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。
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. Themolecular mass was 24.11-94.81 kDa, and all members are hydrophilic proteins. Gene structure analysis showedthat there were significant differences in the number of introns among different subfamilies. The number ofintrons 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 morethan 10. Protein motifs were conserved among TPS subfamilies. The analysis of promoter cis-acting elementsshowed that all promoters of the SmTPSs contained a large number of light-responsive elements, and most ofthem had hormone-responsive elements. Gene expression analysis showed that SmTPS gene family membersexhibited 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 theirfunctions were predicted based on the phylogenetic analysis and expression patterns. This paper providesreference information for the further biosynthesis pathway and regulatory mechanism analysis of terpenoids in S.miltiorrhiza.
作者
高颖
姜金铸
高营营
杨洪涛
刘先菊
刘安
GAO Ying;JIANG Jinzhu;GAO Yingying;YANG Hongtao;LIU Xianju;LIU An(Institute of Chinese Materia Medica,China Academy of Chinese Medical Sciences,Beijing 100700,China;Institute of Botany,Chinese Academy of Sciences,Beijing 100093,China;China Chemical Safety Association,Beijing 100013,China)
出处
《中国实验方剂学杂志》
CAS
CSCD
北大核心
2024年第3期142-151,共10页
Chinese Journal of Experimental Traditional Medical Formulae
基金
国家自然科学基金项目(32202415)
中国中医科学院科技创新工程项目(CI2021A04404,CI2021A04405)
中国中医科学院优秀青年科技人才(创新类)培养专项(ZZ14-YQ-029)
中央公益性科研院所基本科研业务费专项(ZXKT22002)。
关键词
丹参
萜类合酶(TPS)
生物信息学
功能分析
基因家族
Salvia miltiorrhiza
terpenoid synthase(TPS)
bioinformatics
function analysis
gene family
