陆地棉NCS1基因家族的全基因组成员鉴定及分析

doi:10.3969/j.issn.1004-1524.2023.02.01

浙江农业学报 ›› 2023, Vol. 35 ›› Issue (2): 249-258.DOI: 10.3969/j.issn.1004-1524.2023.02.01

陆地棉NCS1基因家族的全基因组成员鉴定及分析

季美君(), 曹孜怡, 王翌婷, 陆静茹, 汪保华()

南通大学生命科学学院,江苏南通 226019

收稿日期:2021-07-20 出版日期:2023-02-25 发布日期:2023-03-14
作者简介:*汪保华,E-mail: bhwang@ntu.edu.cn
季美君(1998—),女,江苏盐城人,硕士研究生,主要研究棉花遗传育种。E-mail: jmj18360491501@163.com
通讯作者: 汪保华
基金资助:
国家重点研发计划(2021YFE0101200);国家自然科学基金(52161145104);大学生创新训练计划(2021117)

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

摘要/Abstract

摘要：

核碱基阳离子转运蛋白-1(NCS1)家族是一个次级活性转运蛋白家族,由细菌、古菌、真菌和植物等2 500多个序列成员组成。在其他研究中发现,该蛋白与溶质特异性转运相关,进而影响植物的生长发育,本研究拟通过分析揭示核碱基阳离子转运蛋白在棉花生长发育中的作用。通过全基因组序列分析鉴定陆地棉NCS1基因家族成员;在此基础上,对这些基因进行定位、结构分析、进化发育分析,并开展启动子顺式作用元件鉴定的系统研究。本研究在全基因组水平一共鉴定出4个陆地棉NCS1基因,染色体定位发现,这些基因分布在A09和D09两条染色体上,motif 结果显示所有NCS1蛋白质中都有NCS1结构域的存在,基因结构分析发现,外显子、内含子结构和长度在亚组表现一致。棉花、拟南芥、水稻、玉米等物种的系统发育分析比较表明,该基因家族在物种进化过程中出现了明显的分化。启动子序列分析则表明,该基因家族中存在有大量与脱落酸、赤霉素反应相关的顺式作用元件。取开花后17和21 d的棉花纤维开展qRT-PCR验证实验,结果表明,NCS1基因家族成员在纤维发育过程中具有显著的调节作用。本研究是首次在陆地棉中对NCS1家族进行全基因组的鉴定分析,为进一步探索核碱基阳离子转运蛋白对棉花生长发育的影响提供理论基础。

关键词: 陆地棉, 生物信息学, NCS1, 基因家族

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

中图分类号:

S562

季美君, 曹孜怡, 王翌婷, 陆静茹, 汪保华. 陆地棉NCS1基因家族的全基因组成员鉴定及分析[J]. 浙江农业学报, 2023, 35(2): 249-258.

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.

图/表 10

参考文献 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

陆地棉NCS1基因家族的全基因组成员鉴定及分析

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

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