杜仲miR172基因家族的生物信息学分析与功能预测

doi:10.3969/j.issn.1004-1524.2022.01.09

浙江农业学报 ›› 2022, Vol. 34 ›› Issue (1): 70-78.DOI: 10.3969/j.issn.1004-1524.2022.01.09

杜仲miR172基因家族的生物信息学分析与功能预测

叶靖(), 杨元玲, 史庆秋, 吴龙飞, 宋国涛^*()

石河子大学农学院林学系,新疆石河子 832003

收稿日期:2020-08-21 出版日期:2022-01-25 发布日期:2022-02-05
通讯作者: 宋国涛
作者简介:* 宋国涛,E-mail: sgtendeavor@hotmail.com
叶靖(1986—),男,重庆长寿人,博士,副教授,研究方向为林木遗传育种。E-mail: yejing@nwafu.edu.cn
基金资助:
石河子大学高层次人才科研启动项目(RCZK201948)

Bioinformatics analysis and function prediction of miR172 gene family in Eucommia ulmoides

YE Jing(), YANG Yuanling, SHI Qingqiu, WU Longfei, SONG Guotao^*()

Department of Forestry, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China

Received:2020-08-21 Online:2022-01-25 Published:2022-02-05
Contact: SONG Guotao

摘要/Abstract

摘要：

为了解杜仲 miR172 家族成员的进化特征及其在杜仲生长发育过程中的作用。从杜仲小RNA高通量测序结果(登录号:SRP216820)及已发表文献中获取杜仲miR172家族前体和成熟体序列,进行序列比对、WebLogo保守性分析、系统发育树构建、前体茎环结构预测、启动子结构分析、靶基因预测及功能预测。结果表明,杜仲miR172家族共有8条前体和8条成熟体序列,且前体序列均能形成稳定的茎环结构;序列比对和 WebLogo 分析表明,除eu-miR172d-5p以外的其他7个成员的成熟体序列保守性较高,但前体序列的保守性均较低;进化分析表明,该家族成熟体进化高度保守,而前体的进化保守性较低;启动子分析表明,杜仲miR172家族启动子包含丰富的光反应原件及激素响应元件和胁迫响应元件,说明其可能调控杜仲的花器官形成和发育及逆境胁迫响应等过程;靶基因预测表明,杜仲miR172家族的靶基因数目较多,其靶基因参与杜仲的生长发育和逆境胁迫等过程,该小RNA家族成员主要调控AP2基因的表达。表明杜仲miR172家族成员在进化过程中既保守又有一定分化,其主要通过调控AP2基因的表达在杜仲生长发育过程中发挥重要调控作用。

关键词: 杜仲, miR172 家族, 进化特征, 靶基因

Abstract:

To understand the evolutionary characteristics of the miR172 family members and their role in the growth and development of Eucommia ulmoides, the precursor and mature sequences of miR172 family were collected from the high-throughput sequencing results (accession number:SRP216820) and published literature related to E. ulmoides. In addition, sequence alignment, WebLogo conservation analysis, phylogenetic tree construction, precursor stem-loop structure prediction, promoter structure analysis, target gene prediction and functional prediction were performed. The E. ulmoides miR172 family contains 8 precursor sequences and 8 mature sequences, and all precursor sequences can form a stable stem-loop structure. Sequence alignment and WebLogo analysis showed that 7 mature sequences (except eu-miR172d-5p) were highly conservative, however the precursor sequences were less conservative. Evolutionary analysis showed that the mature sequences of this family were highly conservative, but the precursor sequences were less conservative. Promoter analysis showed that the E. ulmoides miR172 family promoters contained abundant photoreaction components and hormone response elements and stress response elements, indicating that they may regulate the process of flower organ formation and stress response. Target gene prediction showed that there were many target genes for miR172 family of E. ulmoides, and they were involved in E. ulmoides growth and development and adversity stress, but the miR172 family members mainly regulated the expression of AP2 genes. The E. ulmoides miR172 family members were both conservative and differentiated during evolution, and they play an important regulatory roles in the growth and development of E. ulmoides by regulating AP2 expression.

Key words: Eucommia ulmoides, miR172 family, evolutionary characteristics, target gene

中图分类号:

S727.34

叶靖, 杨元玲, 史庆秋, 吴龙飞, 宋国涛. 杜仲miR172基因家族的生物信息学分析与功能预测[J]. 浙江农业学报, 2022, 34(1): 70-78.

YE Jing, YANG Yuanling, SHI Qingqiu, WU Longfei, SONG Guotao. Bioinformatics analysis and function prediction of miR172 gene family in Eucommia ulmoides[J]. Acta Agriculturae Zhejiangensis, 2022, 34(1): 70-78.

图/表 7

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miRNA名称 miRNA name	光照 Light	干旱 Drought	生物逆境 Biotic stress	激素 Hormone	分生组织表达 Meristem expression	缺氧 Anoxic	昼夜节律控制 Circadian control	类黄酮生物合成 Flavonoid biosynthetic	胚乳表达 Endosperm expression
eu-miR172a	GT1-motif, MRE, Box 4, TCT-motif, LAMP-element, AT1-motif, AE-box,	—	—	TCA-element	—	ARE	—	MBSI	GCN4_motif
eu-miR172a-3p	Sp1, GT1-motif, Box 4, GA-motif, chs-CMA2a, chs-CMA1a, LAMP-element,	MBS	TC-rich repeats	—	CAT-box	ARE	circadian	—	—
eu-miR172b-3p	Sp1, GT1-motif, Box 4, GA-motif, chs-CMA2a, chs-CMA1a, LAMP-element,	MBS	TC-rich repeats	—	CAT-box	ARE	circadian	—	—
eu-miR172c	Box 4, GA-motif, chs-CMA1a, chs-CMA2a, LAMP-element,	MBS	TC-rich repeats	—	CAT-box	ARE	circadian	—	—
eu-miR172c-3p	GT1-motif, MRE, Box 4, TCT-motif, LAMP-element, AT1-motif, AE-box,	MBS	—	TCA-element	—	ARE	—	MBSI	GCN4_motif
eu-miR172d-5p	GT1-motif, Box 4, ATC-motif, GATA-motif, I-box, TCT-motif, AE-box	—	TC-rich repeats	SARE, TCA-element, AuxRR-core	—	—	—	—	—
eu-miR172e-3p	GT1-motif, MRE, Box 4, I-box, TCT-motif, GATA-motif, AE-box	—	TC-rich repeats	SARE, TCA-element, AuxRR-core	—	—	—	—	—
eu-miR172j	GT1-motif, MRE, Box 4, TCCC-motif, LAMP-element, TCT-motif	—	—	TCA-element	—	—	—	MBSI	GCN4_motif

miRNA名称 miRNA name	光照 Light	干旱 Drought	生物逆境 Biotic stress	激素 Hormone	分生组织表达 Meristem expression	缺氧 Anoxic	昼夜节律控制 Circadian control	类黄酮生物合成 Flavonoid biosynthetic	胚乳表达 Endosperm expression
eu-miR172a	GT1-motif, MRE, Box 4, TCT-motif, LAMP-element, AT1-motif, AE-box,	—	—	TCA-element	—	ARE	—	MBSI	GCN4_motif
eu-miR172a-3p	Sp1, GT1-motif, Box 4, GA-motif, chs-CMA2a, chs-CMA1a, LAMP-element,	MBS	TC-rich repeats	—	CAT-box	ARE	circadian	—	—
eu-miR172b-3p	Sp1, GT1-motif, Box 4, GA-motif, chs-CMA2a, chs-CMA1a, LAMP-element,	MBS	TC-rich repeats	—	CAT-box	ARE	circadian	—	—
eu-miR172c	Box 4, GA-motif, chs-CMA1a, chs-CMA2a, LAMP-element,	MBS	TC-rich repeats	—	CAT-box	ARE	circadian	—	—
eu-miR172c-3p	GT1-motif, MRE, Box 4, TCT-motif, LAMP-element, AT1-motif, AE-box,	MBS	—	TCA-element	—	ARE	—	MBSI	GCN4_motif
eu-miR172d-5p	GT1-motif, Box 4, ATC-motif, GATA-motif, I-box, TCT-motif, AE-box	—	TC-rich repeats	SARE, TCA-element, AuxRR-core	—	—	—	—	—
eu-miR172e-3p	GT1-motif, MRE, Box 4, I-box, TCT-motif, GATA-motif, AE-box	—	TC-rich repeats	SARE, TCA-element, AuxRR-core	—	—	—	—	—
eu-miR172j	GT1-motif, MRE, Box 4, TCCC-motif, LAMP-element, TCT-motif	—	—	TCA-element	—	—	—	MBSI	GCN4_motif

miRNA 名称 miRNA name	靶基因ID Target ID	功能注释 Functional annotation
eu-miR172e-3p, eu-miR172j, eu-miR172a, eu-miR172a-3p, eu-miR172b-3p, eu-miR172c, eu-miR172c-3p	c138631.graph_c1	AP2转录因子Transcription factor APETALA2 (AP2)
eu-miR172a, eu-miR172a-3p, eu-miR172b-3p, eu-miR172c, eu-miR172c-3p, eu-miR172j	c138848.graph_c4	泛素羧基末端水解酶12 Ubiquitin carboxyl-terminal hydrolase 12 (UBP12)
eu-miR172e-3p, eu-miR172j	c135016.graph_c0	tRNA (鸟嘌呤(9)-N1)-甲基转移酶 tRNA (guanine(9)-N1)-methyltransferase
eu-miR172a, eu-miR172a-3p, eu-miR172b-3p, eu-miR172c, eu-miR172c-3p, eu-miR172e-3p	c131305.graph_c0	rho GTPase激活蛋白7亚型X2 rho GTPase-activating protein 7 isoform X2
eu-miR172a, eu-miR172a-3p, eu-miR172b-3p, eu-miR172c, eu-miR172c-3p, eu-miR172e-3p, eu-miR172j	c134382.graph_c0	长链酰基辅酶A合成酶6,过氧化物酶 Long chain acyl-CoA synthetase 6, peroxisoma
eu-miR172a, eu-miR172a-3p, eu-miR172b-3p, eu-miR172c, eu-miR172c-3p	c129479.graph_c0	乙酰氨基葡萄糖氨基转移酶活性 Acetylglucosaminyltransferase activity
eu-miR172c-3p	c136450.graph_c1	ATP绑定,锌离子绑定ATP binding, zinc ion binding
eu-miR172d-5p	c124598.graph_c0	RNA绑定,核糖体结构与生物发生RNA binding, structural constituent of ribosome
eu-miR172e-3p, eu-miR172j	c124042.graph_c0	同源盒亮氨酸拉链蛋白REVOLUTA Homeobox-leucine zipper protein REVOLUTA
eu-miR172j, eu-miR172j	c138622.graph_c0	抗病蛋白RPS6 Disease resistance protein RPS6
eu-miR172e-3p, eu-miR172j	c136215.graph_c5	转录调节因子ATRX Transcriptional regulator ATRX
eu-miR172e-3p	c138257.graph_c2	磷脂:二酰基甘油酰基转移酶1 Phospholipid: diacylglycerol acyltransferase 1
eu-miR172j	c137029.graph_c0	钙调神经磷酸酶样磷酸酯酶 Calcineurin-like phosphoesterase
eu-miR172j	c93630.graph_c0	假设蛋白K437DRAFT_294601 Hypothetical protein K437DRAFT_294601

miRNA 名称 miRNA name	靶基因ID Target ID	功能注释 Functional annotation
eu-miR172e-3p, eu-miR172j, eu-miR172a, eu-miR172a-3p, eu-miR172b-3p, eu-miR172c, eu-miR172c-3p	c138631.graph_c1	AP2转录因子Transcription factor APETALA2 (AP2)
eu-miR172a, eu-miR172a-3p, eu-miR172b-3p, eu-miR172c, eu-miR172c-3p, eu-miR172j	c138848.graph_c4	泛素羧基末端水解酶12 Ubiquitin carboxyl-terminal hydrolase 12 (UBP12)
eu-miR172e-3p, eu-miR172j	c135016.graph_c0	tRNA (鸟嘌呤(9)-N1)-甲基转移酶 tRNA (guanine(9)-N1)-methyltransferase
eu-miR172a, eu-miR172a-3p, eu-miR172b-3p, eu-miR172c, eu-miR172c-3p, eu-miR172e-3p	c131305.graph_c0	rho GTPase激活蛋白7亚型X2 rho GTPase-activating protein 7 isoform X2
eu-miR172a, eu-miR172a-3p, eu-miR172b-3p, eu-miR172c, eu-miR172c-3p, eu-miR172e-3p, eu-miR172j	c134382.graph_c0	长链酰基辅酶A合成酶6,过氧化物酶 Long chain acyl-CoA synthetase 6, peroxisoma
eu-miR172a, eu-miR172a-3p, eu-miR172b-3p, eu-miR172c, eu-miR172c-3p	c129479.graph_c0	乙酰氨基葡萄糖氨基转移酶活性 Acetylglucosaminyltransferase activity
eu-miR172c-3p	c136450.graph_c1	ATP绑定,锌离子绑定ATP binding, zinc ion binding
eu-miR172d-5p	c124598.graph_c0	RNA绑定,核糖体结构与生物发生RNA binding, structural constituent of ribosome
eu-miR172e-3p, eu-miR172j	c124042.graph_c0	同源盒亮氨酸拉链蛋白REVOLUTA Homeobox-leucine zipper protein REVOLUTA
eu-miR172j, eu-miR172j	c138622.graph_c0	抗病蛋白RPS6 Disease resistance protein RPS6
eu-miR172e-3p, eu-miR172j	c136215.graph_c5	转录调节因子ATRX Transcriptional regulator ATRX
eu-miR172e-3p	c138257.graph_c2	磷脂:二酰基甘油酰基转移酶1 Phospholipid: diacylglycerol acyltransferase 1
eu-miR172j	c137029.graph_c0	钙调神经磷酸酶样磷酸酯酶 Calcineurin-like phosphoesterase
eu-miR172j	c93630.graph_c0	假设蛋白K437DRAFT_294601 Hypothetical protein K437DRAFT_294601

杜仲miR172基因家族的生物信息学分析与功能预测

Bioinformatics analysis and function prediction of miR172 gene family in Eucommia ulmoides

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