棉花CAD基因家族的生物信息学分析

doi:10.19586/j.2095-2341.2023.0007

生物技术进展 ›› 2023, Vol. 13 ›› Issue (3): 412-424.DOI: 10.19586/j.2095-2341.2023.0007

棉花CAD基因家族的生物信息学分析

胡文冉¹(), 郝晓燕¹, 赵准¹, 邵武奎², 高升旗¹, 李建平¹, 黄全生¹()

^1.新疆农业科学院核技术生物技术研究所，新疆农作物生物技术重点实验室，乌鲁木齐 830091
^2.新疆农业大学生命科学学院，乌鲁木齐 830052

收稿日期:2023-02-02 接受日期:2023-02-28 出版日期:2023-05-25 发布日期:2023-06-12
通讯作者: 黄全生
作者简介:胡文冉 E-mail: huwran@126.com；
基金资助:
新疆维吾尔自治区自然科学基金资助项目(2022D01A88);新疆维吾尔自治区重点实验室开放课题(2021D04002);新疆农作物生物技术重点实验室开放课题(XJYS0302-2020-02)

Bioinformatic Analysis of the CAD Gene Family in Cotton

Wenran HU¹(), Xiaoyan HAO¹, Zhun ZHAO¹, Wukui SHAO², Shengqi GAO¹, Jianping LI¹, Quansheng HUANG¹()

^1.Xinjiang Key Laboratory of Crop Biotechnology，Institute of Nuclear and Biological Technologies，Xinjiang Academy of Agricultural Sciences，Urumqi 830091，China
^2.College of Life Sciences，Xinjiang Agricultural University，Urumqi 830052，China

Received:2023-02-02 Accepted:2023-02-28 Online:2023-05-25 Published:2023-06-12
Contact: Quansheng HUANG

摘要/Abstract

摘要：

苯丙烷代谢是植物重要的次生代谢途径之一，其代谢产物在植物的生长发育中发挥着重要作用。肉桂酸脱氢酶(cinnamyl alcohol dehydrogenase, CAD)是苯丙烷代谢途径的关键酶之一，在棉花纤维品质形成中起着十分重要的调节作用。为了更好地了解CAD基因家族在二倍体雷蒙德氏棉(D₅)和亚洲棉(A₂)、四倍体陆地棉(AD₁)和海岛棉(AD₂)基因组中的数量和分布情况，通过生物信息学方法，在雷蒙德氏棉、亚洲棉、陆地棉和海岛棉全基因组中分别鉴定出16、16、28和25个CAD基因家族成员，进一步分析了这些CAD家族成员进行基因结构、染色体定位、保守域、进化关系及CAD基因在陆地棉不同器官组织中的表达等。结果表明，4个棉种全基因组分别编码16、16、28和25个CAD基因。亚细胞定位将这些棉花CAD基因的表达产物均定位于细胞质。雷蒙德氏棉有14个CAD成员基因分布在5条染色体上，亚洲棉有13个CAD成员基因分布在5条染色体上，陆地棉28个CAD成员基因、海岛棉25个CAD基因分别分布在10条染色体上；内含子/外显子结构分析表明，CAD基因结构较为复杂，均含有内含子和外显子；功能结构域分析发现，有棉花CAD蛋白具有高度保守的ADH_N和ADH_zinc_N 2个功能域；根据系统发育分析结果，将CAD基因家族分成3个亚类。大部分CAD基因在陆地棉的不同器官中均有表达，部分在棉花纤维中表达量较高。分析结果为进一步研究棉花CAD基因家族各成员的功能奠定了理论基础。

关键词: CAD基因家族, 雷蒙德氏棉, 亚洲棉, 陆地棉, 海岛棉, 生物信息学

Abstract:

Phenylpropane metabolism is an important secondary metabolic pathway， and its metabolites play important roles in plant growth and development. Cinnamic acid dehydrogenase （CAD） is one of the key enzymes in phenylpropane metabolism， which plays a very important role in the regulation of cotton fiber quality. The genome ofdiploid cotton Gossypium raimondii （D₅） and Gossypium arboretum （A₂）， the tetraploid cotton Gossypium hirsutum （AD₁）and Gossypium barbadense （AD₂） were analyzed to better understand the quantity and distribution of CAD gene family. By bioinformatics methods， 16， 16， 28 and 25 CAD gene family members were identified from the Gossypium raimondii， Gossypium arboretum， Gossypium hirsutum and Gossypium barbadense genome databases， respectively. The genetic structure， gene localization， subcellular localization， conserved domain and phylogenetic relationship of CAD families were analyzed. The expression of CAD gene in different organs and tissues of Gossypium hirsutum was analyzed. The results showed that 16， 16， 28 and 25 CAD genes were encoded in the whole genome of four cotton varieties. The subcellular localization of the cotton CAD proteins were in the cytoplasm. Gossypium raimondii had 14 CAD member genes distributed on the 5 chromosomes. Gossypium arboretum had 13 CAD member genes distributed on the 5 chromosomes. Gossypium hirsutum had 25 CAD member genes distributed on the 10 chromosomes. Gossypium barbadense had 28 CAD member genes distributed on the 10 chromosomes. The analysis of intron/exon structure showed that the structures of CAD genes were complex， including intron and exon. Through functional domain analysis， it was found that cotton CAD protein contain two functional domains of ADH_N and ADH_zinc_N， which are the conserved domains for most CAD proteins. According to the results of phylogenetic analysis， the CAD gene family was divided into three subfamilies. Most of CAD genes were expressed in different organs of Gossypium hirsutum， and some of them were highly expressed in cotton fiber. The results laid a theoretical foundation for further research on the functions of cotton CAD gene family members.

Key words: CAD gene family, Gossypium raimondii, Gossypium arboretum, Gossypium hirsutum, Gossypium barbadense, bioinformatics

中图分类号:

S562

胡文冉, 郝晓燕, 赵准, 邵武奎, 高升旗, 李建平, 黄全生. 棉花CAD基因家族的生物信息学分析[J]. 生物技术进展, 2023, 13(3): 412-424.

Wenran HU, Xiaoyan HAO, Zhun ZHAO, Wukui SHAO, Shengqi GAO, Jianping LI, Quansheng HUANG. Bioinformatic Analysis of the CAD Gene Family in Cotton[J]. Current Biotechnology, 2023, 13(3): 412-424.

图/表 10

参考文献 32

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基因	基因组登陆号	染色体位置	编码序列长度/ bp	蛋白长度/ aa	分子量/ kD	等电点 pI	亚细胞定位
GrCAD1	Cotton_D_gene_10016775	Chr08	1 068	355	38.45	6.65	细胞质
GrCAD2	Cotton_D_gene_10037629	Chr08	942	313	33.98	6.31	细胞质
GrCAD3	Cotton_D_gene_10012650	Chr07	1 095	364	39.12	5.85	细胞质
GrCAD4	Cotton_D_gene_10038273	Chr08	1 074	357	38.71	5.41	细胞质
GrCAD5	Cotton_D_gene_10016445	Chr10	1 077	358	38.70	5.64	细胞质
GrCAD6	Cotton_D_gene_10033972	Chr09	1 080	359	39.19	7.13	细胞质
GrCAD7	Cotton_D_gene_10036902	Chr07	1 059	352	38.18	6.12	细胞质
GrCAD8	Cotton_D_gene_10014351	Chr07	780	259	28.15	5.99	细胞质
GrCAD9	Cotton_D_gene_10036599	Chr03	1 080	359	39.09	5.58	细胞质
GrCAD10	Cotton_D_gene_10002391	scaffold369	990	329	35.61	6.07	细胞质
GrCAD11	Cotton_D_gene_10002389	scaffold369	1 086	361	39.29	6.26	细胞质
GrCAD12	Cotton_D_gene_10037630	Chr08	741	246	27.09	8.94	细胞质
GrCAD13	Cotton_D_gene_10037632	Chr08	774	257	28.02	8.12	细胞质
GrCAD14	Cotton_D_gene_10037631	Chr08	1 089	362	39.10	6.50	细胞质
GrCAD15	Cotton_D_gene_10014346	Chr07	882	293	31.46	6.25	细胞质
GrCAD16	Cotton_D_gene_10014349	Chr07	1 095	364	39.11	5.75	细胞质

基因	基因组登陆号	染色体位置	编码序列长度/ bp	蛋白长度/ aa	分子量/ kD	等电点 pI	亚细胞定位
GrCAD1	Cotton_D_gene_10016775	Chr08	1 068	355	38.45	6.65	细胞质
GrCAD2	Cotton_D_gene_10037629	Chr08	942	313	33.98	6.31	细胞质
GrCAD3	Cotton_D_gene_10012650	Chr07	1 095	364	39.12	5.85	细胞质
GrCAD4	Cotton_D_gene_10038273	Chr08	1 074	357	38.71	5.41	细胞质
GrCAD5	Cotton_D_gene_10016445	Chr10	1 077	358	38.70	5.64	细胞质
GrCAD6	Cotton_D_gene_10033972	Chr09	1 080	359	39.19	7.13	细胞质
GrCAD7	Cotton_D_gene_10036902	Chr07	1 059	352	38.18	6.12	细胞质
GrCAD8	Cotton_D_gene_10014351	Chr07	780	259	28.15	5.99	细胞质
GrCAD9	Cotton_D_gene_10036599	Chr03	1 080	359	39.09	5.58	细胞质
GrCAD10	Cotton_D_gene_10002391	scaffold369	990	329	35.61	6.07	细胞质
GrCAD11	Cotton_D_gene_10002389	scaffold369	1 086	361	39.29	6.26	细胞质
GrCAD12	Cotton_D_gene_10037630	Chr08	741	246	27.09	8.94	细胞质
GrCAD13	Cotton_D_gene_10037632	Chr08	774	257	28.02	8.12	细胞质
GrCAD14	Cotton_D_gene_10037631	Chr08	1 089	362	39.10	6.50	细胞质
GrCAD15	Cotton_D_gene_10014346	Chr07	882	293	31.46	6.25	细胞质
GrCAD16	Cotton_D_gene_10014349	Chr07	1 095	364	39.11	5.75	细胞质

基因	基因组登陆号	染色体位置	编码序列长度/ bp	蛋白长度/ aa	分子量/ kD	等电点 pI	亚细胞定位
GaCAD1	Ga12G0361	Chr12	1 068	355	38.41	7.05	细胞质
GaCAD2	Ga11G1886	Chr11	987	328	35.17	6.56	细胞质
GaCAD3	Ga12G2139	Chr12	1 098	365	39.70	6.22	细胞质
GaCAD4	Ga14G0143	tig00000498	1 188	395	42.93	5.26	细胞质
GaCAD5	Ga03G2431	Chr03	1 077	358	38.84	5.53	细胞质
GaCAD6	Ga05G1953	Chr05	1 074	357	39.12	6.46	细胞质
GaCAD7	Ga02G0337	Chr02	1 065	354	39.74	6.13	细胞质
GaCAD8	Ga14G1938	tig00016738	339	112	11.76	9.10	细胞质
GaCAD9	Ga02G0499	Chr02	1 080	359	39.07	6.01	细胞质
GaCAD10	Ga02G0339	Chr02	1 086	361	39.22	6.26	细胞质
GaCAD11	Ga14G1937	tig00016738	1 086	361	39.07	7.61	细胞质
GaCAD12	Ga12G2141	Chr12	945	314	34.10	6.45	细胞质
GaCAD13	Ga12G2140	Chr12	1 065	354	37.94	7.15	细胞质
GaCAD14	Ga12G2105	Chr12	1 107	368	39.62	6.64	细胞质
GaCAD15	Ga11G1713	Chr11	783	260	28.16	7.17	细胞质
GaCAD16	Ga11G1714	Chr11	1 095	364	39.13	5.75	细胞质

基因	基因组登陆号	染色体位置	编码序列长度/ bp	蛋白长度/ aa	分子量/ kD	等电点 pI	亚细胞定位
GaCAD1	Ga12G0361	Chr12	1 068	355	38.41	7.05	细胞质
GaCAD2	Ga11G1886	Chr11	987	328	35.17	6.56	细胞质
GaCAD3	Ga12G2139	Chr12	1 098	365	39.70	6.22	细胞质
GaCAD4	Ga14G0143	tig00000498	1 188	395	42.93	5.26	细胞质
GaCAD5	Ga03G2431	Chr03	1 077	358	38.84	5.53	细胞质
GaCAD6	Ga05G1953	Chr05	1 074	357	39.12	6.46	细胞质
GaCAD7	Ga02G0337	Chr02	1 065	354	39.74	6.13	细胞质
GaCAD8	Ga14G1938	tig00016738	339	112	11.76	9.10	细胞质
GaCAD9	Ga02G0499	Chr02	1 080	359	39.07	6.01	细胞质
GaCAD10	Ga02G0339	Chr02	1 086	361	39.22	6.26	细胞质
GaCAD11	Ga14G1937	tig00016738	1 086	361	39.07	7.61	细胞质
GaCAD12	Ga12G2141	Chr12	945	314	34.10	6.45	细胞质
GaCAD13	Ga12G2140	Chr12	1 065	354	37.94	7.15	细胞质
GaCAD14	Ga12G2105	Chr12	1 107	368	39.62	6.64	细胞质
GaCAD15	Ga11G1713	Chr11	783	260	28.16	7.17	细胞质
GaCAD16	Ga11G1714	Chr11	1 095	364	39.13	5.75	细胞质

基因	基因组登陆号	染色体位置	编码序列长度/ bp	蛋白长度/ aa	分子量/ kD	等电点 pI	亚细胞定位
GhCAD1	GH_D12G2651	Chr12	1 068	355	38.45	7.52	细胞质
GhCAD2	GH_D12G0806	Chr12	945	314	33.66	6.59	细胞质
GhCAD3	GH_A12G0990	Chr12	1 086	361	39.24	6.60	细胞质
GhCAD4	GH_A12G0204	Chr12	1 074	357	38.76	5.32	细胞质
GhCAD5	GH_A03G2100	Chr03	1 077	358	38.81	5.53	细胞质
GhCAD6	GH_D05G1877	Chr05	1 080	359	39.18	7.13	细胞质
GhCAD7	GH_D11G2110	Chr11	1 059	352	38.19	6.01	细胞质
GhCAD8	GH_D11G2243	Chr11	1 095	364	39.14	5.85	细胞质
GhCAD9	GH_D03G0499	Chr03	1 080	359	39.09	5.85	细胞质
GhCAD10	GH_A02G1713	Chr02	1 086	361	39.28	6.00	细胞质
GhCAD11	GH_A11G2195	Chr11	1 086	361	39.07	7.61	细胞质
GhCAD12	GH_D12G0807	Chr12	549	182	19.91	7.65	细胞质
GhCAD13	GH_A12G0991	Chr12	1 398	465	50.54	6.02	细胞质
GhCAD14	GH_D12G0808	Chr12	1 089	362	38.99	6.46	细胞质
GhCAD15	GH_A11G2192	Chr11	831	276	29.86	6.59	细胞质
GhCAD16	GH_A11G2193	Chr11	1 095	364	39.13	5.75	细胞质
GhCAD17	GH_D03G0349	Chr03	972	323	34.96	6.71	细胞质
GhCAD18	GH_D03G0347	Chr03	1 086	361	39.19	6.12	细胞质
GhCAD19	GH_D11G3241	Chr11	1 095	364	39.13	5.85	细胞质
GhCAD20	GH_A05G1840	Chr05	1 080	359	39.05	6.41	细胞质
GhCAD21	GH_A12G2629	Chr12	1 068	355	38.38	7.05	细胞质
GhCAD22	GH_A11G2344	Chr11	894	297	31.97	6.23	细胞质
GhCAD23	GH_D12G0217	Chr12	1 074	357	38.71	5.41	细胞质
GhCAD24	GH_A02G1628	Chr02	1 080	359	39.07	5.71	细胞质
GhCAD25	GH_D02G2271	Chr02	663	220	24.01	5.70	细胞质
GhCAD26	GH_D11G2246	Chr11	747	248	26.73	7.14	细胞质
GhCAD27	GH_A12G0994	Chr12	1 137	378	40.94	6.49	细胞质
GhCAD28	GH_A12G0993	Chr12	1 014	337	36.49	6.08	细胞质

棉花CAD基因家族的生物信息学分析

Bioinformatic Analysis of the CAD Gene Family in Cotton

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基因	基因组登陆号	染色体位置	编码序列长度/ bp	蛋白长度/ aa	分子量/ kD	等电点 pI	亚细胞定位
GbCAD1	Gbar_D12G025360	Chr12	1 068	355	38.45	7.52	细胞质
GbCAD2	Gbar_A02G015780	Chr02	981	326	36.30	6.21	细胞质
GbCAD3	Gbar_A12G009020	Chr12	921	306	33.01	6.25	细胞质
GbCAD4	Gbar_A12G002060	Chr12	1 074	357	38.76	5.32	细胞质
GbCAD5	Gbar_A03G020480	Chr03	1 077	358	38.82	5.53	细胞质
GbCAD6	Gbar_D05G018810	Chr05	1 035	344	37.76	6.55	细胞质
GbCAD7	Gbar_D11G021150	Chr11	1 059	352	38.19	6.01	细胞质
GbCAD8	Gbar_D11G022440	Chr11	1 095	364	39.14	5.85	细胞质
GbCAD9	Gbar_D03G004820	Chr03	984	327	35.62	6.19	细胞质
GbCAD10	Gbar_A02G015760	Chr02	1 086	361	39.33	6.26	细胞质
GbCAD11	Gbar_A11G021420	Chr11	1 056	351	37.98	8.63	细胞质
GbCAD12	Gbar_D12G008930	Chr12	549	182	19.94	7.65	细胞质
GbCAD13	Gbar_A12G009010	Chr12	978	325	34.74	6.64	细胞质
GbCAD14	Gbar_D12G008920	Chr12	1 122	373	40.12	6.23	细胞质
GbCAD15	Gbar_D11G022460	Chr11	408	135	14.46	5.62	细胞质
GbCAD16	Gbar_A11G021400	Chr11	1 095	364	39.13	5.75	细胞质
GbCAD17	Gbar_D03G003450	Chr03	792	263	28.34	6.15	细胞质
GbCAD18	Gbar_D03G003430	Chr03	1 086	361	39.16	6.12	细胞质
GbCAD19	Gbar_D11G031180	Chr11	1 098	365	39.26	5.75	细胞质
GbCAD20	Gbar_A05G018170	Chr05	1 080	359	39.17	6.82	细胞质
GbCAD21	Gbar_A12G025440	Chr12	1 068	355	38.38	7.05	细胞质
GbCAD22	Gbar_D02G022410	Chr02	1 077	358	38.82	5.64	细胞质
GbCAD23	Gbar_D12G002300	Chr12	1 074	357	38.71	5.41	细胞质
GbCAD24	Gbar_A11G022760	Chr11	561	186	19.77	7.99	细胞质
GbCAD25	Gbar_A02G014990	Chr02	996	331	36.10	6.46	细胞质

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