棉花学报 ›› 2021, Vol. 33 ›› Issue (6): 469-481.doi: 10.11963/cs20210010
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,*(
)
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, 基金资助:
Wang Yanqing1,2#(),Zheng Jie2#(
),Xu Yanchao2,Cai Xiaoyan2,Zhou Zhongli2,Hou Yuqing2,Wang Kunbo2,Wang Yuhong2,Chen Haodong2,Liu Fang2,*(
),Li Zhikun1,*(
)
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:
【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。
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.
表1
qRT-PCR所用引物序列"
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 |
附表1
亚洲棉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 |
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 |
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3
瑟伯氏棉HDAC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 |
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