Genome-wide identification and analysis of NCS1 gene family in upland cotton

doi:10.3969/j.issn.1004-1524.2023.02.01

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (2): 249-258.DOI: 10.3969/j.issn.1004-1524.2023.02.01

• Crop Science • Next Articles

Genome-wide identification and analysis of NCS1 gene family in upland cotton

JI Meijun(), CAO Ziyi, WANG Yiting, LU Jingru, WANG Baohua()

School of Life Sciences, Nantong University, Nantong 226019,Jiangsu, China

Received:2021-07-20 Online:2023-02-25 Published:2023-03-14
Contact: WANG Baohua

Abstract

Abstract:

The nucleobase-cation-symport-1 (NCS1) family is a family of secondary active transport proteins comprising over 2 500 sequenced members from bacteria, archaea, fungi and plants. In other studies, it has been found that these proteins are related to solute-specific transport, which in turn affects the growth and development of plants. The objective of this study is to reveal the role of nucleobase cation transporter in cotton growth and development. We identified NCS1 gene family members at the genome-wide level in upland cotton. Chromosome mapping, physical and chemical characterization, phylogenetic tree construction, gene structure analysis, and identification of promoter cis-acting elements were performed to systematically analyze members of the gene family. At the genome-wide level, we identified 4 upland cotton NCS1 genes. The chromosome mapping results showed that these genes are distributed on A09 and D09 two chromosomes. All NCS1 proteins have NCS1 domains according to the motif results. Gene structure analysis showed that the structure and length of introns and exons are consistent in the subgroups. Phylogenetic analysis among cotton, Arabidopsis, rice, maize and other species showed that the gene family had obvious differentiation during the evolution of species. Promoter sequence analysis showed that there are a large number of cis-acting elements related to abscisic acid and gibberellin responses in this gene family. qRT-PCR validation experiments were carried out on cotton fibers of 17 and 21 days post anthesis (dpa), and the results showed that NCS1 gene family members have a significant regulatory role in fiber development. This is the first study that the whole genome of NCS1 family has been identified and analyzed in upland cotton, which provides a theoretical basis for further exploration of nucleobase cation transporters on cotton growth and development.

Key words: upland cotton, bioinformatics, NCS1, gene family

CLC Number:

S562

JI Meijun, CAO Ziyi, WANG Yiting, LU Jingru, WANG Baohua. Genome-wide identification and analysis of NCS1 gene family in upland cotton[J]. Acta Agriculturae Zhejiangensis, 2023, 35(2): 249-258.

Figures/Tables 10

References 31

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基因名称 Gene name	上游引物 Forward primers(5'→3')	下游引物 Reverse primers(5'→3')
histidine3	GCCAAGCGTGTCACAATTATG	ACATCACATTGAACCTACCACTACC
Gh_A09G1345	GGTGGCATAGTCTTAGCA	CTGAAACCGACGATAGAA
Gh_A09G1346	TGGCATCTTCAGGTCAAT	AACCAACCAAGGCTCTAA
Gh_D09G1347	ACGATGACCTCAAGCCGACAA	CGCCAGGACAGGGAAAGA
Gh_D09G1348	AATGATGACCTCAAGCCGACAA	CACCCACAACAAACCAAAGCA

基因名称 Gene name	上游引物 Forward primers(5'→3')	下游引物 Reverse primers(5'→3')
histidine3	GCCAAGCGTGTCACAATTATG	ACATCACATTGAACCTACCACTACC
Gh_A09G1345	GGTGGCATAGTCTTAGCA	CTGAAACCGACGATAGAA
Gh_A09G1346	TGGCATCTTCAGGTCAAT	AACCAACCAAGGCTCTAA
Gh_D09G1347	ACGATGACCTCAAGCCGACAA	CGCCAGGACAGGGAAAGA
Gh_D09G1348	AATGATGACCTCAAGCCGACAA	CACCCACAACAAACCAAAGCA

物种 Species	基因名 Gene name	基因ID Gene ID	氨基酸数量 Amino acid length	亚细胞定位 Subcellular localization
陆地棉	GhNCS1	Gh_A09G1345	570	叶绿体,线粒体Chloroplast,mitochondrion
Gossypium hirsutum	GhNCS2	Gh_A09G1346	557	叶绿体,质膜Chloroplast, plasma membrane
	GhNCS3	Gh_D09G1347	573	叶绿体,线粒体Chloroplast,mitochondrion
	GhNCS4	Gh_D09G1348	554	叶绿体,质膜Chloroplast, plasma membrane
拟南芥Arabidopsis thaliana	ATNCS1	AT5G03555	599	质膜Plasma membrane
番茄Lycopersicon esculentum	SlNCS1	Solyc09g008550.3	501	质膜Plasma membrane
水稻Oryza sativa	OsNCS1	Os02g0666700	538	叶绿体,质膜Chloroplast, plasma membrane
玉米Zea mays	ZmNCS1	Zm00001d017531	541	质膜,叶绿体,细胞质
				Plasma membrane, chloroplast, cytoplasm
可可Theobroma cacao	TcNCS1	EOY08031	579	叶绿体Chloroplast
葡萄Vitis vinifera	VvNCS1	VIT_08s0007g04550.t01	511	叶绿体Chloroplast
高粱Sorghum bicolor	SBNCS1	KXG31048	544	质膜Plasma membrane

物种 Species	基因名 Gene name	基因ID Gene ID	氨基酸数量 Amino acid length	亚细胞定位 Subcellular localization
陆地棉	GhNCS1	Gh_A09G1345	570	叶绿体,线粒体Chloroplast,mitochondrion
Gossypium hirsutum	GhNCS2	Gh_A09G1346	557	叶绿体,质膜Chloroplast, plasma membrane
	GhNCS3	Gh_D09G1347	573	叶绿体,线粒体Chloroplast,mitochondrion
	GhNCS4	Gh_D09G1348	554	叶绿体,质膜Chloroplast, plasma membrane
拟南芥Arabidopsis thaliana	ATNCS1	AT5G03555	599	质膜Plasma membrane
番茄Lycopersicon esculentum	SlNCS1	Solyc09g008550.3	501	质膜Plasma membrane
水稻Oryza sativa	OsNCS1	Os02g0666700	538	叶绿体,质膜Chloroplast, plasma membrane
玉米Zea mays	ZmNCS1	Zm00001d017531	541	质膜,叶绿体,细胞质
				Plasma membrane, chloroplast, cytoplasm
可可Theobroma cacao	TcNCS1	EOY08031	579	叶绿体Chloroplast
葡萄Vitis vinifera	VvNCS1	VIT_08s0007g04550.t01	511	叶绿体Chloroplast
高粱Sorghum bicolor	SBNCS1	KXG31048	544	质膜Plasma membrane

基因 Gene	非同义替换率 Ka	同义替换率 Ks	选择压力比值 Ka/Ks
GhNCS2&GhNCS4	0.991436	1.02657	0.965776
GhNCS2&GhNCS1	0.982483	1.05538	0.930925
GhNCS2&GhNCS3	0.978506	1.0674	0.91672
GhNCS4&GhNCS1	0.983082	1.0533	0.933336
GhNCS4&GhNCS3	0.979421	1.06429	0.920259
GhNCS1&GhNCS3	0.006621	0.037711	0.175571

Genome-wide identification and analysis of NCS1 gene family in upland cotton

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