谷子GH5基因家族全基因组鉴定和表达分析

doi:10.3969/j.issn.1004-1524.2021.10.02

浙江农业学报 ›› 2021, Vol. 33 ›› Issue (10): 1797-1807.DOI: 10.3969/j.issn.1004-1524.2021.10.02

谷子GH5基因家族全基因组鉴定和表达分析

孟亚轩(), 孙颖琦, 赵心月, 王凤霞, 瓮巧云, 刘颖慧^*()

河北北方学院农林科技学院,河北张家口 075000

收稿日期:2020-12-15 出版日期:2021-10-25 发布日期:2021-11-02
作者简介:*刘颖慧,E-mail: leely519@126.com
孟亚轩(1997—),男,河北保定人,硕士研究生,主要从事植物生理学研究。E-mail: 997027363@qq.com
通讯作者: 刘颖慧
基金资助:
河北省重点研发计划(19226420D);河北省重点研发计划(21326302D);河北省重点研发计划(16226310D)

Identification and expression analysis of millet GH5 gene family

MENG Yaxuan(), SUN Yingqi, ZHAO Xinyue, WANG Fengxia, WENG Qiaoyun, LIU Yinghui^*()

College of Agriculture and Forestry Science and Technology, Hebei North University, Zhangjiakou 075000, China

Received:2020-12-15 Online:2021-10-25 Published:2021-11-02
Contact: LIU Yinghui

摘要/Abstract

摘要：

糖苷水解酶5(GH5)属于最大的糖苷水解酶家族,在细胞壁合成与降解过程中发挥重要作用。为解读谷子GH5基因家族特性,通过生物信息学方法对谷子进行全基因组扫描,鉴定并分析谷子GH5家族成员。结果表明,谷子具有18个GH5基因(命名为SiGH5-1~SiGH5-18),不均匀分布在8条染色体上。SiGH5蛋白具有保守结构域,叠合比对发现不同物种GH5蛋白结构高度保守。多物种系统发育树分析表明,GH5蛋白具有种属特异性特点。基因结构分析发现,同一分支的GH5蛋白具有相似的基序分布,GH5成员具有外显子改组现象。表达谱分析发现,谷子GH5家族基因属诱导型表达,其中,SiGH5-8、SiGH5-17在谷子各器官和非生物胁迫过程中均具有较高表达量。启动子分析鉴定到大量激素类响应元件,暗示GH5家族成员通过响应植物内源激素发挥调控作用。

关键词: 谷子, GH5基因家族, 生物信息学, 蛋白结构, 表达分析

Abstract:

Glycoside hydrolase 5 (GH5) belonged to the largest family of glycoside hydrolyases involved in the cell wall synthesis and degradation in plant. To identify and systematically characterize GH5 gene family, whole genome scan and bio-informatics analysis in millet were performed. In this study, total 18 GH5 genes were identified in millet, which unevenly distributed on eight chromosomes. By the gene structure and evolutionary analysis, SiGH5 proteins had a conserved domain, and overlapping alignment found that GH5 protein structures were highly conserved. Multi-species phylogenetic tree analysis indicated that GH5 proteins had species-specific characteristics. Gene structure analysis showed that the 18 GH5 genes contained exons and introns structure, some gene had the exon shuffling phenomenon. Expression analysis revealed that millet GH5 genes were specifically expressed in one or more organs, and significantly induced under different abiotic stress. In addition, a large number of hormone-responsive elements were identified in promoter region,which implied millet GH5 genes might play important role in response to plant growth and stresses.

Key words: millet, GH5 gene family, bioinformatics analysis, protein structure, expression analysis

中图分类号:

S511

孟亚轩, 孙颖琦, 赵心月, 王凤霞, 瓮巧云, 刘颖慧. 谷子GH5基因家族全基因组鉴定和表达分析[J]. 浙江农业学报, 2021, 33(10): 1797-1807.

MENG Yaxuan, SUN Yingqi, ZHAO Xinyue, WANG Fengxia, WENG Qiaoyun, LIU Yinghui. Identification and expression analysis of millet GH5 gene family[J]. Acta Agriculturae Zhejiangensis, 2021, 33(10): 1797-1807.

图/表 12

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基因名称 Gene name	转录名 Transcript name	位置 Location/bp	外显子数量 Number of extron	开放阅读框长度 Length of open reading fragment/bp	亚细胞定位 Subcellular location	蛋白质Protein
基因名称 Gene name	转录名 Transcript name	位置 Location/bp	外显子数量 Number of extron	开放阅读框长度 Length of open reading fragment/bp	亚细胞定位 Subcellular location	氨基酸数量 Amino acid number/ aa	分子量 Molecular weight/ku	等电点 Isoelec- tric point
SiGH5-1	KQL30310	Chr01.29829643-29831492	3	1 850	叶绿体Chloroplast	556	59.66	6.10
SiGH5-2	KQL31659	Chr01.39063114-39064817	4	1 704	细胞质Cytoplasm	410	44.71	6.12
SiGH5-3	KQL13587	Chr03.5378556-5381974	8	3 419	细胞壁Cell wall	541	59.52	8.00
SiGH5-4	KQL16047	Chr03.27514790-27518321	5	3 532	叶绿体、细胞质	499	56.24	6.68
					Chloroplast, cytoplasm
SiGH5-5	KQL09905	Chr04.7339963-7344080	10	4 118	细胞壁Cell wall	539	60.40	5.25
SiGH5-6	KQL10447	Chr04.15288452-15292978	5	4 527	细胞壁、细胞质	438	48.76	8.51
					Cell wall, cytoplasm
SiGH5-7	KQL06275	Chr05.32331156-32333994	3	2 839	细胞质Cytoplasm	428	45.85	9.34
SiGH5-8	KQL06959	Chr05.36712724-36715959	5	3 236	细胞质Cytoplasm	464	51.50	6.68
SiGH5-9	KQL02231	Chr06.31102783-31106162	10	3 380	细胞壁Cell wall	526	59.01	4.93
SiGH5-10	KQK96704	Chr07.14261700-14264284	2	2 585	叶绿体Chloroplast	578	62.46	9.12
SiGH5-11	KQK97746	Chr07.23041168-23045609	3	4 442	细胞膜Cell membrane	557	61.17	6.47
SiGH5-12	KQK97753	Chr07.23047335-23050440	3	3 106	叶绿体Chloroplast	554	59.71	7.81
SiGH5-13	KQK99686	Chr07.34214668-34216588	5	1 921	叶绿体、细胞壁	419	46.91	5.10
					Chloroplast, cell wall
SiGH5-14	KQK93353	Chr08.710113-711489	5	1 377	细胞质Cytoplasm	285	31.69	5.70
SiGH5-15	KQK86298	Chr09.1179023-1181193	4	2 171	细胞质Cytoplasm	480	52.38	8.66
SiGH5-16	KQK89267	Chr09.22784605-22789592	9	4 988	细胞壁Cell wall	492	54.71	5.16
SiGH5-17	KQK89268	Chr09.22801684-22805751	8	4 068	细胞壁Cell wall	511	56.29	5.10
SiGH5-18	KQK89274	Chr09.22899258-22905994	7	6 737	细胞壁Cell wall	451	50.76	6.38

基因名称 Gene name	转录名 Transcript name	位置 Location/bp	外显子数量 Number of extron	开放阅读框长度 Length of open reading fragment/bp	亚细胞定位 Subcellular location	蛋白质Protein
基因名称 Gene name	转录名 Transcript name	位置 Location/bp	外显子数量 Number of extron	开放阅读框长度 Length of open reading fragment/bp	亚细胞定位 Subcellular location	氨基酸数量 Amino acid number/ aa	分子量 Molecular weight/ku	等电点 Isoelec- tric point
SiGH5-1	KQL30310	Chr01.29829643-29831492	3	1 850	叶绿体Chloroplast	556	59.66	6.10
SiGH5-2	KQL31659	Chr01.39063114-39064817	4	1 704	细胞质Cytoplasm	410	44.71	6.12
SiGH5-3	KQL13587	Chr03.5378556-5381974	8	3 419	细胞壁Cell wall	541	59.52	8.00
SiGH5-4	KQL16047	Chr03.27514790-27518321	5	3 532	叶绿体、细胞质	499	56.24	6.68
					Chloroplast, cytoplasm
SiGH5-5	KQL09905	Chr04.7339963-7344080	10	4 118	细胞壁Cell wall	539	60.40	5.25
SiGH5-6	KQL10447	Chr04.15288452-15292978	5	4 527	细胞壁、细胞质	438	48.76	8.51
					Cell wall, cytoplasm
SiGH5-7	KQL06275	Chr05.32331156-32333994	3	2 839	细胞质Cytoplasm	428	45.85	9.34
SiGH5-8	KQL06959	Chr05.36712724-36715959	5	3 236	细胞质Cytoplasm	464	51.50	6.68
SiGH5-9	KQL02231	Chr06.31102783-31106162	10	3 380	细胞壁Cell wall	526	59.01	4.93
SiGH5-10	KQK96704	Chr07.14261700-14264284	2	2 585	叶绿体Chloroplast	578	62.46	9.12
SiGH5-11	KQK97746	Chr07.23041168-23045609	3	4 442	细胞膜Cell membrane	557	61.17	6.47
SiGH5-12	KQK97753	Chr07.23047335-23050440	3	3 106	叶绿体Chloroplast	554	59.71	7.81
SiGH5-13	KQK99686	Chr07.34214668-34216588	5	1 921	叶绿体、细胞壁	419	46.91	5.10
					Chloroplast, cell wall
SiGH5-14	KQK93353	Chr08.710113-711489	5	1 377	细胞质Cytoplasm	285	31.69	5.70
SiGH5-15	KQK86298	Chr09.1179023-1181193	4	2 171	细胞质Cytoplasm	480	52.38	8.66
SiGH5-16	KQK89267	Chr09.22784605-22789592	9	4 988	细胞壁Cell wall	492	54.71	5.16
SiGH5-17	KQK89268	Chr09.22801684-22805751	8	4 068	细胞壁Cell wall	511	56.29	5.10
SiGH5-18	KQK89274	Chr09.22899258-22905994	7	6 737	细胞壁Cell wall	451	50.76	6.38

项目Item	谷子Setaria italica
大豆Glycine max	0.58
高粱Sorghum bicolor	1.56
水稻Oryza sativa	1.09
拟南芥Arabidopsis thaliana	1.76
小立碗藓Physcomitrella patens	1.71
玉米Zea mays	1.48

项目Item	谷子Setaria italica
大豆Glycine max	0.58
高粱Sorghum bicolor	1.56
水稻Oryza sativa	1.09
拟南芥Arabidopsis thaliana	1.76
小立碗藓Physcomitrella patens	1.71
玉米Zea mays	1.48

谷子基因名 Gene names of Setaria italica	玉米基因名 Gene names of Zea mays	非同义突变概率 Nonsynonymous (K_a)	同义突变概率 Synonymous (K_s)	进化指数 Evolution index (K_a/K_s)
SiGH5-1	Zm00001d050974	0.087 0	0.208 8	0.418 2
SiGH5-2	Zm00001d052158	0.173 4	0.302 8	0.572 8
SiGH5-3	Zm00001d010039	0.742 2	1.373 5	0.540 3
SiGH5-4	Zm00001d035149	0.219 3	0.420 8	0.521 0
SiGH5-5	Zm00001d044877	0.131 2	0.293 7	0.446 6
SiGH5-6	Zm00001d045873	0.080 0	0.327 8	0.246 6
SiGH5-7	Zm00001d043965	0.091 0	0.282 6	0.325 2
SiGH5-8	Zm00001d043443	0.064 0	0.148 6	0.436 5
SiGH5-11	Zm00001d025696	0.075 0	0.373 3	0.201 0
SiGH5-12	Zm00001d003281	0.104 4	0.196 4	0.531 5
SiGH5-13	Zm00001d005052	0.077 0	0.321 8	0.241 2
SiGH5-14	Zm00001d005052	0.096 0	0.318 9	0.303 9
SiGH5-15	Zm00001d034723	0.145 5	0.201 1	0.723 6

谷子GH5基因家族全基因组鉴定和表达分析

Identification and expression analysis of millet GH5 gene family

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