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

doi:10.3969/j.issn.1004-1524.2022.01.09

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (1): 70-78.DOI: 10.3969/j.issn.1004-1524.2022.01.09

• Horticultural Science • Previous Articles Next Articles

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

Abstract

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

CLC Number:

S727.34

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.

Figures/Tables 7

References 30

[1]	JOVER-GIL S, CANDELA H, PONCE M R. Plant microRNAs and development[J]. The International Journal of Developmental Biology, 2005, 49(5/6): 733-744. DOI URL
[2]	XU L, WANG Y, ZHAI L L, et al. Genome-wide identification and characterization of cadmium-responsive microRNAs and their target genes in radish (Raphanus sativus L.) roots[J]. Journal of Experimental Botany, 2013, 64(14): 4271-4287. DOI URL
[3]	VOINNET O. Origin, biogenesis, and activity of plant MicroRNAs[J]. Cell, 2009, 136(4): 669-687. DOI URL
[4]	WAHEED S, ZENG L H. The critical role of miRNAs in regulation of flowering time and flower development[J]. Genes, 2020, 11(3): 319. DOI URL
[5]	LUO Y, GUO Z H, LI L. Evolutionary conservation of microRNA regulatory programs in plant flower development[J]. Developmental Biology, 2013, 380(2): 133-144. DOI URL
[6]	SHAMIMUZZAMAN M, VODKIN L. Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing[J]. BMC Genomics, 2012, 13: 310. DOI URL
[7]	李栋栋. 脱落酸调控草莓果实成熟的分子机理和关键miRNA调控因子的探究[D]. 杭州: 浙江大学, 2019.
	LI D D. The mechanism of abscisic acid regulated strawberry fruit ripening and identification of key miRNAs involved[D]. Hangzhou: Zhejiang University, 2019. (in Chinese with English abstract)
[8]	鲁海琴, 陈丽, 陈磊, 等. Bna-novel-miR311-HSC70-1模块调控甘蓝型油菜响应热胁迫的机制[J]. 作物学报, 2020, 46(10): 1474-1484. DOI
	LU H Q, CHEN L, CHEN L, et al. Mechanism research of Bna-novel-miR311-HSC70-1 module regulating heat stress response in Brassica napus L[J]. Acta Agronomica Sinica, 2020, 46(10): 1474-1484.(in Chinese with English abstract)
[9]	吴隽香, 刘益勇, 赵恩鹏, 等. 茄科蔬菜中miRNA响应低温胁迫研究进展[J]. 分子植物育种, 2021, 19(4): 1163-1168.
	WU J X, LIU Y Y, ZHAO E P, et al. Research progress on miRNA response to low temperature stress in Solanaceae vegetables[J]. Molecular Plant Breeding, 2021, 19(4): 1163-1168.(in Chinese with English abstract)
[10]	孟淑君, 张雪海, 王琪月, 等. 水稻根系盐胁迫响应miRNA和tRF的鉴定[J]. 中国农业科学, 2020, 53(4): 669-682.
	MENG S J, ZHANG X H, WANG Q Y, et al. Identification of miRNAs and tRFs in response to salt stress in rice roots[J]. Scientia Agricultura Sinica, 2020, 53(4): 669-682.(in Chinese with English abstract)
[11]	杨丽娟, 李世访, 卢美光. miRNA在植物病原调控方面的研究进展[J]. 生物技术通报, 2020, 36(1): 101-109. DOI
	YANG L J, LI S F, LU M G. miRNA-mediated Regulation Involved in Plant Pathogen[J]. Biotechnology Bulletin, 2020, 36(1): 101-109.(in Chinese with English abstract)
[12]	李昕晏, 崔杰, 李俊良, 等. miRNA调控植物抗逆机制的研究现状[J]. 江苏农业科学, 2019, 47(21): 63-66.
	LI X Y, CUI J, LI J L, et al. Research status of miRNA regulating plant stress resistance mechanism[J]. Jiangsu Agricultural Sciences, 2019, 47(21): 63-66.(in Chinese)
[13]	王劲东, 周豫, 余佳雯, 等. miR172-AP2模块调控植物生长发育及逆境响应的研究进展[J]. 植物学报, 2020, 55(2): 205-215. DOI
	WANG J D, ZHOU Y, YU J W, et al. Advances in the regulation of plant growth and development and stress response by miR172-AP2 module[J]. Chinese Bulletin of Botany, 2020, 55(2): 205-215.(in Chinese with English abstract)
[14]	PARK W, LI J J, SONG R T, et al. CARPEL FACTORY, a dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana[J]. Current Biology, 2002, 12(17): 1484-1495. DOI URL
[15]	GLAZIŃSKA P, ZIENKIEWICZ A, WOJCIECHOWSKI W, et al. The putative miR172 target gene InAPETALA2-like is involved in the photoperiodic flower induction of Ipomoea nil[J]. Journal of Plant Physiology, 2009, 166(16): 1801-1813. DOI URL
[16]	WANG L, SUN S Y, JIN J Y, et al. Coordinated regulation of vegetative and reproductive branching in rice[J]. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(50): 15504-15509.
[17]	LAUTER N, KAMPANI A, CARLSON S, et al. microRNA172 down-regulates glossy15 to promote vegetative phase change in maize[J]. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102(26): 9412-9417.
[18]	WANG Y W, LI P C, CAO X F, et al. Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules[J]. Biochemical and Biophysical Research Communications, 2009, 378(4): 799-803. DOI URL
[19]	MARTIN A, ADAM H, DÍAZ-MENDOZA M, et al. Graft-transmissible induction of potato tuberization by the microRNA miR172[J]. Development (Cambridge, England), 2009, 136(17): 2873-2881. DOI URL
[20]	ZHOU L G, LIU Y H, LIU Z C, et al. Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa[J]. Journal of Experimental Botany, 2010, 61(15): 4157-4168. DOI URL
[21]	ZHOU X F, WANG G D, SUTOH K, et al. Identification of cold-inducible microRNAs in plants by transcriptome analysis[J]. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 2008, 1779(11): 780-788.
[22]	HAN Y Y, ZHANG X, WANG W, et al. The suppression of WRKY44 by GIGANTEA-miR172 pathway is involved in drought response of Arabidopsis thaliana[J]. PLoS One, 2013, 8(11): e73541. DOI URL
[23]	HWANG E W, SHIN S J, PARK S C, et al. Identification of miR172 family members and their putative targets responding to drought stress in Solanum tuberosum[J]. Genes & Genomics, 2011, 33(2): 105-110.
[24]	张志翔. 中国林业出版社[M]. 北京: 中国林业出版社, 2008.
[25]	TAKENO S, BAMBA T, NAKAZAWA Y, et al. Quantification of trans-1, 4-polyisoprene in Eucommia ulmoides by Fourier transform infrared spectroscopy and pyrolysis-gas chromatography/mass spectrometry[J]. Journal of Bioscience and Bioengineering, 2008, 105(4): 355-359. DOI URL
[26]	黎云昆. 一个树种的国家战略[J]. 中国林业产业, 2011(7): 18-22.
	LI Y K. National strategy for a tree species[J]. China Forestry Industry, 2011(7): 18-22.(in Chinese)
[27]	WANG L, DU H Y, WUYUN T N. Genome-wide identification of MicroRNAs and their targets in the leaves and fruits of Eucommia ulmoides using high-throughput sequencing[J]. Frontiers in Plant Science, 2016, 7: 1632.
[28]	徐子涵, 胡凤荣. miR172参与植物发育调控的研究进展[J]. 生物技术通报, 2020, 36(8): 173-184. DOI
	XU Z H, HU F R. Research progress of miR172 in plant development and regulation[J]. Biotechnology Bulletin, 2020, 36(8): 173-184.(in Chinese with English abstract)
[29]	刘炜婳, 林玉玲, 林争春, 等. 植物miR172家族成员进化与分子特性分析[J]. 热带作物学报, 2018, 39(3): 525-533.
	LIU W H, LIN Y L, LIN Z C, et al. Analysis of evolution and molecular characteristics of miR172 family members in plants[J]. Chinese Journal of Tropical Crops, 2018, 39(3): 525-533.(in Chinese with English abstract)
[30]	李文静, 王杏茹, 刘涛, 等. 芥蓝miR172家族成员进化特性比较及时空表达分析[J]. 西北植物学报, 2018, 38(8): 1443-1450.
	LI W J, WANG X R, LIU T, et al. Evolutionary characteristics and analysis of miR172 family members in Chinese kale[J]. Acta Botanica Boreali-Occidentalia Sinica, 2018, 38(8): 1443-1450.(in Chinese with English abstract)

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

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

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