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中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志
中国生物工程杂志  2023, Vol. 43 Issue (1): 1-17    DOI: 10.13523/j.cb.2209054
研究报告     
决明GRAS基因家族全基因组鉴定及其在盐和干旱胁迫条件下的表达分析
冯昭*(),刘世鹏,覃洋
陕西中医药大学医学技术学院 咸阳 712046
Genome-wide Identification of GRAS Gene Family in Senna tora L. and Its Expression Analysis under Salt and Drought Stress
FENG Zhao*(),LIU Shi-peng,QIN Yang
College of Medical Technology, Shaanxi University of Chinese Medicine, Xianyang 712046, China
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摘要：

目的: 基于决明(Senna tora L.)全基因组数据,对GRAS家族成员、理化性质、基因结构、进化关系以及胁迫条件下的表达模式进行鉴定和分析。方法: 将决明基因组蛋白数据与拟南芥GRAS成员进行比对,分别利用TBtools、MEGA-X、CLUSTALW、MEME等生物信息学软件和工具,对决明GRAS基因家族成员进行分析。利用qRT-PCR(quantitative real-time PCR)检测干旱和盐胁迫条件下决明根中GRAS基因的表达情况。结果: 50个StGRAS分为9个亚家族,不均等地分布在13条染色体上。结构分析表明,StGRAS34和StGRAS12分别与蒺藜苜蓿(Medicago truncatula)结瘤信号蛋白NSP1和NSP2高度同源。StGRAS的启动子区域多含有与胁迫响应、激素调节等相关的响应元件。qRT-PCR结果表明,在盐胁迫条件下,StGRAS表达具有明显差异;在干旱胁迫条件下,绝大多数检测基因能够快速响应,表达显著升高;两种胁迫条件下,StGRAS28和StGRAS29表达趋势互补,具有协同调控关系。结论: GRAS基因家族能够广泛参与胁迫响应,其中StGRAS28与StGRAS29可能共同参与介导决明根的盐与干旱胁迫应答,StGRAS34和StGRAS12分别作为决明共生结瘤的NSP1和NSP2,可能与增强结瘤因子信号诱导相关,这为进一步挖掘和研究GRAS基因在决明响应胁迫和共生固氮过程所发挥的作用提供了基础。
关键词： 决明;  GRAS基因家族;  基因表达分析;  盐胁迫;  干旱胁迫    
Abstract:

Objective: Based on the whole-genome data of Cassia (Senna tora L.), this study aimed to identify and analyze the physicochemical properties, gene structure, evolutionary relationship, and expression patterns of its GRAS gene family members under stress conditions. Methods: The S. tora genomic protein data were compared with Arabidopsis GRAS members using bioinformatics software and websites such as TBtools, MEGA-X, CLUSTALW, and MEME to analyze the S. tora GRAS gene family members. The expression of GRAS genes in the root under drought and salt stress conditions was examined using qRT-PCR (quantitative real-time PCR). Results: 50 StGRAS were unequally distributed on 13 chromosomes and divided into 9 subfamilies. Structural analysis showed that StGRAS34 and StGRAS12 are highly homologous to Medicago truncatula nodulation signaling proteins NSP1 and NSP2, respectively. The promoter region of StGRAS contained many elements related to stress response and hormone regulation. qRT-PCR showed that StGRAS expression was significantly different under salt stress conditions; under drought stress conditions, most of the detected genes were able to respond rapidly with significantly higher expression, and the expression trends of StGRAS28 and StGRAS29 were complementary with synergistic regulation under both salt and drought stress conditions. Conclusion: The GRAS gene family is widely involved in stress response, among which StGRAS28 and StGRAS29 may be jointly involved in mediating salt and drought stress response in S. tora root. StGRAS34 and StGRAS12, as NSP1 and NSP2 of S. tora symbiotic nodulation, respectively, may be associated with enhanced nodulation factor signal induction, which provides a basis for further exploration and study of the role of GRAS genes in S. tora response to stress and symbiotic nitrogen fixation.
Key words: Senna tora L.    GRAS gene family    Gene expression analysis    Salt stress    Drought stress
收稿日期: 2022-09-20 出版日期: 2023-02-14
ZTFLH:  Q78R282  
通讯作者: *冯昭 电子信箱:fengzhao2018@163.com   
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引用本文:

冯昭, 刘世鹏, 覃洋. 决明GRAS基因家族全基因组鉴定及其在盐和干旱胁迫条件下的表达分析[J]. 中国生物工程杂志, 2023, 43(1): 1-17.

FENG Zhao, LIU Shi-peng, QIN Yang. Genome-wide Identification of GRAS Gene Family in Senna tora L. and Its Expression Analysis under Salt and Drought Stress. China Biotechnology, 2023, 43(1): 1-17.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2209054    或    https://manu60.magtech.com.cn/biotech/CN/Y2023/V43/I1/1

Gene Gene ID Forward primer sequence(5'→3') Reverse primer sequence(5'→3') Size/bp
StGRAS11 Sto05g121000 GCGATCTGTTGGAGGCCT CCCCAGGACGGCAATTGA 140
StGRAS12 Sto05g121870 AACGCCTTGCACGCTTTG CGGTGAAGTGGGCGAACT 139
StGRAS13 Sto05g134220 CTGCTCCAGTTTGGCGGA CGTGCCTTTCCACTCGGT 113
StGRAS14 Sto05g160010 ACGGGCGAAGTGAAGGTG GGGTTTCCCCGAAGCGAA 80
StGRAS15 Sto05g160250 TGGGTTTGGGAATGTGCACT GTGACCTGTCCTGCCAGC 134
StGRAS20 Sto06g185380 CCCCGCATCCGTATCACC TGGACAGCCTCTTCCCGA 82
StGRAS22 Sto06g198020 ACTCCAACCAACGCCTCG GTGTGGGTGTGGATGGGG 109
StGRAS23 Sto06g199910 CTCCGACGATCTTCCGCC CACACCCCGACGAAACGA 149
StGRAS26 Sto07g218070 CCCTTCGGTGATGGGTCG TTGGGTTCCAGCACCAGC 87
StGRAS28 Sto07g225180 TCAAACGGGTCGGGAAGC ACACAGGAATCGCCGGTC 106
StGRAS29 Sto07g227960 GCTCCATTCCCTCCTCGC CTGCTGATGGACCACCCG 112
StGRAS30 Sto08g235890 GTGTCGGGGTTCTGTCGG GCAACCTACCCTCTCGGC 83
StGRAS33 Sto08g255120 TGGTCGAGCAAGAAGGCG GCCGCGAAGTAATGCAGC 94
StGRAS42 Sto11g369400 CACGACCACGACGGAACA GCGACGTTTCTGGAGGCT 125
StGRAS45 Sto12g376020 TGTTCTGCTGCTGCTGGC CCGGGGAAGAAGGCTTGG 94
表1  qRT-PCR引物
Gene Gene ID CDS
length/bp		 Protein
length/aa		 Molecular
mass/kDa		 pI Subcellular localization
StGRAS1 Sto01g017730 1 824 607 66.71 5.51 Nuclear
StGRAS2 Sto01g020800 2 181 726 78.26 5.67 Nuclear
StGRAS3 Sto01g021890 2 268 755 85.73 5.34 Nuclear
StGRAS4 Sto02g028340 2 562 853 96.29 5.85 Nuclear
StGRAS5 Sto03g062080 2 169 722 102.51 6.26 Nuclear
StGRAS6 Sto03g066880 1 518 505 56.96 5.97 Nuclear
StGRAS7 Sto04g087560 1 968 655 73.02 6.06 Nuclear
StGRAS8 Sto04g088080 1 731 576 65.52 5.89 Cytoplasmic
StGRAS9 Sto04g090370 2 244 747 84.88 5.19 Nuclear
StGRAS10 Sto04g113810 2 097 698 76.95 5.22 Nuclear
StGRAS11 Sto05g121000 1 887 628 70.05 4.74 Nuclear
StGRAS12 Sto05g121870 1 398 465 51.60 5.51 Nuclear
StGRAS13 Sto05g134220 1 458 485 52.54 5.15 Nuclear
StGRAS14 Sto05g160010 1 362 453 49.13 5.38 Mitochondrion
StGRAS15 Sto05g160250 1 401 466 52.66 5.90 Nuclear
StGRAS16 Sto05g160270 1 506 501 56.30 6.19 Extracellular
StGRAS17 Sto06g164970 2 199 732 80.93 5.32 Nuclear
StGRAS18 Sto06g166670 1 899 632 71.03 5.00 Nuclear
StGRAS19 Sto06g168190 2 361 786 88.84 5.99 Nuclear
StGRAS20 Sto06g185380 1 809 602 67.97 5.84 Endomembrane system
StGRAS21 Sto06g197830 2 733 910 101.33 6.15 Cytoplasmic
StGRAS22 Sto06g198020 2 469 822 92.04 8.43 Nuclear
StGRAS23 Sto06g199910 1 539 512 57.26 6.55 Chloroplast
StGRAS24 Sto07g209900 2 049 682 76.36 7.16 Chloroplast
StGRAS25 Sto07g218030 1 902 633 72.33 6.63 Nuclear
StGRAS26 Sto07g218070 2 445 814 91.98 5.12 Nuclear
StGRAS27 Sto07g218090 2 328 775 87.23 6.14 Nuclear
StGRAS28 Sto07g225180 2 301 766 86.16 5.98 Nuclear
StGRAS29 Sto07g227960 1 752 583 65.84 6.69 Endomembrane system
StGRAS30 Sto08g235890 2 250 749 84.60 6.28 Nuclear
StGRAS31 Sto08g238980 3 120 1 039 118.57 6.15 Nuclear
StGRAS32 Sto08g248410 2 031 676 74.54 5.55 Chloroplast
StGRAS33 Sto08g255120 1 467 488 55.32 6.35 Nuclear
StGRAS34 Sto09g280170 1 803 600 66.51 6.09 Nuclear
StGRAS35 Sto09g304260 1 935 644 70.34 5.47 Nuclear
StGRAS36 Sto09g307310 1 782 593 66.25 4.97 Chloroplast
StGRAS37 Sto09g308510 2 832 943 104.65 6.05 Cytoplasmic
Gene Gene ID CDS
length/bp		 Protein
length/aa		 Molecular
mass/kDa		 pI Subcellular localization
StGRAS38 Sto10g341020 2 043 680 75.11 6.19 Nuclear
StGRAS39 Sto11g354210 1 902 633 70.35 5.92 Nuclear
StGRAS40 Sto11g366550 1 317 438 48.33 5.85 Chloroplast
StGRAS41 Sto11g366710 1 536 511 57.93 6.03 Extracellular
StGRAS42 Sto11g369400 1 965 654 73.38 6.09 Chloroplast, thylakoid, membrane
StGRAS43 Sto12g374940 1 890 629 71.10 5.82 Cytoplasmic
StGRAS44 Sto12g376000 2 052 683 76.52 5.52 Nuclear
StGRAS45 Sto12g376020 2 322 773 87.33 5.42 Nuclear
StGRAS46 Sto12g376040 2 241 746 84.58 6.11 Nuclear
StGRAS47 Sto12g379970 3 138 1 045 117.69 8.74 Nuclear
StGRAS48 Sto13g429550 1 659 552 61.38 5.63 Nuclear
StGRAS49 Sto13g440380 1 593 530 60.70 5.39 Nuclear
StGRAS50 Sto13g440390 2 706 901 102.51 6.26 Endomembrane system
表2  决明GRAS基因家族理化性质及亚细胞定位信息
图1  决明与拟南芥、水稻、蒺藜苜蓿、大豆GRAS基因家族系统发育树分析
图2  决明GRAS家族基因结构和保守基序分析
图3  决明GRAS家族保守结构域序列比对
图4  StGRAS基因染色体分布
图5  决明种内GRAS基因片段重复分析
图6  决明分别与拟南芥、水稻、蒺藜苜蓿、大豆的GRAS基因家族共线性分析
图7  决明GRAS基因启动子顺式作用元件分析
图8  决明StGRAS34、StGRAS12分别与蒺藜苜蓿和大豆NSP1、NSP2蛋白质三级结构
图9  决明StGRASs在不同组织及不同生长发育阶段的表达热图
图10  经盐和干旱处理后20 d对照与处理植株的生长表型与根毛生长情况
图11  经盐处理后0~24 h 15个StGRASs在决明根中的相对表达量
图12  经干旱处理后0~24 h 15个StGRASs在决明根中的相对表达量
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