青年专项(17-1-1-51-jch);国家自然科学基金(31701464);山东省农业科学院农业科技创新工程(CXGC2016B02);山东省农业科学院农业科技创新工程(CXGC2018E21);山东省良种工程项目(2017LZGC003);广东省重点领域研究计划(2020B020219003);青岛市科技惠民专项(19-6-1-61-nsh)

Genome-Wide Identification and Characteristic Analyzation of the TCP Transcription Factors Family in Peanut

Wang Tong1(), Zhao Xiaodong2, Zhen Pingping3, Chen Jing1, Chen Mingna1, Chen Na1, Pan Lijuan1, Wang Mian1, Xu Jing1, Yu Shanlin1, Chi Xiaoyuan1(), Zhang Jiancheng1()   

  1. 1Shandong Peanut Research Institute/Key Laboratary of Peanut Biology and Genetic Improvement of Ministry of Agriculture and Rural Affairs, Qingdao 266100, Shandong, China
    2Linyi Academy of Agricultural Sciences, Linyi 276012, Shandong, China
    3Agriculture and Rural Bureau of Linyi County, Dezhou 251500, Shandong, China
  • Received:2020-07-23 Revised:2020-10-27 Online:2021-04-15 Published:2021-04-16
  • Contact: Chi Xiaoyuan,Zhang Jiancheng

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摘要：

TCP基因家族是植物中一类重要的转录因子,参与植物整个生长发育阶段的调控,尤其在花器官和分生组织中发挥重要作用。目前,在花生中尚无TCP相关基因的报道。为研究花生各TCP转录因子的生物调控作用,以及为进一步分析花生TCP基因提供参考信息,利用生物信息学方法在全基因组水平对花生TCP家族基因进行鉴定,分析其染色体定位、系统进化、基因结构、保守基序和基因表达模式。结果分别从花生野生种和栽培种鉴定出19个和32个TCP基因,不均匀分布在9个野生种染色体和14个栽培种染色体上。系统进化分析表明,51个花生TCP基因可划分为亚家族Ⅰ（PCF）和亚家族Ⅱ两个亚类,其中亚家族Ⅱ包括2个分支,CIN和CYC/TB1。这些基因都含有高度保守的bHLH结构域,但其内含子结构存在较大差异,内含子数量及长度分布与基因的系统进化有较大关系,其中亚家族Ⅰ成员的内含子较少,亚家族Ⅱ内含子较多,且长度差异较大。表达谱分析显示,仅有7个基因在各组织中呈现显著差异性表达,其中有6个基因的差异表达与分生组织和花器官有关,推测其在花生茎尖和花的生长发育过程中起重要作用。

关键词: 花生, TCP转录因子, 全基因鉴定, 基因表达

Abstract:

The transcription factor TCPs is very important and plays multiple roles in plants, which is involved in the regulation of plant growth throughout the whole development stage, especially in flower organs and meristem. However, no information on this gene family in peanut was reported. The objective of this study is to identify and characterize the peanut TCP family genes, and to provide a basis for studying the theoretical roles of TCP genes in the regulation of peanut growth and development, and also to provide valuable information for TCP genes cloning in peanut. The TCP family genes were identified from peanut genome through bioinformatics methods, and the chromosomal location, phylogenetic evolution, gene structure, conserved motif and gene expression patterns of peanut TCP genes were analyzed. Results showed that 19 and 32 peanut TCP genes were identified in nine wild species chromosomes and 14 cultivar chromosomes, respectively. Phylogenetic analysis displayed the 51 peanut TCP genes could be divided into two subclasses: classⅠ(PCF) and classⅡ, furthermore, the classⅡ was divided into two clades: CIN and CYC/TB1. These genes all contained highly conserved bHLH domains, but their intron structures were quite different. The number and length of introns in these genes were largely related to the phylogenetic evolution. Genes in classⅠ had less introns, nevertheless the number of introns was much more in classⅡ, and there were many differences of intron length between class I and classⅡ. Moreover, the expression profile of peanut TCP family genes showed that only seven genes were differentially expressed in tissues, and six of which were related to meristems and flowers. It is suggested that these genes could play important roles in the growth and development of peanut stems tips and flowers.

Key words: Peanut, TCP transcription factor, Whole-gene identification, Gene expression

表1

花生中TCP基因家族基本信息

基因编号
Code No.		 氨基酸数
Amino acid number		 分子量
Molecular mass (kD)		 等电点
pI		 染色体位置
Chromosome location (bp)		 亚细胞定位
Subcellular location		 外显子数
Exon number
Du1RN6D 84 9.94 10.94 A01: 38362763-38364266(+) 高尔基体 3
Du31JVP 149 15.88 8.67 A02: 93698897-93699375(+) 细胞核 2
DuJKM1G 139 14.92 10.16 A03: 1146898-1147314(+) 细胞核 1
Du3K3P7 431 46.58 8.32 A03: 26177414-26179364(-) 叶绿体 5
Du6M9JS 457 47.01 7.10 A04: 2833799-2835169(+) 细胞核 1
Du6MF1G 396 43.94 8.96 A04: 120573975-120575319(-) 叶绿体 3
DuJ06JT 333 36.36 6.55 A08: 32597179-32599158(-) 细胞核 3
Du0YU93 298 32.59 8.37 A10: 102683116-102684850(+) 细胞核 5
DuD4D3B 430 47.20 9.71 A10: 105227329-105229071(+) 细胞核 3
DuPG28A 164 18.21 10.46 A04: 119147168-119149150(+) 细胞核 3
IpH57JT 128 14.49 10.06 B01: 46465219-46466868(+) 细胞核 5
IpX255Z 140 15.04 10.35 B03: 3045361-3045780(+) 细胞核 1
IpY6QYT 284 31.38 9.05 B03: 23558367-23559380(-) 叶绿体 2
Ip4Z7UA 425 45.80 6.84 B03: 29032433-29034246(-) 细胞核 4
IpY5APX 456 47.15 7.14 B04: 4092175-4093542(+) 叶绿体 1
IpTU4HL 390 42.88 9.43 B04: 130737935-130739655(-) 细胞核 3
IpZ17TF 313 34.06 6.60 B08: 11054251-11056427(-) 细胞核 3
IpEDM7N 256 29.06 9.92 B10: 121980287-121981189(-) 细胞核 2
IpLUF2N 427 46.80 9.62 B10: 131879700-131881139(+) 细胞核 2
Hy3CY5UQ.1 244 27.51 10.53 1: 40133651-40137664(+) 细胞质和细胞核 6
Hy5LBE6G.1 477 53.18 7.54 1: 108380381-108382890(+) 细胞核 2
Hy6V3SWS.1 438 47.46 7.72 1: 111396243-111397559(+) 细胞核 1
HyNAZY29.1 138 14.94 10.16 3: 1322159-1322575(+) 细胞核 1
Hy7QL5S6.1 645 70.83 7.31 3: 28296178-28298188(-) 细胞核 2
HyJF9204.1 466 51.69 8.61 3: 141164292-141170983(-) 细胞核 4
HyJF9204.2 471 52.12 8.29 3: 141167176-141170983(-) 细胞核 1
HyABQ1RQ.1 496 51.40 7.35 4: 2968102-2969592(+) 细胞核 1
Hy47Q1NW.1 456 50.28 8.27 4: 126017493-126020268(-) 细胞核 3
HyXF5UIG.1 393 42.71 6.85 6: 101537588-101541638(-) 细胞核 6
HyD15RR9.1 352 38.54 6.63 8: 34637022-34640267(-) 细胞核 3
HyCX086V.1 448 47.76 8.94 9: 109849678-109852244(+) 细胞核 3
HyDG8AQJ.1 434 48.52 6.83 9: 110621159-110623060(-) 细胞核 4
HyU9727D.1 432 47.83 9.79 10: 105064759-105066057(-) 细胞核 1
HyN9U68C.1 351 38.55 8.92 10: 110274281-110276042(+) 细胞核 3
Hy18WYEQ.1 428 46.74 9.47 10: 112845226-112847602(+) 叶绿体 3
HyQ9YRAB.1 439 47.58 7.72 11: 123697432-123698751(-) 细胞核 1
HyM1TALC.1 131 14.16 10.16 13: 3108557-3109882(+) 细胞核 2
HyT0E7SC.1 658 72.68 6.73 13: 30175294-30177526(-) 细胞核 2
HyQI2904.1 469 52.34 8.09 13: 45539292-45541730(-) 细胞核 2
HyUL2QPJ.1 583 64.76 8.31 13: 144071693-144077814(-) 细胞核 6
HyUL2QPJ.2 457 50.64 9.21 13: 144072664-144077814(-) 细胞核 1
Hy22FU97.1 495 51.47 7.38 14: 4287692-4289179(+) 细胞核 1
HyQ1RL33.1 471 51.37 8.27 14: 140464278-140466478(-) 细胞核 3
HyKNN8RN.1 363 39.33 6.61 16: 132806525-132807987(-) 细胞核 4
HyQ2VML3.1 168 17.96 4.99 18: 4831951-4833441(-) 细胞核 2
Hy6TI82F.1 352 38.53 6.63 18: 12213609-12216824(-) 细胞核 3
HyI9FULJ.1 151 16.61 9.22 18: 47354288-47354743(+) 细胞核 1
HyW24P9U.1 266 27.84 10.39 19: 153036959-153037759(-) 细胞核 1
Hy5684ZR.1 379 39.72 6.11 19: 157994787-157997637(+) 细胞核 2
HyTU0X8W.1 410 45.48 6.82 19: 157353782-157355014(+) 细胞核 1
Hy46V6T7.1 428 46.70 9.34 20: 139422745-139425095(+) 叶绿体 3

图1

野生种（a）和栽培种（b）花生TCP家族基因的染色体分布

图2

花生与水稻TCP家族蛋白序列进化关系和亚组分类 黑色、蓝色和绿色弧线分别为PCF亚家族、CYC/TB1亚家族和CIN亚家族;Du表示Arachis duranensis,Ip表示Arachis ipaensis,Hy表示Arachis hypogaea,下同

图3

花生TCP家族基因的进化树及基因结构分析 黑色为PCF类,蓝色为CYC/TB1类,绿色为CIN类

图4

花生TCP家族蛋白保守结构域分析 (a)是花生51个TCP蛋白bHLH结构域的多序列比对;(b)是TCP保守基序组成

图5

花生TCP家族基因的组织表达模式

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