陆地棉抗坏血酸过氧化物酶基因家族全基因组生物信息学分析

doi:10.11963/issn.1002-7807.201701003

棉花学报 ›› 2017, Vol. 29 ›› Issue (1): 17-28.doi: 10.11963/issn.1002-7807.201701003

陆地棉抗坏血酸过氧化物酶基因家族全基因组生物信息学分析

刘娜^1,^*,*(),吴金华^1,^2,^*,*(),安亚茹¹,杨君¹,张艳¹,王省芬¹,马峙英^1,^2,^*()

1. 河北农业大学农学院/教育部华北作物种质资源研究与利用重点实验室/河北省作物种质资源重点实验室,河北保定 071001
2. 河北农业大学作物学博士后科研流动站,河北保定 071001

收稿日期:2016-03-03 出版日期:2017-01-15 发布日期:2017-01-15
通讯作者: 刘娜,吴金华,马峙英 E-mail:liu_na_1991@126.com;nxywjh@126.com;mzhy@mail.hebau.edu.cn
作者简介:刘娜（1991―），女，硕士研究生，liu_na_1991@126.com；吴金华，nxywjh@126.com
基金资助:
国家自然科学基金(31401426);河北省自然科学基金（C2015204060）;河北农业大学作物学科梯队建设基金（TD2016C319）

Bioinformatics Analysis of the Ascorbate Peroxidase Gene Family in the Gossypium hirsutum L. Genome

Liu Na^1,^*,*(), Wu Jinhua^1,^2,^*,*(), An Yaru¹, Yang Jun¹, Zhang Yan¹, Wang Xingfen¹, Ma Zhiying^1,^2,^*()

1. College of Agronomy of Hebei Agricultural University / North China Key Laboratory for Crop Germplasm Resources of the Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei, Baoding, Hebei 071001, China
2. Postdoctoral Research Station of Crop Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China

Received:2016-03-03 Online:2017-01-15 Published:2017-01-15
Contact: Na Liu,Jinhua Wu,Zhiying Ma E-mail:liu_na_1991@126.com;nxywjh@126.com;mzhy@mail.hebau.edu.cn

摘要/Abstract

摘要： 目的抗坏血酸过氧化物酶（Ascorbate peroxidase,APX）是过氧化物酶家族中的1类成员,可以清除活性氧。APX家族的生物信息学分析有助于更好地了解该家族基因。方法利用生物信息学方法,从中国农业科学院棉花研究所提供的陆地棉序列中鉴定出14条APX基因家族序列,并对这14个成员的染色体定位、亚细胞定位、进化关系、理化性质、信号肽、保守基序以及其编码蛋白的结构特征进行了预测分析,并初步分析了部分基因的表达。结果 APX基因分布广泛,分散在不同的染色体上;且大部分APX蛋白定位在细胞质,是亲水性脂溶蛋白;有3个保守基序,保守性较强;基因起源和进化比较复杂;二级结构的主要元件为α-螺旋和无规则卷曲。根据表达分析推测,第1亚组和第2亚组的基因在棉纤维发育的不同时期起作用。结论这些结果有望为APX家族成员的结构与功能挖掘提供参考。

关键词: 陆地棉; APX基因家族; 生物信息学分析; 纤维发育

Abstract:

[Objective] Ascorbate peroxidase (APX) is a type of peroxidase, which can scavenge reactive oxygen species. The objective of this study was to further characterize the APX gene families. [Method] Using bioinformatics methods, we identified 14 members of the APX gene family using the Gossypium hirsutum L. genomic sequence provided by the Institute of Cotton Research of the Chinese Academy of Agricultural Sciences. Systematic analyses focused on chromosome locations, subcellular localizations, evolutionary relationships, physicochemical properties, structure, and the presence of signal peptides and conserved motifs. Preliminary expression analyses were completed for selected genes related to fiber development. [Results] The APX gene family members were distributed on almost all chromosomes. Most of the encoded hydrophilic and lipid-soluble enzymes were localized to the cytoplasm. They had three conserved motifs, and the associated gene sequences were highly conserved. The origin and evolution of the APX genes was complex. Additionally, the predicted secondary structures of the main motifs consisted of α-helices and random coils. Genes in the first and second subgroups were speculated to affect different cotton fiber development stages. [Conclusion] These results may be useful for future studies of the structures and functions of APX family members.

Key words: Gossypium hirsutum L.; APX gene family; bioinformatics analysis; fiber development

刘娜, 吴金华, 安亚茹, 杨君, 张艳, 王省芬, 马峙英. 陆地棉抗坏血酸过氧化物酶基因家族全基因组生物信息学分析[J]. 棉花学报, 2017, 29(1): 17-28.

Liu Na, Wu Jinhua, An Yaru, Yang Jun, Zhang Yan, Wang Xingfen, Ma Zhiying. Bioinformatics Analysis of the Ascorbate Peroxidase Gene Family in the Gossypium hirsutum L. Genome[J]. Cotton Science, 2017, 29(1): 17-28.

0
/ / 推荐

导出引用管理器 EndNote|Reference Manager|ProCite|BibTeX|RefWorks

链接本文: https://journal.cricaas.com.cn/Jweb_mhxb/CN/10.11963/issn.1002-7807.201701003

https://journal.cricaas.com.cn/Jweb_mhxb/CN/Y2017/V29/I1/17

参考文献

[1]	Caverzan A, Passaia G, Rosa S B, et al.Plant responses to stresses: role of ascorbate peroxidase in the antioxidant protection[J]. Genetics and Molecular Biology, 2012, 35(4): 1011-1019.
[2]	Mittler R, Vanderauwera S, Suzuki N, et al.ROS signaling: the new wave[J]. Trends Plant Science, 2011, 16(6): 300-309.
[3]	Mittler R, Vanderauwera S, Gollery M, et al.Reactive oxygen gene network of plants[J]. Trends Plant Science, 2004, 9(10): 490-498.
[4]	Mittler R.Oxidative stress, antioxidants and stress tolerance[J]. Trends Plant Science, 2002, 7(9): 405-410.
[5]	张维静, 陆海, 杜希华. 抗坏血酸过氧化物酶在植物抵抗氧化胁迫中的作用[J]. 山东师范大学学报(自然科学版), 2008, 23(4): 113-115.
[5]	Zhang Weijing, Lu Hai, Du Xihua.The function of ascorbate peroxidases in plant resistance to oxidative stress[J]. Journal of Shandong Normal University (Natural Science), 2008, 23(4): 113-115.
[6]	苗雨晨, 白玲, 苗琛, 等. 植物谷胱甘肽过氧化物酶研究进展[J]. 植物学通报, 2005, 22(3): 350-356.
[6]	Miao Yuchen, Bai Ling, Miao Chen, et al.Progress in plant glutathione peroxidase[J]. Chinese Bulletin of Botany, 2005, 22(3): 350-356.
[7]	Mathews M C, Summers C B, Felton G W.Ascorbate peroxidase: a novel antioxidant enzyme in insects[J]. Archive of Insect Biochemistry and Physiology, 1997, 34(1): 57-68.
[8]	Shigeoka S, Ishikawa T, Tamoi M, et al.Regulation and function of ascorbate peroxidase isoenzymes[J]. Journal of Experimental Botany, 2002, 53(372): 1305-1319.
[9]	Panchuk II, Volkov RA, Schoeffl F.Heat stress and heat shock transcription factor-dependent expression and activity of ascorbate peroxidase in Arabidopsis[J]. Plant Physiology, 2002, 129(2): 838-853.
[10]	Narendra S, Venkataramani S, Shen Guoxin, et al.The Arabidopsis ascorbate peroxidase 3 is a peroxisomal membrane-bound antioxidant enzyme and is dispensable for Arabidopsis growth and development[J]. Journal of Experimental Botany, 2006, 57(12): 3033-3042.
[11]	Teixeira F K, Menezes-Benavente L, Margis R, et al.Analysis of the molecular evolutionary history of the ascorbate peroxidase gene family: inferences from the rice genome[J]. Journal of Molecular Evolution, 2004, 59(6): 761-770.
[12]	Teixeira F K, Menezes-Benavente L, Galv?o V C, et al.Rice ascorbate peroxidase gene family encodes functionally diverse isoforms localized in different subcellular compartments[J]. Planta, 2006, 224(2): 300-314.
[13]	李泽琴, 李静晓, 张根发. 植物抗坏血酸过氧化物酶的表达调控以及对非生物胁迫的耐受作用[J]. 遗传, 2013, 35(1): 45-54.
[13]	Li Zeqin, Li Jingxiao, Zhang Genfa.Expression regulation of plant ascorbate peroxidase and its tolerance to abiotic stresses[J]. Hereditas, 2013, 35(1): 45-54.
[14]	郭庆勋, 张春雨, 王晶莹, 等. 九台晚李PGIP基因的克隆及生物信息学分析[J]. 植物遗传资源学报, 2010, 11(5): 650-653.
[14]	Guo Qingxun, Zhang Chunyu, Wang Jingying, et al.Cloning and bioinformatic analysis of PGIP gene from Jiutaiwanli[J]. Journal of Plant Genetic Resources, 2010, 11(5): 650-653.
[15]	Schultz J, Milpetz F, Bork P, et al.A simple modular architecture research tool: identification of signaling domains[J]. Proceedings of the National Academy of Sciences of the United States of America, 1998, 95(11): 5857-5864.
[16]	Finn R D, Tate J, Mistry J, et al.The Pfam protein families database[J]. Nucleic Acids Research, 2008, 36: 281-288.
[17]	周喆, 张彩霞, 张利义,等. 苹果LysM基因家族的生物信息学及表达分析[J]. 中国农业科学, 2014, 47(13): 2602-2612.
[17]	Zhou Zhe, Zhang Caixia, Zhang Liyi, et al.Bioinformatics and expression analysis of the LysM gene family in apple[J]. Scientia Agricultura Sinica, 2014, 47(13): 2602-2612.
[18]	Finn R D, Clements J, Eddy S R.HMMER web server: interactive sequence similarity searching[J]. Nucleic Acids Research, 2011, 39(S2): W29-W37.
[19]	樊连梅, 刘更森, 刘成连, 等. 苹果金属硫蛋白基因MdFjMT2克隆及生物信息学分析[J]. 植物遗传资源学报, 2011, 12(5): 782-789.
[19]	Fan Lianmei, Liu Gengsen, Liu Chenglian, et al.Cloning and bioinformatic analysis of metallothionein-like protein gene (MdFjMT2) from apple (Malus domestica)[J]. Journal of Plant Genetic Resources, 2011, 12(5): 782-789.
[20]	Nobuyuki N, Junko T, Roos A A, et al.Xyloglucan endo-transglycosylase-mediated xyloglucan rearrangements in developing wood of hybrid aspen[J]. Plant Physiology, 2011, 155(1): 399-413.
[21]	罗聪, 何新华, 陈虎, 等. 芒果APl同源基因的克隆及其生物信息学分析[J]. 基因组学与应用生物学, 2009, 28(5): 851-858.
[21]	Luo Cong, He Xinhua, Chen Hu, et al.Cloning and bioinformatic analysis of the AP1 homolog gene from mango[J]. Genomics and Applied Biology, 2009, 28(5): 851-858.
[22]	Lee J, Burns T H, Light G, et al.Xyloglucan endotransglycosylase/hydrolase genes in cotton and their role in fiber elongation[J]. Planta, 2010, 232(5): 1191-1205.
[23]	Hon G, Crooks G E, Chandonia J M, et al.Web logo: a sequence logo generator[J]. Genome Research, 2004, 14(6): 1188-1190.
[24]	刘国元, 吴嫚, 于霁雯, 等. 雷蒙德氏棉Argonaute基因家族的生物信息学预测与分析[J]. 棉花学报, 2014, 26(5): 411-419.
[24]	Liu Guoyuan, Wu Man, Yu Jiwen, et al.Genome-wide identification of Argonaute gene family in G. raimondii using bioinformatic analysis[J]. Cotton Science, 2014, 26(5): 411-419.
[25]	龙婷, 雷洁萍, 宋涛, 等. 棉铃虫类胰蛋白酶的生物信息学分析[J]. 湖北农业科学, 2013, 52(20): 5047-5050.
[25]	Long Ting, Lei Jieping, Song Tao, et al.Bioinformatics analysis of putative trypsins of Helicoverpa armigera[J]. Hubei Agricultural Sciences, 2013, 52(20): 5047-5050.
[26]	王超, 杨传平, 王玉成, 等. 白桦抗坏血酸过氧化物酶(APX)基因克隆及表达分析[J]. 东北林业大学学报, 2009, 37(3): 79-81, 88.
[26]	Wang Chao, Yang Chuanping, Wang Yucheng.Cloning and expression analysis of an APX gene from Betula platyphyla[J]. Journal of Northeast Forestry University, 2009, 37(3): 79-81, 88.
[27]	马箐. 过量表达毛白杨APX基因增强植物对非生物胁迫的抗性[D]. 济南: 山东师范大学, 2012.
[27]	Ma Qing.Overexpression of APX gene from Populus tomentosa enhance plant tolerance to abiotic stress[D]. Jinan: Shandong Normal University, 2012.
[28]	D'Arcy-Lameta A, Ferrari-Iliou R, Contour-Ansel D, et al. Isolation and characterization of four ascorbate peroxidase cDNAs responsive to water deficit in cowpea leaves[J]. Annals of Botany, 2006, 97(1): 133-140.
[29]	Sarowar S, Kim E N, Kim Y J, et al.Overexpression of a pepper ascorbate peroxidase-like1 gene in tobacco plants enhances tolerance to oxidative stress and pathogens[J]. Plant Science, 2005, 169(1): 55-63.

陆地棉抗坏血酸过氧化物酶基因家族全基因组生物信息学分析

Bioinformatics Analysis of the Ascorbate Peroxidase Gene Family in the Gossypium hirsutum L. Genome

RichHTML

PDF (PC)

赞

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

Metrics

本文评价

推荐阅读 10

[1]	赵曾强,张析,李潇玲,张薇. GhEIN3基因对棉花枯萎病胁迫响应的功能分析[J]. 棉花学报, 2022, 34(3): 173-186.
[2]	吴健锋,樊志浩,武连杰,胡晓旺,韩知里,高巍,龙璐. 陆地棉衰老相关基因GhSAG101的克隆及抗病功能分析[J]. 棉花学报, 2022, 34(3): 187-197.
[3]	田一波,潘奥,陈劲,周仲华,袁小玲,刘志. 陆地棉ACX基因家族的鉴定与功能分析[J]. 棉花学报, 2022, 34(3): 215-226.
[4]	张素君,李兴河,王海涛,唐丽媛,蔡肖,刘存敬,张香云,张建宏. 陆地棉主要育种性状SSR关联位点的验证及优异材料鉴定[J]. 棉花学报, 2022, 34(2): 120-136.
[5]	徐婷婷,张弛,冯震,刘其宝,李黎贝,俞啸天,张雅楠,喻树迅. 陆地棉基因GhMIPS1A的克隆及功能分析[J]. 棉花学报, 2022, 34(2): 93-106.
[6]	陈琴,李多露,赵杰银,高文举,陈全家,曲延英. 陆地棉UDPGP基因家族的鉴定及抗旱性分析[J]. 棉花学报, 2022, 34(1): 12-22.
[7]	上官小霞,曹俊峰,杨琴莉,吴霞. 棉花纤维发育的分子机理研究进展[J]. 棉花学报, 2022, 34(1): 33-47.
[8]	贺浪,张华崇,司宁,简桂良. 陆地棉GhBZR1基因的克隆及功能研究[J]. 棉花学报, 2021, 33(6): 435-447.
[9]	李丹,赵存鹏,赵丽英,刘旭,刘素恩,王凯辉,王兆晓,耿军义,郭宝生. 棉花类表皮特异性分泌糖蛋白基因GhA01EP1的克隆和功能分析[J]. 棉花学报, 2021, 33(6): 448-458.
[10]	王雪慧,陈丽锦,赵若林,程海亮,张友平,王巧连,吕丽敏,宋国立,左东云. 陆地棉纤维起始期优势表达基因GhCRPK1的克隆及功能研究[J]. 棉花学报, 2021, 33(6): 459-468.
[11]	姜辉,郑锦秀,王永翠,张超,王秀丽,陈莹,高明伟,王家宝,柴启超,赵军胜. 陆地棉L-D₁等位基因特异性分子标记的开发及应用[J]. 棉花学报, 2021, 33(5): 412-421.
[12]	卞英杰,王寒涛,魏恒玲,张蒙,李弈,喻树迅. 陆地棉叶片发育相关基因GhRH39克隆与功能分析[J]. 棉花学报, 2021, 33(4): 319-327.
[13]	张岚,程琦,梁士辰,邓雨潇,潘玉欣. 棉花UGPase基因鉴定与生物信息学分析[J]. 棉花学报, 2021, 33(4): 337-346.
[14]	程成,李斌,王雅丽,赵楠,苏莹,聂虎帅,华金平. 转FBP7::iaaM基因陆地棉育种应用初报[J]. 棉花学报, 2021, 33(4): 368-376.
[15]	徐鹏,郭琪,徐珍珍,孟珊,陈天子,沈新莲. 基于重测序鉴定SbHKT基因在陆地棉基因组中的插入位点[J]. 棉花学报, 2021, 33(4): 377-383.