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

• 作物科学 • 下一篇

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
通讯作者: 汪保华
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
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

[1]	KRYPOTOU E, EVANGELIDIS T, BOBONIS J, et al. Origin, diversification and substrate specificity in the family of NCS1/FUR transporters[J]. Molecular Microbiology, 2015, 96(5): 927-950.
[2]	SIOUPOULI G, LAMBRINIDIS G, MIKROS E, et al. Cryptic purine transporters in Aspergillus nidulans reveal the role of specific residues in the evolution of specificity in the NCS1 family[J]. Molecular Microbiology, 2017, 103(2):319-332.
[3]	MA P, PATCHING S G, IVANOVA E, et al. Allantoin transport protein, PucI, from Bacillus subtilis: evolutionary relationships, amplified expression, activity and specificity[J]. Microbiology (Reading, England), 2016, 162(5):823-836.
[4]	SAIER M H, YEN M R, NOTO K, et al. The transporter classification database: recent advances[J]. Nucleic Acids Research, 2009, 37(suppl_1): D274-D278.
[5]	JACKSON S M, PATCHING S G, IVONOVA E, et al. Mhp1, the Na⁺-hydantoin membrane transport protein[M]//Encyclopedia of biophysics. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013: 1514-1521.
[6]	KAZMIER K, CLAXTON D P, MCHAOURAB H S. Alternating access mechanisms of LeuT-fold transporters: trailblazing towards the promised energy landscapes[J]. Current Opinion in Structural Biology, 2017, 45:100-108.
[7]	SHIMAMURA T, WEYAND S, BECKSTEIN O, et al. Molecular basis of alternating access membrane transport by the sodium-hydantoin transporter Mhp1[J]. Science, 2010, 328(5977): 470-473.
[8]	MOFFATT B A, ASHIHARA H. Purine and pyrimidine nucleotide synthesis and metabolism[J]. Frontiers in Bioscience, 2002, 1: e0018.
[9]	KAFER C, ZHOU L, SANTOSO D, et al. Regulation of pyrimidine metabolism in plants[J]. Frontiers in Bioscience: a Journal and Virtual Library, 2004, 9:1611-1625.
[10]	ZRENNER R, STITT M, SONNEWALD U, et al. Pyrimidine and purine biosynthesis and degradation in plants[J]. Annual Review of Plant Biology, 2006, 57:805-836.
[11]	ASHIHARA H, SANO H, CROZIER A. Caffeine and related purine alkaloids: Biosynthesis, catabolism, function and genetic engineering[J]. Phytochemistry, 2008, 69(4): 841-856.
[12]	FRÉBORT I, KOWALSKA M, HLUSKA T, et al. Evolution of cytokinin biosynthesis and degradation[J]. Journal of Experimental Botany, 2011, 62(8): 2431-2452.
[13]	GILLISSEN B, BÜRKLE L, ANDRÉ B, et al. A new family of high-affinity transporters for adenine, cytosine, and purine derivatives in Arabidopsis[J]. The Plant Cell, 2000, 12(2): 291-300.
[14]	BÜRKLE L, CEDZICH A, DÖPKE C, et al. Transport of cytokinins mediated by purine transporters of the PUP family expressed in phloem, hydathodes, and pollen of Arabidopsis[J]. The Plant Journal, 2003, 34(1): 13-26.
[15]	CEDZICH A, STRANSKY H, SCHULZ B, et al. Characterization of cytokinin and adenine transport in Arabidopsis cell cultures[J]. Plant Physiology, 2008, 148(4):1857-1867.
[16]	MANSFIELD T A, SCHULTES N P, MOURAD G S. AtAzg1 and AtAzg2 comprise a novel family of purine transporters in Arabidopsis[J]. FEBS Letters, 2009, 583(2): 481-486.
[17]	RAPP M, SCHEIN J, HUNT K A, et al. The solute specificity profiles of nucleobase cation symporter 1 (NCS₁) from Zea mays and Setaria viridis illustrate functional flexibility[J]. Protoplasma, 2016, 253(2):611-623.
[18]	FINN R D, COGGILL P, EBERHARDT R Y, et al. The Pfam protein families database: towards a more sustainable future[J]. Nucleic Acids Research, 2016, 44(D1): D279-D285.
[19]	VOORRIPS R E. MapChart: software for the graphical presentation of linkage maps and QTLs[J]. Journal of Heredity, 2002, 93(1):77-78.
[20]	WANG Y P, TANG H B, DEBARRY J D, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity[J]. Nucleic Acids Research, 2012, 40(7): e49.
[21]	BAILEY T L, WILLIAMS N, MISLEH C, et al. MEME: discovering and analyzing DNA and protein sequence motifs[J]. Nucleic Acids Research, 2006, 34(suppl_2): W369-W373.
[22]	HU B, JIN J P, GUO A Y, et al. GSDS 2.0: an upgraded gene feature visualization server[J]. Bioinformatics, 2015, 31(8):1296-1297.
[23]	ZHANG C H, RAIKHEL N V, HICKS G R. CLASPing microtubules and auxin transport[J]. Developmental Cell, 2013, 24(6): 569-571.
[24]	TAMURA K, STECHER G, PATERSON D, et al. MEGA6: molecular evolutionary genetics analysis version 6.0[J]. Molecular Biology and Evolution, 2013, 30(12):2725-2729.
[25]	LESCOT M, DÉHAIS P, THIJS G, et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences[J]. Nucleic Acids Research, 2002, 30(1):325-327.
[26]	FRILLINGOS S. Insights to the evolution of Nucleobase-Ascorbate Transporters (NAT/NCS₂ family) from the Cys-scanning analysis of xanthine permease XanQ[J]. International Journal of Biochemistry and Molecular Biology, 2012, 3(3): 250-272.
[27]	DIALLINAS G, GOURNAS C. Structure-function relationships in the nucleobase-ascorbate transporter (NAT) family: lessons from model microbial genetic systems[J]. Channels (Austin, Tex), 2008, 2(5): 363-372.
[28]	SCHEIN J R, HUNT K A, MINTON J A, et al. The nucleobase cation symporter 1 of Chlamydomonas reinhardtii and that of the evolutionarily distant Arabidopsis thaliana display parallel function and establish a plant-specific solute transport profile[J]. Plant Physiology and Biochemistry, 2013, 70: 52-60.
[29]	YOUND J D, YAO S Y M, BALDWIN J M, et al. The human concentrative and equilibrative nucleoside transporter families, SLC28 and SLC29[J]. Molecular Aspects of Medicine, 2013, 34(2/3): 529-547.
[30]	PAN W C, ZHENG P P, ZHANG C, et al. The effect of abre binding factor 4-mediated fyve 1 on salt stress tolerance in Arabidopsis[J]. Plant Science, 2020, 296:110489.
[31]	IMAN A, HUNTLEY R B, MOURAD G S, et al. Apple nucleobase cation symporter 1 transports guanine and the toxic guanine analog 6-thioguanine[J]. Physiological and Molecular Plant Pathology, 2020, 111:101492.

编辑推荐

Metrics

阅读次数

全文

680

HTML			PDF

最新录用	在线预览	正式出版	最新录用	在线预览	正式出版
0	0	129	0	0	551

来源	本网站	其他网站

次数	410	270
比例	60%	40%

摘要

305

最新录用	在线预览	正式出版

0	0	305

	来源	本网站

	次数	305
	比例	100%

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

RichHTML

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

图/表 10

参考文献 31

相关文章 15

编辑推荐

Metrics

本文评价

[1]	梁成刚, 汪燕, 关志秀, 韦春玉, 邓娇, 黄娟, 孟子烨, 石桃雄. 苦荞蔗糖转运体家族FtSUCs的鉴定与生物信息学分析[J]. 浙江农业学报, 2022, 34(8): 1591-1598.
[2]	向淅, 王思悦, 蒲俊宏, 唐雯璐, 陈清. 低温短日照诱导五叶草莓成花诱导的机理研究[J]. 浙江农业学报, 2022, 34(8): 1661-1668.
[3]	楚志刚, 田云芳. 蕙兰一个PEBP家族基因的克隆及生物信息学分析[J]. 浙江农业学报, 2022, 34(8): 1679-1691.
[4]	刘鹏程, 张继, 邱淦远, 龚俞, 李雪松, 李维, 张依裕, 刘若余. 关岭牛TBC1D7基因单核苷酸多态性筛查及生物信息学分析[J]. 浙江农业学报, 2022, 34(7): 1402-1411.
[5]	李文辰, 刘鑫, 齐泽铮, 于璐, 王芳. 灰皮支黑豆GmPUB24基因的生物信息学与胞囊线虫诱导表达分析[J]. 浙江农业学报, 2022, 34(6): 1124-1132.
[6]	刘凯, 谢楠, 郭炜, 马恒甲. 三角鲂MHCⅠα基因全长cDNA克隆与生物信息学分析[J]. 浙江农业学报, 2022, 34(6): 1162-1174.
[7]	夏煜琪, 孙宇, 刘志鑫, 孙瑞青, 杨楠, 蒲金基, 张贺. 杧果转录因子BES1s家族全基因组鉴定及生物信息学分析[J]. 浙江农业学报, 2022, 34(5): 984-994.
[8]	余艳玲, 罗洪林, 罗辉, 冯鹏霏, 潘传燕, 宋漫玲, 肖蕊, 张永德. 卵形鲳鲹生肌调节因子基因家族的鉴定及在胚胎中的表达[J]. 浙江农业学报, 2022, 34(4): 695-705.
[9]	刘同金, 徐铭婕, 汪精磊, 刘良峰, 崔群香, 包崇来, 王长义. 萝卜ALMT基因家族的鉴定与表达[J]. 浙江农业学报, 2022, 34(4): 746-755.
[10]	樊有存, 张红岩, 杨旭升, 韩芊, 刘玉皎, 武学霞. 蚕豆耐盐相关基因VfHKT1;1的克隆、生物信息学分析及表达特性[J]. 浙江农业学报, 2022, 34(4): 756-765.
[11]	李小兰, 张瑞, 郝兰兰, 王鸿. 桃NAC家族基因生物信息学分析及其响应低温胁迫的表达特征[J]. 浙江农业学报, 2022, 34(4): 766-780.
[12]	杨卫军, 董艳蕾, 吴秋芳, 张美玲, 韩丽滨, 张元臣. 棉蚜ATP合成酶基因AgoATPb的克隆与表达[J]. 浙江农业学报, 2022, 34(2): 329-336.
[13]	许金根, 靳二辉, 王重龙, 顾有方, 李庆岗. 猪CAST基因多态性与生物信息学分析[J]. 浙江农业学报, 2022, 34(1): 17-23.
[14]	蔡方阳, 赵懿琛, 李义, 赵德刚. 杜仲ABC转运蛋白基因家族成员鉴定与分析[J]. 浙江农业学报, 2021, 33(9): 1581-1591.
[15]	赵秀平, 王双, 闫星伊, 段强, 张帅, 陈永胜, 李国瑞. 稻瘟病菌MGG-01005的表达纯化与生物信息学分析[J]. 浙江农业学报, 2021, 33(3): 470-478.