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基于冬凌草全长转录组的TIFY基因家族鉴定与表达分析

练从龙 兰金旭 杨晶凡 李晶晶 杨灏 陈随清

练从龙,兰金旭,杨晶凡,等. 基于冬凌草全长转录组的TIFY基因家族鉴定与表达分析 [J]. 福建农业学报,2024,39(X):1−12
引用本文: 练从龙,兰金旭,杨晶凡,等. 基于冬凌草全长转录组的TIFY基因家族鉴定与表达分析 [J]. 福建农业学报,2024,39(X):1−12
LIAN C L, LAN J X, YANG J F, et al. Identification and Expression Analysis of TIFY Gene Family in Isodon rubescens [J]. Fujian Journal of Agricultural Sciences,2024,39(X):1−12
Citation: LIAN C L, LAN J X, YANG J F, et al. Identification and Expression Analysis of TIFY Gene Family in Isodon rubescens [J]. Fujian Journal of Agricultural Sciences,2024,39(X):1−12

基于冬凌草全长转录组的TIFY基因家族鉴定与表达分析

基金项目: 河南省科技研发计划联合基金项目(优势学科培育类)(232301420078);河南省中药材产业技术体系(豫农科教[2018]14号);2019年中医药公共卫生服务补助专项“全国中药资源普查项目”(豫财社[2019]40号)
详细信息
    作者简介:

    练从龙(1988 — ),男,博士,讲师,主要从事药用植物生理生态与分子生物学研究,E-mail:770379183@qq.com

    通讯作者:

    陈随清(1965 — ),男,博士,教授,主要从事中药资源与质量评价研究,E-mail:chsq@hactcm.edu.cn

  • 中图分类号: R286

Identification and Expression Analysis of TIFY Gene Family in Isodon rubescens

  • 摘要:   目的  TIFY 蛋白是JA信号通路的关键调节因子,在植物生长发育、非生物胁迫以及次生代谢产物的积累中具有显著的调控作用。揭示冬凌草的TIFY基因可为冬凌草的抗逆性改良育种和次生代谢产物合成研究提供理论依据。  方法  基于冬凌草三代全长转录组序列,通过生物信息学方法对冬凌草TIFY基因家族进行鉴定和分析,并采用RT-qPCR 技术分析其不同组织中的表达特性。  结果  (1)成功从冬凌草中共鉴定出12个TIFY家族基因成员;(2)理化性质分析表明其氨基酸长度范围是124~378 aa;分子量大小为13 924.89~39 692.38 Da;等电点的范围5.05~9.69;除IrTIFY10为稳定蛋白,其他均为不稳定蛋白;IrTIFYs的亚细胞定位均在细胞核,均为亲水性蛋白,且不含信号肽。(3)结构分析表明IrTIFY家族蛋白成员无跨膜结构,二级结构中含量最多的结构类型为无规则卷曲;且含有多个磷酸化位点。(4)密码子偏好性分析结果表明IrTIFY基因家族密码子偏好性较弱,稍倾向于使用以A或U结尾的密码子;(5)启动子元件分析表明冬凌草TIFY家族成员中存在多个光响应元件、激素响应元件、和逆境响应元件等,但不同成员之间的元件存在差异。(6)进化树分析表明冬凌草TIFY家族12个成员分为PPD(IrTIFY2)、ZML(IrTIFY3/8/10)、TIFY(IrTIFY7/12)和JAZ(IrTIFY1/4/5/6/9/11)4个亚家族,进化上与同为唇形科的丹参(Salvia miltiorrhiza)亲缘关系最近。(7)RT-qPCR分析结果显示冬凌草TIFY家族12个成员在不同组织中的表达量均表现为叶>茎>根,且大部分成员存在显著差异。  结论  基于以上结果,推测TIFY基因家族在对冬凌草的生长发育过程中发挥重要的调控作用,并且可能参与调控冬凌草次生代谢产物的合成,为进一步深入研究冬凌草TIFY基因家族的功能奠定基础和提供思路。
  • 图  1  冬凌草TIFY家族蛋白三级结构预测分析

    (A) IrTIFY1蛋白;(B) IrTIFY2蛋白;(C) IrTIFY3蛋白;(D) IrTIFY4蛋白;(E) IrTIFY5蛋白;(F) IrTIFY6蛋白;(G) IrTIFY7蛋白;(H) IrTIFY8蛋白;(I) IrTIFY9蛋白;(J) IrTIFY10蛋白;(K) IrTIFY11蛋白;(L) IrTIFY12蛋白

    Figure  1.  Tertiary structure prediction analysis of TIFY protein family in I. rubescens

    (A) IrTIFY1 protein;(B) IrTIFY2 protein;(C) IrTIFY3 protein;(D) IrTIFY4 protein;(E) IrTIFY5 protein;(F) IrTIFY6 protein;(G) IrTIFY7 protein;(H) IrTIFY8 protein;(I) IrTIFY9 protein;(J) IrTIFY10 protein;(K) IrTIFY11 protein;(L) IrTIFY12 protein

    图  2  冬凌草TIFY家族蛋白保守结构域比对分析

    Figure  2.  Alignment analysis of the conserved domain of TIFY family proteins of I. rubescens

    图  3  冬凌草TIFY家族蛋白结构域可视化分析

    Figure  3.  Visualization of conserved protein domain analysis of TIFY protein family in I. rubescens

    图  4  冬凌草TIFY家族蛋白保守基序

    Figure  4.  Schematic diagram of conserved protein motif analysis of TIFY protein family in I. rubescens

    图  5  冬凌草TIFY家族成员启动子元件分析

    Figure  5.  Cis-element analysis of TIFYs promoters in I. rubescens

    图  6  冬凌草TIFY家族系统树分析

    Ir:冬凌草;At:拟南芥;Sm:丹参;Os:水稻。

    Figure  6.  Phylogenetic trees of TIFY gene family in I. rubescens

    Ir:Isodon rubescens;At:Arabidopsis thaliana;Sm:Salvia miltiorrhiza;Os:Oryza sativa; Ptr: Populus trichocarpa.

    图  7  冬凌草TIFY家族成员的不同组织表达分析

    小写字母代表在 0.05 水平上差异显著。

    Figure  7.  Expressions of TIFYs in different organs of I. rubescens plant

    Data with lowercase letters represent significant differences at P<0.05.

    表  1  荧光定量 PCR 引物序列

    Table  1.   Primer sequences for fluorescent quantitative PCR

    基因名称
    Gene name
    正向引物序列(5′-3′)
    Forward primer sequence
    (5′-3′)
    反向引物序列(5′-3′)
    Reverse primer sequence
    (5′-3′)
    UBQ CTGAGGCTTCGTGGAGGGAT TGTAGTCTGCAAGAGTCCTT
    IrTIFY1 TGTCACCCCTTTCGTTCACC AGTCATCGGAGGGCCATTTC
    IrTIFY2 TTGATAAGCCGCTCCACCAG TTTCCGCCTCACCAGTTGTT
    IrTIFY3 CGAGAACTGGGATTCAGGCA TGTTCGCCCACATTAACCCA
    IrTIFY4 ACGGAAAGCATCTCTGGCTC ACCTGCATTCTTGCTCTGGT
    IrTIFY5 ACGCTTGGCTTCACTCCTAC CCTCGGGCTTAATCTGGGTC
    IrTIFY6 GCCGCTCCAAATTCAGAGGA TCCGGAGGGTTCAACTACCA
    IrTIFY7 GCGATCATATCGTTGGCGAG GCGATCTCTTCATCGACAGC
    IrTIFY8 GGGGAACAGATGGCAATGGA CGGCGCATCATTGGAGTAGA
    IrTIFY9 AGGAGGCAACCAGGGAAATC CATTGAGGGCTGGGGTTGAG
    IrTIFY10 TATGATGCGACGTGGACCAG TAATGGCGTTTGCAGGAGGT
    IrTIFY11 ATTACGTCGAGGGCCATTCC ACTCGTGCTCGGGTTCATTT
    IrTIFY12 TGGGTAGTTTGAGCAGGCAG CCGGCTCCAACTCCAATCAA
    下载: 导出CSV

    表  2  冬凌草TIFY家族蛋白理化性质分析

    Table  2.   Physicochemical properties of TIFY protein family in I. rubescens

    基因名称
    Gene name
    转录组基因ID
    Gene ID in transcriptome
    长度
    Length/aa
    分子量
    molecular weight/Da
    等电点
    Isoelectric point
    不稳定指数
    Instability index
    脂肪族指数
    Aliphatic index
    亲水性平均值
    Grand average of hydropathicity
    IrTIFY1 D-tissues_transcript_12000 356 37,515.67 9.01 58.96 76.97 −0.169
    IrTIFY2 D-tissues_transcript_12412 344 37,381.18 8.09 50.35 69.22 −0.633
    IrTIFY3 D-tissues_transcript_13824 343 37,606.01 5.05 49.03 66.56 −0.567
    IrTIFY4 D-tissues_transcript_14652 299 31,555.55 8.59 56.46 58.83 −0.438
    IrTIFY5 D-tissues_transcript_15941 229 24,182.28 7.81 53.98 72.71 −0.315
    IrTIFY6 D-tissues_transcript_16425 173 18,692.28 8.99 41.53 75.78 −0.409
    IrTIFY7 D-tissues_transcript_17017 124 13,924.89 9.69 66.65 77.26 −0.473
    IrTIFY8 D-tissues_transcript_27842 299 32,514.88 6.17 40.31 58.66 −0.819
    IrTIFY9 D-tissues_transcript_48324 250 27,235.7 8..93 68.06 66.4 −0.634
    IrTIFY10 D-tissues_transcript_51903 300 32,486.03 5.63 37.71 59.2 −0.761
    IrTIFY11 D-tissues_transcript_53470 273 29,436.81 9.15 56.22 65.79 −0.778
    IrTIFY12 D-tissues_transcript_57396 378 39,692.38 9.22 46.47 46.8 −0.815
    下载: 导出CSV

    表  3  冬凌草TIFY家族蛋白二级结构分析

    Table  3.   Secondary structure analysis of TIFY protein family in I. rubescens

    基因名称
    Gene name
    转录组基因ID
    Gene ID in transcriptome
    α-螺旋
    α-helix/%
    延伸链
    Extension/%
    β-转角
    β-angle/%
    无规则卷曲
    Random curling/%
    IrTIFY1 D-tissues_transcript_12000 11.24 12.36 2.53 73.88
    IrTIFY2 D-tissues_transcript_12412 19.77 7.56 3.2 69.48
    IrTIFY3 D-tissues_transcript_13824 22.45 10.79 5.83 60.93
    IrTIFY4 D-tissues_transcript_14652 12.04 11.37 2.68 73.91
    IrTIFY5 D-tissues_transcript_15941 17.9 12.66 4.37 65.07
    IrTIFY6 D-tissues_transcript_16425 23.12 13.29 5.78 57.8
    IrTIFY7 D-tissues_transcript_17017 27.56 11.81 5.51 55.12
    IrTIFY8 D-tissues_transcript_27842 19.06 11.71 4.68 64.55
    IrTIFY9 D-tissues_transcript_48324 20 7.6 4 68.4
    IrTIFY10 D-tissues_transcript_51903 18 13.33 4.67 64
    IrTIFY11 D-tissues_transcript_53470 13.92 6.59 2.93 76.56
    IrTIFY12 D-tissues_transcript_57396 7.41 12.43 2.65 77.51
    下载: 导出CSV

    表  4  冬凌草TIFY蛋白磷酸化位点、信号肽、跨膜结构和亚细胞定位分析

    Table  4.   Phosphorylation site, signal peptide, transmembrane structure and subcellular localization analysis of TIFY protein family in I. rubescens

    基因名称
    Gene name
    磷酸化位点
    Phosphorylation
    sites
    丝氨酸
    Serine
    苏氨酸
    Threonine
    酪氨酸
    Tyrosine
    信号肽值
    Signal peptides
    value
    有无信号肽
    Signal peptides
    跨膜位置
    Trsns membrane
    localization
    跨膜结构数
    Trsns membrane
    domain
    亚细胞定位
    Subcellular
    localization
    IrTIFY1 54 32 20 2 0.001 无 no 膜外outside 0 细胞核 Nuclear
    IrTIFY2 44 25 16 3 0.0007 无 no 膜外 outside 0 细胞核 Nuclear
    IrTIFY3 38 20 17 1 0.0007 无 no 膜外 outside 0 细胞核 Nuclear
    IrTIFY4 36 29 6 1 0.0005 无 no 膜外 outside 0 细胞核 Nuclear
    IrTIFY5 20 18 2 0 0.0013 无 no 膜外 outside 0 细胞核 Nuclear
    IrTIFY6 18 14 4 0 0.0018 无 no 膜外 outside 0 细胞核 Nuclear
    IrTIFY7 18 13 4 1 0.0014 无 no 膜外 outside 0 细胞核 Nuclear
    IrTIFY8 27 18 9 0 0.0011 无 no 膜外 outside 0 细胞核 Nuclear
    IrTIFY9 32 25 5 2 0.0012 无 no 膜外 outside 0 细胞核 Nuclear
    IrTIFY10 33 20 10 2 0.0022 无 no 膜外 outside 0 细胞核 Nuclear
    IrTIFY11 38 32 6 0 0.0035 无 no 膜外 outside 0 细胞核 Nuclear
    IrTIFY12 59 41 16 2 0.0011 无 no 膜外 outside 0 细胞核 Nuclear
    下载: 导出CSV

    表  5  冬凌草TIFY家族蛋白密码子偏好性分析

    Table  5.   Codon bias analysis of TIFY protein family in I. rubescens

    基因名称
    Gene name
    转录组基因号
    Gene ID in transcriptome
    有效密码子数
    ENC
    GC/% GC1s/% GC2s/% GC3s/%
    IrTIFY1 D-tissues_transcript_12000 50.869 44.06 47.06 44.85 40.26
    IrTIFY2 D-tissues_transcript_12412 55.717 46.92 45.85 50.19 44.72
    IrTIFY3 D-tissues_transcript_13824 59.099 45.66 46.24 42.37 48.39
    IrTIFY4 D-tissues_transcript_14652 54.066 43.83 43.44 39.62 48.45
    IrTIFY5 D-tissues_transcript_15941 55.686 48.84 47.13 52.27 47.13
    IrTIFY6 D-tissues_transcript_16425 52.629 46.55 44.21 44.21 51.23
    IrTIFY7 D-tissues_transcript_17017 54.526 43.25 39.22 37.93 52.59
    IrTIFY8 D-tissues_transcript_27842 58.699 44.06 42.25 48.49 41.45
    IrTIFY9 D-tissues_transcript_48324 50.617 40.31 37.7 42.67 40.58
    IrTIFY10 D-tissues_transcript_51903 53.436 49.66 50.77 50.26 47.96
    IrTIFY11 D-tissues_transcript_53470 56.905 43.92 42.18 41.19 48.39
    IrTIFY12 D-tissues_transcript_57396 60.714 46.35 49.59 38.39 51.07
    下载: 导出CSV
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出版历程
  • 收稿日期:  2023-10-11
  • 修回日期:  2023-12-02
  • 网络出版日期:  2024-03-28

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