Identification and expression analysis of millet GH5 gene family

doi:10.3969/j.issn.1004-1524.2021.10.02

Acta Agriculturae Zhejiangensis ›› 2021, Vol. 33 ›› Issue (10): 1797-1807.DOI: 10.3969/j.issn.1004-1524.2021.10.02

• Crop Science • Previous Articles Next Articles

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

Abstract

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

CLC Number:

S511

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.

Figures/Tables 12

References 32

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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

Identification and expression analysis of millet GH5 gene family

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