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

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

Abstract

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

CLC Number:

S513

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.

Figures/Tables 8

References 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