铁皮石斛糖苷水解酶GH3基因家族鉴定及表达模式分析

doi:10.3969/j.issn.1004-1524.20230502

浙江农业学报 ›› 2024, Vol. 36 ›› Issue (4): 790-799.DOI: 10.3969/j.issn.1004-1524.20230502

铁皮石斛糖苷水解酶GH3基因家族鉴定及表达模式分析

李亚萍¹(), 金福来², 黄宗贵³, 张涛⁴, 段晓婧¹, 姜武¹, 陶正明¹^,^*(), 陈家栋¹

1.浙江省亚热带作物研究所,浙江温州 325005
2.温州市金福来农业科技有限公司,浙江温州 325005
3.温州市种子站,浙江温州 325052
4.温州市农业技术推广中心,浙江温州 325052

收稿日期:2023-04-18 出版日期:2024-04-25 发布日期:2024-04-29
作者简介:李亚萍(1997—),女,河南开封人,硕士研究生,主要从事药用植物有效成分合成机制研究。E-mail: Lyy100400@163.com
通讯作者: *陶正明,E-mail: 312633768@qq.com
基金资助:
国家自然科学基金(32102485);温州市农业新品种选育协作组项目(2019ZX003-4);温州市农业高新园区开放性项目(KN20210005);温州市科技特派员专项项目(X20210018);乐清市农业重点科技项目(2022N026);乐清市农业重点科技项目(2022N046);温州市科协服务科技创新项目(kjfw73)

Identification and expression pattern analysis of glycoside hydrolase GH3 gene family in Dendrobium officinale

LI Yaping¹(), JIN Fulai², HUANG Zonggui³, ZHANG Tao⁴, DUAN Xiaojing¹, JIANG Wu¹, TAO Zhengming¹^,^*(), CHEN Jiadong¹

1. Zhejiang Institute of Subtropical Crops, Wenzhou 325005, Zhejiang, China
2. Wenzhou Jinfulai Agricultural Science and Technology Co., Ltd., Wenzhou 325005, Zhejiang, China
3. Wenzhou Seed Station, Wenzhou 325052, Zhejiang, China
4. Wenzhou Agricultural Technology Promotion Center, Wenzhou 325052, Zhejiang, China

Received:2023-04-18 Online:2024-04-25 Published:2024-04-29
Contact: TAO Zhengming

摘要/Abstract

摘要：

利用生物信息学方法对铁皮石斛 GH3 基因家族成员进行筛选、鉴定,对其基因结构、蛋白理化性质、亚细胞定位、系统进化、蛋白质二级结构及跨膜预测、基序及染色体定位进行分析,同时分析GH3 基因家族在不同组织以及低磷与正常磷水平下的表达模式。在铁皮石斛全基因组中筛选得到13个GH3家族基因,其中一个基因存在可变剪切,表达为14个GH3蛋白。GH3基因家族蛋白可分为3个亚家族,各亚家族中不同基因相对保守;各成员均含有内含子与外显子,内含子相位在0~2,13个基因分布在8染色体上。GH3基因家族在铁皮石斛的8个组织中均有表达,其中白根和花蕾表达量高,茎和唇瓣低,推测GH3基因家族可能参与铁皮石斛根系生长以及开花现蕾。低磷与正常磷水平表达结果表明,低磷水平下叶中基因LOC110110392、LOC110100144表达上调,根中基因LOC110095762、LOC110107269表达上调。该研究对铁皮石斛糖苷水解酶GH3 基因家族成员生物信息学、在不同组织以及正常磷与低磷条件下的表达水平进行研究分析,筛选响应低磷信号的糖苷水解酶基因,为后期研究糖苷水解酶参与低磷条件下铁皮石斛多糖代谢调节机制提供研究基础。

关键词: 铁皮石斛, 糖苷水解酶GH3, 生物信息学分析, 基因表达模式

Abstract:

Bioinformatics methods were used to screen and identify the members of the GH3 gene family of Dendrobium officinale, and analyze their gene structure, protein physical and chemical properties, subcellular localization, phylogeny, protein secondary structure and transmembrane prediction, motifs, and chromosome localization. We analyzed the expression patterns of the GH3 gene family in different tissues and under low and normal phosphorus levels. Thirteen GH3 family genes were screened from the genome of D. officinale, with one gene exhibiting variable splicing and expressing 14 GH3 proteins. GH3 gene family proteins can be divided into three subfamilies, in which different genes are relatively conservative. Each member gene contains intron and exon, the phase of intron is between 0 and 2, and 13 genes are distributed on chromosome 8. The GH3 gene is expressed in all 8 tissues of D. officinale, with high expression levels in white roots and flower buds, and low expression levels in stems and lips. It is speculated that the GH3 gene may be involved in the root growth and flowering stage of D. officinale. The expression results of low and normal phosphorus levels showed that under low phosphorus levels, the expression of genes LOC110110392 and LOC110100144 in leaves was upregulated, while the expression of genes LOC110095762 and LOC110107269 in roots was upregulated. The bioinformatics of the members of the glycoside hydrolase GH3 gene family of D. officinale, the expression level in different tissues and under normal phosphorus and low phosphorus conditions were studied and analyzed, and the glycoside hydrolase genes responding to low phosphorus signals were screened, providing a research basis for the further study of glycoside hydrolase involved in the regulation mechanism of polysaccharide metabolism in D. officinale under low phosphorus conditions.

Key words: Dendrobium officinale, glycoside hydrolase GH3, bioinformatics analysis, gene expression pattern

中图分类号:

S567

李亚萍, 金福来, 黄宗贵, 张涛, 段晓婧, 姜武, 陶正明, 陈家栋. 铁皮石斛糖苷水解酶GH3基因家族鉴定及表达模式分析[J]. 浙江农业学报, 2024, 36(4): 790-799.

LI Yaping, JIN Fulai, HUANG Zonggui, ZHANG Tao, DUAN Xiaojing, JIANG Wu, TAO Zhengming, CHEN Jiadong. Identification and expression pattern analysis of glycoside hydrolase GH3 gene family in Dendrobium officinale[J]. Acta Agriculturae Zhejiangensis, 2024, 36(4): 790-799.

图/表 10

参考文献 20

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蛋白ID Protein ID	基因ID Gene ID	染色体 Chromosome	基因长度 Length/bp	CDS序列号 CDS ID
XP_028554809.1	LOC110095762	NW_021319658.1	4 029	XM_028698976.1
XP_028554802.1	LOC110095760	NW_021319658.1	13 801	XM_028698969.1
XP_028549622.1	LOC114578346	NW_021318505.1	3 024	XM_028693789.1
XP_028549465.1	LOC110107249	NW_021318505.1	2 586	XM_028693632.1
XP_028549390.1	LOC110107248	NW_021318505.1	4 203	XM_028693557.1
XP_020705298.1	LOC110116159	NW_021420086.1	6 817	XM_020849639.2
XP_020697503.1	LOC110110392	NW_021319315.1	4 737	XM_020841844.2
XP_020693131.1	LOC110107269	NW_021318505.1	5 362	XM_020837472.2
XP_020689109.1	LOC110104374	NW_021319682.1	4 260	XM_020833450.2
XP_020684254.1	LOC110100884	NW_021319733.1	5 838	XM_020828595.2
XP_020683228.1	LOC110100144	NW_021319820.1	43 378	XM_020827569.2
XP_020677781.1	LOC110096263	NW_021528311.1	2 964	XM_020822122.1
XP_020677766.1	LOC110096253	NW_021528311.1	5 580	XM_020822107.2
XP_020677074.1	LOC110095760	NW_021319658.1	13 801	XM_020821415.2

蛋白ID Protein ID	基因ID Gene ID	染色体 Chromosome	基因长度 Length/bp	CDS序列号 CDS ID
XP_028554809.1	LOC110095762	NW_021319658.1	4 029	XM_028698976.1
XP_028554802.1	LOC110095760	NW_021319658.1	13 801	XM_028698969.1
XP_028549622.1	LOC114578346	NW_021318505.1	3 024	XM_028693789.1
XP_028549465.1	LOC110107249	NW_021318505.1	2 586	XM_028693632.1
XP_028549390.1	LOC110107248	NW_021318505.1	4 203	XM_028693557.1
XP_020705298.1	LOC110116159	NW_021420086.1	6 817	XM_020849639.2
XP_020697503.1	LOC110110392	NW_021319315.1	4 737	XM_020841844.2
XP_020693131.1	LOC110107269	NW_021318505.1	5 362	XM_020837472.2
XP_020689109.1	LOC110104374	NW_021319682.1	4 260	XM_020833450.2
XP_020684254.1	LOC110100884	NW_021319733.1	5 838	XM_020828595.2
XP_020683228.1	LOC110100144	NW_021319820.1	43 378	XM_020827569.2
XP_020677781.1	LOC110096263	NW_021528311.1	2 964	XM_020822122.1
XP_020677766.1	LOC110096253	NW_021528311.1	5 580	XM_020822107.2
XP_020677074.1	LOC110095760	NW_021319658.1	13 801	XM_020821415.2

蛋白ID Protein ID	氨基酸长度 Amino acid/aa	分子量 Molecular weight/u	等电点 Isoelectric point	不稳定指数 Instability index	脂肪指数 Aliphatic index	总平均疏水指数 GRAVY	亚细胞定位 Location
XP_028554809.1	624	68 931.43	7.56	32.67	94.34	-0.092	质体/细胞质Plastid/cytoplasm
XP_028554802.1	569	62 043.3	6.15	24.64	92.92	-0.009	质体Plastid
XP_028549622.1	434	48 049.32	7.14	28.64	91.84	-0.04	叶绿体Chloroplast
XP_028549465.1	182	19 743.06	9.46	30.44	100.77	0.207	线粒体Mitochondrion
XP_028549390.1	626	68 173.11	6.47	27.63	92.67	-0.049	细胞外/质体Extracellular/plastid
XP_020705298.1	629	69 196.69	6.64	32.68	94.07	-0.01	质体Plastid
XP_020697503.1	617	67 640.07	6.67	33.83	87.59	-0.135	细胞外Extracellular
XP_020693131.1	631	69 537.96	6.55	30.51	91.28	-0.041	细胞质Cytoplasm
XP_020689109.1	795	86 669.85	6.25	41.01	86.65	-0.106	叶绿体Chloroplast
XP_020684254.1	788	85 006.68	8.26	34.65	87.77	-0.099	细胞外Extracellular
XP_020683228.1	614	67 201.81	5.72	32.41	92.1	-0.05	细胞质Cytoplasm
XP_020677781.1	624	67 993.29	5.83	24.91	86.23	-0.192	细胞外Extracellular
XP_020677766.1	766	82 994.27	6.29	28.41	83.73	-0.121	细胞外Extracellular
XP_020677074.1	655	71 534.72	8.23	24.08	93.08	-0.024	线粒体/叶绿体
							Mitochondrion/chloroplast

蛋白ID Protein ID	氨基酸长度 Amino acid/aa	分子量 Molecular weight/u	等电点 Isoelectric point	不稳定指数 Instability index	脂肪指数 Aliphatic index	总平均疏水指数 GRAVY	亚细胞定位 Location
XP_028554809.1	624	68 931.43	7.56	32.67	94.34	-0.092	质体/细胞质Plastid/cytoplasm
XP_028554802.1	569	62 043.3	6.15	24.64	92.92	-0.009	质体Plastid
XP_028549622.1	434	48 049.32	7.14	28.64	91.84	-0.04	叶绿体Chloroplast
XP_028549465.1	182	19 743.06	9.46	30.44	100.77	0.207	线粒体Mitochondrion
XP_028549390.1	626	68 173.11	6.47	27.63	92.67	-0.049	细胞外/质体Extracellular/plastid
XP_020705298.1	629	69 196.69	6.64	32.68	94.07	-0.01	质体Plastid
XP_020697503.1	617	67 640.07	6.67	33.83	87.59	-0.135	细胞外Extracellular
XP_020693131.1	631	69 537.96	6.55	30.51	91.28	-0.041	细胞质Cytoplasm
XP_020689109.1	795	86 669.85	6.25	41.01	86.65	-0.106	叶绿体Chloroplast
XP_020684254.1	788	85 006.68	8.26	34.65	87.77	-0.099	细胞外Extracellular
XP_020683228.1	614	67 201.81	5.72	32.41	92.1	-0.05	细胞质Cytoplasm
XP_020677781.1	624	67 993.29	5.83	24.91	86.23	-0.192	细胞外Extracellular
XP_020677766.1	766	82 994.27	6.29	28.41	83.73	-0.121	细胞外Extracellular
XP_020677074.1	655	71 534.72	8.23	24.08	93.08	-0.024	线粒体/叶绿体
							Mitochondrion/chloroplast

蛋白ID Protein ID	跨膜区 Transmembrane helices	α-螺旋 Alpha-helix (Hh)/%	延伸链 Extended strand (Ee)/%	β-转角 Beta turn (Tt)/%	无规卷曲 Random coil (Cc)/%
XP_028554809.1	否No	35.74	15.71	5.77	42.79
XP_028554802.1	否No	35.15	16.17	6.15	42.53
XP_028549622.1	否No	32.26	14.75	6.91	46.08
XP_028549465.1	是Yes	46.70	12.64	4.40	36.26
XP_028549390.1	是Yes	36.58	15.34	5.75	42.33
XP_020705298.1	否No	36.25	15.90	5.72	42.13
XP_020697503.1	是Yes	33.39	15.72	6.16	44.73
XP_020693131.1	是Yes	36.13	15.37	5.71	42.79
XP_020689109.1	是Yes	27.55	20.25	5.66	46.54
XP_020684254.1	是Yes	28.43	21.57	6.22	43.78
XP_020683228.1	否No	35.83	14.98	5.37	43.81
XP_020677781.1	否No	25.00	23.40	8.17	43.43
XP_020677766.1	否No	27.68	21.54	7.05	43.73
XP_020677074.1	否No	35.57	15.57	5.95	42.90

铁皮石斛糖苷水解酶GH3基因家族鉴定及表达模式分析

Identification and expression pattern analysis of glycoside hydrolase GH3 gene family in Dendrobium officinale

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