棉花HDAC基因家族鉴定及其在黄萎病菌侵染下的表达分析

doi:10.11963/cs20210010

棉花学报 ›› 2021, Vol. 33 ›› Issue (6): 469-481.doi: 10.11963/cs20210010

棉花HDAC基因家族鉴定及其在黄萎病菌侵染下的表达分析

王艳情^1,^2#(),郑杰^2#(),许艳超²,蔡小彦²,周忠丽²,侯宇清²,王坤波²,王玉红²,陈浩东²,刘方^2,^*(),李志坤^1,^*()

1.河北农业大学/华北作物改良与调控国家重点实验室,河北保定 071001
2.中国农业科学院棉花研究所/棉花生物学国家重点实验室,河南安阳 455000

收稿日期:2021-02-05 出版日期:2021-11-15 发布日期:2022-04-14
通讯作者: 刘方,李志坤 E-mail:wyq1118@163.com;zhengjieself@163.com;liufcri@163.com;lzk790319@163.com
作者简介:王艳情（1996―）,女,硕士研究生, wyq1118@163.com;|郑杰（1990―）,男,博士研究生, zhengjieself@163.com
基金资助:
中央级公益性科研院所基本科研业务费专项(1610162021039);中央级公益性科研院所基本科研业务费专项(16101620201050);中央级公益性科研院所基本科研业务费专项(1610162021017);湖南省自然科学基金青年基金(2019JJ50307)

Identification of cotton HDAC gene family and expression analysis of HDAC genes under Verticillium dahliae stress

Wang Yanqing^1,^2#(),Zheng Jie^2#(),Xu Yanchao²,Cai Xiaoyan²,Zhou Zhongli²,Hou Yuqing²,Wang Kunbo²,Wang Yuhong²,Chen Haodong²,Liu Fang^2,^*(),Li Zhikun^1,^*()

1. Hebei Agricultural University/State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China
2. Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China

Received:2021-02-05 Online:2021-11-15 Published:2022-04-14
Contact: Liu Fang,Li Zhikun E-mail:wyq1118@163.com;zhengjieself@163.com;liufcri@163.com;lzk790319@163.com

摘要/Abstract

摘要：

【目的】组蛋白去乙酰化酶（Histone deacetylases,HDAC）在植物发育及抗病应答中发挥重要作用,本研究旨在鉴定棉花HDAC基因家族成员并对其在黄萎病抗性中的作用进行分析。【方法】利用生物信息学方法对棉花基因组中HDAC基因家族成员进行鉴定,并对其理化性质、系统发育关系、基因结构进行系统分析。利用实时荧光定量聚合酶链式反应分析了黄萎病菌诱导下瑟伯氏棉HADC基因的表达模式。【结果】陆地棉、亚洲棉和瑟伯氏棉基因组中分别包括30、15和13个HDAC基因。棉花HDAC分为RPD3/HDA1、HD2和SIR2三个亚族,同一亚族成员间具有相似的基因结构和保守基序。棉花HDACs基因启动子中含有大量的激素应答、胁迫响应以及植物生长发育相关的顺式作用元件。瑟伯氏棉GthHDAC基因响应乙烯、水杨酸和茉莉酸的诱导;在黄萎病菌胁迫下,多数GthHDAC基因上调表达,表明该基因家族可能通过乙烯/茉莉酸和水杨酸等信号通路调控棉花黄萎病抗性。【结论】本研究从全基因组水平上鉴定了亚洲棉、陆地棉和瑟伯氏棉中58个HDAC家族基因,并明确了瑟伯氏棉HDAC家族成员在黄萎病菌胁迫下的表达模式。黄萎病菌处理后,大部分GthHDAC基因在叶片中上调表达,并且受到乙烯、水杨酸和茉莉酸的诱导。

关键词: 棉花; HDAC; 抗黄萎病; 全基因组家族鉴定; 基因表达

Abstract:

[Objective] Histone deacetylases (HDAC) plays an important role in plant development and disease resistance. Here, we intend to identify the members of HDAC gene family and its function in Verticillium wilt resistance of cotton. [Method] In this study, HDAC genes were identified and their physical and chemical properties, phylogenetic relationships, gene structures were analyzed by bioinformatics analysis. The expression patterns of HDAC genes under Verticillium dahliae stress were tested by qRT-PCR (Quantitative real-time polymerase chain reaction). [Result] A total of 30, 15, and 13 HDAC genes were identified in Gossypium hirsutum, G. arboreum, and G. thurberi, respectively. These genes were divided into RPD3/HDA1, HD2 and SIR2 groups and possessed similar structures and conserved motifs in each group. A large number of cis-acting elements related to hormone response, stress response and plant growth and development were identified in the promoters of HDAC genes. The results also showed that HDAC genes could be induced by ethylene (ET), salicylic acid (SA) and jasmonic acid (JA) and up-regulated under Verticillium dahliae infection, which indicated HDAC genes probably involved in Verticillium wilt resistance by ET/JA and/or SA signding pathways in cotton. [Conclusion] In this study, a total of 58 HDAC genes were identified. Under the treatment of wilt, most of GthHDAC genes were up-regulated in the leaves of G. thurberi, and some GthHDAC genes were induced by ET, SA and JA. These results proved that HDAC can be used in the future research to understand the molecular mechanism of Verticillium wilt tolerance in cotton.

Key words: cotton; HDAC; Verticillium wilt resistance; genome-wide gene family identification; gene expression

王艳情, 郑杰, 许艳超, 蔡小彦, 周忠丽, 侯宇清, 王坤波, 王玉红, 陈浩东, 刘方, 李志坤. 棉花HDAC基因家族鉴定及其在黄萎病菌侵染下的表达分析[J]. 棉花学报, 2021, 33(6): 469-481.

Wang Yanqing, Zheng Jie, Xu Yanchao, Cai Xiaoyan, Zhou Zhongli, Hou Yuqing, Wang Kunbo, Wang Yuhong, Chen Haodong, Liu Fang, Li Zhikun. Identification of cotton HDAC gene family and expression analysis of HDAC genes under Verticillium dahliae stress[J]. Cotton Science, 2021, 33(6): 469-481.

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链接本文: https://journal.cricaas.com.cn/Jweb_mhxb/CN/10.11963/cs20210010

https://journal.cricaas.com.cn/Jweb_mhxb/CN/Y2021/V33/I6/469

图/表 12

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附表2

陆地棉HDAC家族的理化性质"

基因名称 Gene ID	基因名称 Gene name	开放阅读框长度 ORF length/bp	GC含量 GC content/%	外显子数量 Exon number	外显子长度 Exon length/bp	内含子平均长度 Intron length/bp	蛋白质长度Protein length/aa	蛋白相对分子质量Protein size/kDa	等电点 Isoelectric point	染色体位置Chromosome	亚细胞定位 Subcellular localization
Ghir_A01G001410.1	GhHDAC1	1 500	42.9	8	333.1	328.6	499	56.175	4.968	A01	nucl
Ghir_A01G020190.1	GhHDAC2	813	44.4	9	90.3	239.3	270	29.486	4.7	A01	nucl
Ghir_A03G007210.1	GhHDAC3	1 416	47.7	6	316.2	556.2	471	53.095	5.076	A03	cyto
Ghir_A03G008200.1	GhHDAC4	1 968	41.9	15	166.1	1 240.80	655	73.015	5.326	A03	nucl
Ghir_A03G018610.1	GhHDAC5	1 056	42.5	8	258	337.7	351	39.546	4.474	A03	cyto
Ghir_A05G008720.1	GhHDAC6	888	45.5	10	158.3	129.1	295	31.442	4.365	A05	nucl
Ghir_A05G039400.1	GhHDAC7	1 209	44.3	11	293.5	471	402	44.735	9.438	A05	chlo
Ghir_A05G039610.1	GhHDAC8	1 350	44.3	9	181.9	420.3	449	48.664	6.928	A05	chlo
Ghir_A07G020200.1	GhHDAC9	723	42.2	8	90.4	188.9	240	26.563	4.821	A07	nucl
Ghir_A09G010110.1	GhHDAC10	840	45.5	10	174.6	142.8	279	29.734	4.66	A09	nucl
Ghir_A09G010210.1	GhHDAC11	1 290	40.2	14	92.1	243.8	429	49.084	4.897	A09	cyto
Ghir_A11G034800.1	GhHDAC12	909	43.8	9	281	296.3	302	32.739	4.485	A11	nucl
Ghir_A12G027820.1	GhHDAC13	1 725	43.6	18	144.5	429.9	574	63.258	6.314	A12	nucl
Ghir_A13G013780.1	GhHDAC14	975	42.9	12	211.5	417.8	324	35.922	8.217	A13	cyto
Ghir_A13G019980.1	GhHDAC15	699	43.1	9	537.8	137.4	232	25.795	6.615	A13	cyto
Ghir_A13G023460.1	GhHDAC16	1 107	42.6	4	276.8	841.3	368	40.374	5.338	A13	cyto
Ghir_D01G001410.1	GhHDAC17	1 500	43.1	8	282.6	335.9	499	56.258	4.968	D01	nucl
Ghir_D01G021720.1	GhHDAC18	744	45.2	8	93	280.1	247	26.565	5.113	D01	nucl
Ghir_D02G019970.1	GhHDAC19	1 398	44.7	7	294.6	413.5	465	52.653	5.131	D02	nucl
Ghir_D03G010660.1	GhHDAC20	1 908	41.4	14	136.3	561.2	635	71.015	4.889	D03	cyto
Ghir_D03G011510.1	GhHDAC21	1 416	47.7	6	321.8	550	471	53.062	5.149	D03	cyto
Ghir_D04G003510.1	GhHDAC22	1 332	43.8	9	168.2	412.6	443	47.954	6.984	D04	chlo
Ghir_D05G008730.1	GhHDAC23	882	45.5	10	141.2	132.4	293	31.378	4.373	D05	nucl
Ghir_D09G009840.1	GhHDAC24	861	45.6	10	137.8	143.1	286	30.434	4.596	D09	nucl
Ghir_D09G009940.1	GhHDAC25	1 290	40.2	14	92.1	242.7	429	49.106	4.837	D09	cyto
Ghir_D11G035640.1	GhHDAC26	915	44.4	8	165.9	278.1	304	32.876	4.43	D11	nucl
Ghir_D12G027930.1	GhHDAC27	1 740	43.9	18	152.1	428.3	579	63.804	6.182	D12	nucl
Ghir_D13G014460.1	GhHDAC28	1 398	41.5	14	145.9	415.7	465	51.921	9.244	D13	nucl
Ghir_D13G020760.1	GhHDAC29	996	44.1	13	163.3	254.6	331	37.281	8.726	D13	chlo
Ghir_D13G024090.1	GhHDAC30	1 143	43.3	3	477.7	1,284.50	380	41.633	5.65	D13	cyto

附表2

附表3

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基因名称 Gene name	上游引物 Forward primer	下游引物 Reverse primer
GthHDAC1	ATGTTGCCAGATGTTGGTGCTA	TTGGATGGTGGATGGTGTTGT
GthHDAC2	GTAATACAAGCGGTTCGTCAG	ACAGGGCACTATTTGCTTCAT
GthHDAC3	GTGGTGCTGACTCCCTTTCTG	CGTGTTGAGGCATCTTGTCGT
GthHDAC4	AAGGAGCAACACTTAATCTACCA	TGACCATCATACATCCCAATC
GthHDAC5	GCAGGTGTCACAAGTTTAGGC	TTGGTGCTTTGGTCAATGAGT
GthHDAC6	CATCTTTCCCAGGCTTCACT	CCTCCTCGCTTTCTTCTTCA
GthHDAC7	CTTCTACAACTATCGTCCCAATG	GACTCACCAAGTGTCGCATC
GthHDAC8	GTTACCGGAGGTGGAGGAT	ACCTGGAGCATGTTGGATG
GthHDAC9	CAGATCCTGGTGCCAGTCATG	CTCAAAGCCTTGCTCAAATACTAAA
GthHDAC10	TTTTATGCGTCTCCTTTCTCA	GAAGCTCCTCCAGAGTGATTT
GthHDAC11	GGGACTGCAACTGTTGACTA	TTCTATCACGAGCAAACCTG
GthHDAC12	GTCCTTACGGTTTCGCTTCAT	TCGCATACCCATATCCCTTGT
GthHDAC13	ACTGGACCATCCGCATAGCA	GGCAACCGCATCCATCACTA
GthUBQ7	GCATTCCACCTGACCAACA	CGCATTAGGGCACTCTTTT

基因名称 Gene ID	基因名称 Gene name	开放阅读框长度 ORF length/bp	GC含量 GC content/%	外显子数量 Exon number	外显子长度 Exon length/bp	内含子平均长度 Intron length/bp	蛋白质长度Protein length/aa	蛋白相对分子质量Protein size/kDa	等电点 Isoelectric point	染色体位置Chromosome	亚细胞定位 Subcellular localization
Ga01G0161	GaHDAC1	1 500	42.9	7	214.3	362.7	499	56.175	4.968	Chr01	nucl
Ga01G1929	GaHDAC2	1 968	41.9	15	131.2	1 261.30	655	73.016	5.172	Chr01	nucl
Ga01G2034	GaHDAC3	1 368	47.2	7	195.4	686.5	455	51.404	5.325	Chr01	nucl
Ga02G1604	GaHDAC4	900	45.1	8	112.5	261.6	299	32.484	4.578	Chr02	nucl
Ga03G2237	GaHDAC5	1 458	43.8	7	208.3	305.2	485	54.88	4.948	Chr03	nucl
Ga04G1766	GaHDAC6	1 167	44.4	11	106.1	475.8	388	43.114	9.438	Chr04	chlo
Ga04G1786	GaHDAC7	1 332	44	9	148	422.8	443	47.857	6.552	Chr04	chlo
Ga05G0904	GaHDAC8	849	45.8	9	94.3	147.8	282	29.956	4.427	Chr05	nucl
Ga09G1097	GaHDAC9	813	45.8	9	90.3	166.1	270	28.637	4.645	Chr09	nucl
Ga09G1110	GaHDAC10	1 290	40.2	14	92.1	244.1	429	49.113	4.961	Chr09	cyto
Ga11G0099	GaHDAC11	915	43.4	8	114.4	302.1	304	32.97	4.422	Chr11	nucl
Ga12G0127	GaHDAC12	1 740	43.7	17	102.4	406.6	579	63.743	6.181	Chr12	nucl
Ga13G1664	GaHDAC13	1 317	41.5	13	101.3	452.3	438	49.118	8.478	Chr13	nucl
Ga13G2333	GaHDAC14	1 257	44	13	96.7	258.1	418	46.714	8.868	Chr13	chlo
Ga13G2700	GaHDAC15	1 143	43	3	381	1 248.00	380	41.521	5.329	Chr13	chlo

基因名称 Gene ID	基因名称 Gene name	开放阅读框长度 ORF length/bp	GC含量 GC content/%	外显子数量 Exon number	外显子长度 Exon length/bp	内含子平均长度 Intron length/bp	蛋白质长度Protein length/aa	蛋白相对分子质量Protein size/kDa	等电点 Isoelectric point	染色体定位Chromosome localization	亚细胞定位 Subcellular localization
Gthu32375	GthHDAC1	1 416	47.74%	7	250.71	554	471	53.079	5.21	D02	cyto
Gthu33146	GthHDAC2	1 941	41.89%	14	137.64	601.38	646	71.852	5.29	D02	cyto
Gthu13364	GthHDAC3	1 788	42.73%	11	161.54	210.7	595	68.211	5.21	D03	nucl
Gthu45696	GthHDAC4	1 494	43.84%	10	148.4	343.33	497	54.240	6.19	D04	chlo
Gthu46021	GthHDAC5	1 284	43.93%	11	115.72	387.5	427	47.387	9.32	D04	chlo
Gthu22455	GthHDAC6	654	46.94%	8	80.75	201	217	22.985	5.7	D05	nucl
Gthu39470	GthHDAC7	486	43.00%	4	120.5	310	161	17.921	4.61	D06	chlo
Gthu42243	GthHDAC8	1 227	39.93%	14	86.642	269.53	408	46.421	4.92	D09	mito
Gthu42425	GthHDAC9	585	41.88%	5	116	198	194	21.142	4.42	D09	nucl
Gthu07686	GthHDAC10	1 587	42.79%	18	81.16	400.05	528	58.855	6.42	D12	nucl
Gthu15391	GthHDAC11	1 263	43.55%	13	96.153	257.16	420	46.782	8.4	D13	chlo
Gthu15946	GthHDAC12	1 215	42.88%	4	302.76	614.25	404	44.193	5.79	D13	cyto
Gthu34219	GthHDAC13	1 398	41.49%	14	98.857	415.54	465	51.919	9.07	D13	nucl

棉花HDAC基因家族鉴定及其在黄萎病菌侵染下的表达分析

Identification of cotton HDAC gene family and expression analysis of HDAC genes under Verticillium dahliae stress

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