玉米miR395基因家族生物信息学分析及靶基因预测

doi:10.11924/j.issn.1000-6850.casb2021-0492

中国农学通报 ›› 2022, Vol. 38 ›› Issue (14): 30-37.doi: 10.11924/j.issn.1000-6850.casb2021-0492

所属专题：生物技术；玉米

玉米miR395基因家族生物信息学分析及靶基因预测

王丽¹^,²(), 路运才¹()

¹黑龙江大学现代农业与生态环境学院,哈尔滨 150080
²黑龙江省肇东市农业技术推广中心,黑龙江肇东 151100

收稿日期:2021-03-20 修回日期:2021-06-13 出版日期:2022-05-15 发布日期:2022-06-07
通讯作者: 路运才
作者简介:王丽,女,1996年出生,黑龙江双鸭山人,硕士,研究方向：玉米种质资源利用及逆境生理方面研究。通信地址：150080 黑龙江省哈尔滨市南岗区学府路74号黑龙江大学现代农业与生态环境学院,E-mail： 15764539804@163.com。
基金资助:
国家十三五重点研发计划“玉米分子设计育种”(2016YFD0101803);黑龙江省自然科学基金联合引导项目“利用连锁和关联分析发掘玉米抗低温出苗优异等位基因”(LH2019C056)

miR395 Gene Family in Maize: Bioinformatics Analysis and Target Gene Prediction

WANG Li¹^,²(), LU Yuncai¹()

¹College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin 150080
²Heilongjiang Zhaodong Agricultural Technology Extension Center, Zhaodong, Heilongjiang 151100

Received:2021-03-20 Revised:2021-06-13 Online:2022-05-15 Published:2022-06-07
Contact: LU Yuncai

摘要/Abstract

摘要：

MicroRNA(miRNA)具有调控基因表达的作用,为了揭示玉米miR395基因家族进化规律、表达模式及功能,开展了基因定位、多序列比对、顺式作用元件分析、二级结构分析、靶基因预测及表达模式分析。结果共鉴定到16个成员,且均集中分布在第2号、第10号染色体上;19个碱基完全相同,表明在进化过程中具有高度保守性;具有18个ABRE类顺式作用元件,推测其通过参与调节ABA信号传导,提高玉米抗逆性;多数靶向基因参与硫酸盐同化,初步推测玉米miR395基因家族参与玉米硫代谢;转录组分析发现zma-miR395基因家族中一些成员为下调表达模式。研究结果为后续玉米相关基因的功能解析奠定了基础。

关键词: 玉米, miR395基因家族, 生物信息学分析, 靶基因, 表达模式

Abstract:

MicroRNA (miRNA) has the function of regulating gene expression. In order to reveal the evolutionary rule, expression pattern and function of the maize miR395 gene family, we conducted gene mapping, multiple sequence alignment, cis-acting element analysis, secondary structure analysis, target gene prediction and analysis of expression pattern. The results showed that a total of 16 members were identified and all members were located on chromosome 2 and chromosome 10. 19 bases of zma-miR395 gene were identical, which proved that the gene family sequence was very conservative in evolution. There were 18 ABRE-type cis-acting elements, which were speculated to be involved in regulating ABA signaling to improve the maize resistance. Most of the targeted genes were involved in sulfate assimilation, and the zma-miR395 gene family participated in the sulfur metabolism of maize. Transcriptome data analysis showed that some members of the zma-miR395 gene family were down-regulated. The results can provide reference for the related maize gene function analysis.

Key words: maize, miR395 gene family, bioinformatics analysis, target gene, expression pattern

中图分类号:

S513

王丽, 路运才. 玉米miR395基因家族生物信息学分析及靶基因预测[J]. 中国农学通报, 2022, 38(14): 30-37.

WANG Li, LU Yuncai. miR395 Gene Family in Maize: Bioinformatics Analysis and Target Gene Prediction[J]. Chinese Agricultural Science Bulletin, 2022, 38(14): 30-37.

图/表 8

参考文献 31

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Mature miR395	Result
zma-miR395a-5p	--GUUCUCCUCAAACCACUUCAGUU
zma-miR395a-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395b-5p	--GUUCCCUACAAGC-ACUUCACAA
zma-miR395b-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395c-5p	--GUUCCCUGCAAAC-ACUUCACCA
zma-miR395c-3p	GUGAAGUGUUUGGAGGAACUC----
zma-miR395d-5p	--GUUCUAUGCAAGC-ACUUCACGA
zma-miR395d-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395e-5p	--GUUCCCUUCAAGC-ACUUCACAU
zma-miR395e-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395f-5p	--GUUACCUACAAGC-ACGUCUCGA
zma-miR395f-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395g-5p	--GUUCUAUGCAAGC-ACUUCACGA
zma-miR395g-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395h-5p	--GUUCCCUUCAAGC-ACUUCACAU
zma-miR395h-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395i-5p	--GUUCCCUACAAGC-ACUUCACGA
zma-miR395i-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395j-5p	--GUUCCCUUCAAGC-ACUUCACAU
zma-miR395j-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395k-5p	--GUUUCCUUCAAGC-ACUUCACAU
zma-miR395k-3p	GUGAAGUGUUUGAGGAAACUC----
zma-miR395l-5p	--GUUCCUUCCAAAC-ACUUCACCA
zma-miR395l-3p	GUGAAGUGUUUGGAGGAACUC----
zma-miR395m-5p	--GUUCCUUUCAAAC-ACUUCACAU
zma-miR395m-3p	GUGAAGUGUUUGGAGGAACUC----
zma-miR395n-5p	--GUUCUCUACAAGC-ACUUCACGA
zma-miR395n-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395o-5p	--GUUCUCUUCAAGC-ACUUCACGA
zma-miR395o-3p	GUGAAGUGUUUGGGUGAACUC----
zma-miR395p-5p	--GUUCCCUUCAAGC-ACUUCACAU
zma-miR395p-3p	GUGAAGUGUUUGGGGGAACUC----

Mature miR395	Result
zma-miR395a-5p	--GUUCUCCUCAAACCACUUCAGUU
zma-miR395a-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395b-5p	--GUUCCCUACAAGC-ACUUCACAA
zma-miR395b-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395c-5p	--GUUCCCUGCAAAC-ACUUCACCA
zma-miR395c-3p	GUGAAGUGUUUGGAGGAACUC----
zma-miR395d-5p	--GUUCUAUGCAAGC-ACUUCACGA
zma-miR395d-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395e-5p	--GUUCCCUUCAAGC-ACUUCACAU
zma-miR395e-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395f-5p	--GUUACCUACAAGC-ACGUCUCGA
zma-miR395f-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395g-5p	--GUUCUAUGCAAGC-ACUUCACGA
zma-miR395g-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395h-5p	--GUUCCCUUCAAGC-ACUUCACAU
zma-miR395h-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395i-5p	--GUUCCCUACAAGC-ACUUCACGA
zma-miR395i-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395j-5p	--GUUCCCUUCAAGC-ACUUCACAU
zma-miR395j-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395k-5p	--GUUUCCUUCAAGC-ACUUCACAU
zma-miR395k-3p	GUGAAGUGUUUGAGGAAACUC----
zma-miR395l-5p	--GUUCCUUCCAAAC-ACUUCACCA
zma-miR395l-3p	GUGAAGUGUUUGGAGGAACUC----
zma-miR395m-5p	--GUUCCUUUCAAAC-ACUUCACAU
zma-miR395m-3p	GUGAAGUGUUUGGAGGAACUC----
zma-miR395n-5p	--GUUCUCUACAAGC-ACUUCACGA
zma-miR395n-3p	GUGAAGUGUUUGGGGGAACUC----
zma-miR395o-5p	--GUUCUCUUCAAGC-ACUUCACGA
zma-miR395o-3p	GUGAAGUGUUUGGGUGAACUC----
zma-miR395p-5p	--GUUCCCUUCAAGC-ACUUCACAU
zma-miR395p-3p	GUGAAGUGUUUGGGGGAACUC----

	MYB	G-box	TGA-element	ABRE	ABRE3a	ABRE4	AC-II	STRE	W box	TCT-motif	WRE3	CCAAT-box
zma-miR395a	6	2	2	2	0	0	1	1	0	0	0	0
zma-miR395b	0	0	0	0	0	0	1	1	1	0	0	0
zma-miR395c	1	1	1	1	0	0	0	0	0	0	0	0
zma-miR395d	0	0	0	0	0	0	1	1	0	0	0	0
zma-miR395e	0	1	0	1	1	1	1	1	0	0	0	0
zma-miR395f	0	0	0	0	0	0	1	1	1	0	0	0
zma-miR395g	0	0	0	0	0	0	1	1	0	0	0	0
zma-miR395h	0	1	0	1	1	1	1	1	0	0	0	0
zma-miR395i	0	0	0	0	0	0	1	1	1	0	0	0
zma-miR395j	0	1	0	1	1	1	1	1	0	0	0	0
zma-miR395k	0	0	0	0	0	0	0	0	0	1	0	0
zma-miR395l	0	1	0	1	1	1	0	0	0	0	0	0
zma-miR395m	2	0	0	0	0	0	0	0	0	0	1	0
zma-miR395n	0	0	0	0	0	0	1	1	0	0	0	0
zma-miR395o	2	1	0	1	1	1	1	1	0	0	0	1
zma-miR395p	1	0	0	0	0	0	1	1	0	0	0	0
total	12	8	3	8	5	5	12	12	3	1	1	1

	MYB	G-box	TGA-element	ABRE	ABRE3a	ABRE4	AC-II	STRE	W box	TCT-motif	WRE3	CCAAT-box
zma-miR395a	6	2	2	2	0	0	1	1	0	0	0	0
zma-miR395b	0	0	0	0	0	0	1	1	1	0	0	0
zma-miR395c	1	1	1	1	0	0	0	0	0	0	0	0
zma-miR395d	0	0	0	0	0	0	1	1	0	0	0	0
zma-miR395e	0	1	0	1	1	1	1	1	0	0	0	0
zma-miR395f	0	0	0	0	0	0	1	1	1	0	0	0
zma-miR395g	0	0	0	0	0	0	1	1	0	0	0	0
zma-miR395h	0	1	0	1	1	1	1	1	0	0	0	0
zma-miR395i	0	0	0	0	0	0	1	1	1	0	0	0
zma-miR395j	0	1	0	1	1	1	1	1	0	0	0	0
zma-miR395k	0	0	0	0	0	0	0	0	0	1	0	0
zma-miR395l	0	1	0	1	1	1	0	0	0	0	0	0
zma-miR395m	2	0	0	0	0	0	0	0	0	0	1	0
zma-miR395n	0	0	0	0	0	0	1	1	0	0	0	0
zma-miR395o	2	1	0	1	1	1	1	1	0	0	0	1
zma-miR395p	1	0	0	0	0	0	1	1	0	0	0	0
total	12	8	3	8	5	5	12	12	3	1	1	1

miRNA_Acc.	Target_Acc.	Inhibition	Target_Desc.
zma-miR395a/b/d/e/f/g/h/i/j/o/p-3p	TC466492	Cleavage	Derlin4
zma-miR395b/i-5p	FL271305	Cleavage	Proline-rich protein verprolin
zma-miR395a/b/c/d/e/f/g/h/i/j/l/m/n/o/p-3p	TC476140	Cleavage	ATP sulfurylase
zma-miR395a/b/c/d/e/f/g/h/i/j/k/l/m/n/o/p-3p	FL283189	Cleavage
zma-miR395a/b/c/d/e/f/g/h/i/j/l/m/n/o/p-3p	FL290739	Cleavage
zma-miR395a/b/c/d/e/f/g/h/i/j/k/l/m/n/o/p-3p	FL331200	Cleavage
zma-miR395a/b/c/d/e/f/g/h/i/j/l/m/n/o/p-3p	CO462284	Cleavage
zma-miR395a/b/c/d/e/f/g/h/i/j/k/l/m/n/o/p-3p	TC476789	Cleavage
zma-miR395a/b/c/d/e/f/g/h/i/j/l/m/n/p-3p	TC511410	Cleavage	Photosystem I reaction center subunit VI
zma-miR395o-3p	FL440195	Cleavage	Glycosyltransferase
	CO454638	Cleavage
	TC458232	Cleavage
zma-miR395d/g-5p	TC494779	Translation	MYB-transcription factor 14
zma-miR395a/b/c/d/e/f/g/h/i/j/l/m/n/p-3p	FL044816	Cleavage	Alternative oxidase
zma-miR395a/b/c/d/e/f/g/h/i/j/l/m/n/p-3p	TC474095	Cleavage	Alternative oxidase
zma-miR395c/l/m-3p	CD976760	Cleavage	Casein kinase II subunit alpha
zma-miR395c-5p	TC461396	Translation	BHLH transcription factor PTF1
zma-miR395e/h/j/p-5p	TC541685	Translation	DNA-directed RNA polymerase

玉米miR395基因家族生物信息学分析及靶基因预测

miR395 Gene Family in Maize: Bioinformatics Analysis and Target Gene Prediction

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