Identification and Expression Pattern of<italic style="font-style: italic"> Salvia miltiorrhiza</italic> Terpenoid Synthase Gene Family

GAO Ying; JIANG Jinzhu; GAO Yingying; YANG Hongtao; LIU Xianju; LIU An

doi:10.13422/j.cnki.syfjx.20231612

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Identification and Expression Pattern of Salvia miltiorrhiza Terpenoid Synthase Gene Family

更新时间：2023-12-28

- Identification and Expression Pattern of Salvia miltiorrhiza Terpenoid Synthase Gene Family
- Chinese Journal of Experimental Traditional Medical Formulae Vol. 30, Issue 3, Pages: 142-151(2024)
- 作者机构：
  
  1.中国中医科学院中药研究所，北京 100700
  2.中国科学院植物研究所，北京 100093
  3.中国化学品安全协会，北京 100013
- 作者简介：
- 基金信息：
- DOI：10.13422/j.cnki.syfjx.20231612
  CLC： R284.2;R289;R287;R22;R2-031;R33;R24
- Published：05 February 2024，
  
  Published Online：20 November 2023，
  
  Received：14 August 2023，
- 稿件说明：
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高颖,姜金铸,高营营等.丹参萜类合酶基因家族的鉴定和表达模式分析[J].中国实验方剂学杂志,2024,30(03):142-151.

GAO Ying,JIANG Jinzhu,GAO Yingying,et al.Identification and Expression Pattern of Salvia miltiorrhiza Terpenoid Synthase Gene Family[J].Chinese Journal of Experimental Traditional Medical Formulae,2024,30(03):142-151.
高颖,姜金铸,高营营等.丹参萜类合酶基因家族的鉴定和表达模式分析[J].中国实验方剂学杂志,2024,30(03):142-151. DOI： 10.13422/j.cnki.syfjx.20231612.

GAO Ying,JIANG Jinzhu,GAO Yingying,et al.Identification and Expression Pattern of Salvia miltiorrhiza Terpenoid Synthase Gene Family[J].Chinese Journal of Experimental Traditional Medical Formulae,2024,30(03):142-151. DOI： 10.13422/j.cnki.syfjx.20231612.

摘要

目的

利用生物信息学方法从基因组层面对丹参萜类合酶（

SmTPS

）基因家族成员进行全面鉴定和功能预测。

方法

从国家基因组科学数据中心（NGDC）、美国国家生物技术信息中心（NCBI）、拟南芥信息资源中心（TAIR）和番茄功能基因组学数据库（TFGD）分别获取丹参、拟南芥和番茄基因组与转录组数据。借助Perl语言、TBtools等工具对

SmTPS

进行全基因组鉴定与生物信息学分析。

结果

共鉴定出52个TPS成员分布在丹参的8条染色体上；编码氨基酸数目在207~822 aa；等电点在4.76~9.16，分子质量为24.11~94.81 kDa，所有成员均为亲水蛋白。基因结构分析表明不同亚族成员之间内含子数差异明显，72.6% TPS-a、TPS-b、TPS-g亚族成员为6，88.9% TPS-c、TPS-e/f亚族成员

10；蛋白motif相对保守。顺式作用元件分析表明，

SmTPSs

启动子区均含有大量光响应元件，大多数

SmTPSs

启动子区含有激素响应元件。基因表达模式分析显示

SmTPS

家族成员存在组织表达特异性，24个基因响应外源茉莉酸甲酯。

结论

基于已发表丹参基因组，鉴定得到52个

SmTPS

家族成员，结合系统进化与表达模式对其功能进行了预测。该文为丹参中萜类化合物生物合成及调控机制全面解析提供了参考信息。

Abstract

Objective

Bioinformatics methods were used to systematically identify the

Salvia miltiorrhiza

terpenoid synthase （

SmTPS

）

gene family members and predict their functions from the perspective of the genome.

Method

The genome and transcriptome data of

S. miltiorrhiza

，

Arabidopsis thaliana

， and tomato were obtained from the national genomics data center （NGDC）， national center for biotechnology information （NCBI）， the

Arabidopsis

information resource （TAIR）， and tomato functional genomics database （TFGD）， and the whole genome identification and bioinformatics analysis of the

SmTPS

gene family member were carried out with the help of Perl language programming， Tbtools， and other bioinformatics tools.

Result

A total of 52

TPS

gene family members were identified， and they were distributed on eight chromosomes of

S. miltiorrhiza

. Their coding amino acid number was 207-822 aa. The isoelectric points were 4.76-9.16. The molecular mass was 24.11-94.81 kDa， and all members are hydrophilic proteins. Gene structure analysis showed that there were significant differences in the number of introns among different subfamilies. The number of introns in 72.6% of TPS-a， b， and g subfamilies was 6， and that in 88.9% of TPS-c and e/f subfamilies was more than 10. Protein motifs were conserved among TPS subfamilies. The analysis of promoter

cis

-acting elements showed that all promoters of the

SmTPSs

contained a large number of light-responsive elements， and most of them had hormone-responsive elements. Gene expression analysis showed that

SmTPS

gene family members exhibited tissue-specific expression， and 24 of them responded to exogenous methyl jasmonate.

Conclusion

Based on the published

S. miltiorrhiza

genome， 52

SmTPS

gene family members were identified， and their functions were predicted based on the phylogenetic analysis and expression patterns. This paper provides reference information for the further biosynthesis pathway and regulatory mechanism analysis of terpenoids in

S. miltiorrhiza.

关键词

丹参萜类合酶（TPS）生物信息学功能分析基因家族

Keywords

Salvia miltiorrhizaterpenoid synthase （TPS）bioinformaticsfunction analysisgene family

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Identification and Expression Pattern of Salvia miltiorrhiza Terpenoid Synthase Gene Family

DOI：10.13422/j.cnki.syfjx.20231612

摘要

Abstract

关键词

Keywords

references