Crops ›› 2021, Vol. 37 ›› Issue (2): 35-44.doi: 10.16035/j.issn.1001-7283.2021.02.005

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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 E-mail:wtwtp@126.com;chi000@126.com;13863920622@163.com

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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

Table 1

The information of TCP family genes in peanut"

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

Fig.1

Chromosome distribution of TCP family genes in wild (a) and cultivated (b) peanut"

Fig.2

Phylogenetic relationship and subgroup classification of peanut and rice TCP family proteins The curved lines with black, blue and green indicate the PCF, CYC/TB1 and CIN clade, respectively; Du represents Arachis duranensis, Ip represents Arachis ipaensis, Hy represents Arachis hypogaea. The same below"

Fig.3

Evolutionary tree and gene structure analysis of peanut TCP family genes Black is PCF clade, blue is CYC/TB1 clade, green is CIN clade"

Fig.4

Bioinformatics analysis of conserved domains of peanut TCP family proteins (a) is the multiple sequence alignment of 51 TCP proteins bHLH domain; (b) is motif logo of TCP conserved domains"

Fig.5

Tissues expression profiles of peanut TCP family genes"

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