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作物杂志,2022, 第4期: 37–45 doi: 10.16035/j.issn.1001-7283.2022.04.006

• 遗传育种·种质资源·生物技术 • 上一篇    下一篇

基于转录组数据的生姜ZoWRKY基因家族鉴定及逆境响应分析

姜玉松1,2(), 李洪雷2, 李哲馨2, 徐晓玉1, 李隆云3, 黄孟军1,2,3()   

  1. 1西南大学资源环境学院,400715,重庆
    2重庆文理学院特色植物研究院,402160,重庆
    3重庆市中药研究院中药生药研究所,400065,重庆
  • 收稿日期:2021-03-31 修回日期:2021-09-10 出版日期:2022-08-15 发布日期:2022-08-22
  • 通讯作者: 黄孟军
  • 作者简介:姜玉松,研究方向为植物病害防控及逆境胁迫应答,E-mail： jysong@126.com
  • 基金资助:
    国家自然科学基金青年科学基金(31501273);中国博士后科学基金(2021M700623);重庆市教育委员会科技项目(KJZD-K201801301);重庆市教育委员会科技项目(KJQN202001337);重庆市自然科学基金(cstc2020jcyj-msxmX0925);重庆市自然科学基金(cstc2019jcyj-msxmX0697)

Identification and Expression Analysis of the ZoWRKY Family in Stress Responses Based on Transcriptome Data of Ginger (Zingiber officinale Roscoe)

Jiang Yusong1,2(), Li Honglei2, Li Zhexin2, Xu Xiaoyu1, Li Longyun3, Huang Mengjun1,2,3()   

  1. 1College of Resources and Environment, Southwest University, Chongqing 400715, China
    2Institute for Special Plants, Chongqing University of Arts and Sciences, Chongqing 402160, China
    3Institute of Chinese Materia Medica, Chongqing Academy of Chinese Materia Medica, Chongqing 400065, China
  • Received:2021-03-31 Revised:2021-09-10 Online:2022-08-15 Published:2022-08-22
  • Contact: Huang Mengjun

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摘要：

WRKY是一类植物特有的转录因子家族,每个成员都含有高度保守的WRKY结构域,广泛参与植物的生长发育、信号传导和逆境胁迫应答等过程。本研究基于生姜转录组数据鉴定了ZoWRKY家族成员。结果显示,在340.2Mb的生姜转录组数据中,共获得78个具有ORF序列的ZoWRKY家族成员,分为Ⅰ、Ⅱ和Ⅲ 3个亚族,其中亚族Ⅱ又分为Ⅱ-a、Ⅱ-b、Ⅱ-c、Ⅱ-d和Ⅱ-e。逆境响应表达分析显示,分布在Ⅱ-c、Ⅱ-d和Ⅲ等的21个ZoWRKY响应土壤湿度,而分布在Ⅰ、Ⅱ-a和Ⅱ-c等的19个ZoWRKY响应青枯菌侵染,推测ZoWRKY在生姜逆境响应中具有重要功能。对后续开展生姜WRKY的研究、促进抗性育种和提高产量具有重要意义。

关键词: 生姜, WRKY, 转录因子, 逆境响应

Abstract:

The WRKY proteins was a group of plant-specific transcription factors that shared WRKY conserved domains. They perform crucial roles in growth, development, signal transduction and stress response. Based on RNA-Seq data from ginger, researchers were able to identify and analyse members of the ZoWRKY family (Zingiber officinale Roscoe). The results showed that a toal of 78 putative ZoWRKY family members with complete ORF sequences were identified in 340.2Mb total nucleotides. These candidate genes could be clustered into three subfamilies:Ⅰ, Ⅱ and Ⅲ, respectively, and subfamilyⅡcould be further divided into Ⅱ-a,Ⅱ-b,Ⅱ-c,Ⅱ-d and Ⅱ-e group. The expression patterns of ZoWRKY genes showed that 21 members significantly responded to moisture stress, which were mainly distributed in Ⅱ-c,Ⅱ-d, and Ⅲ. After infected by Ralstonia solanacearum, 19 of ZoWRKY genes were differentially expressed, and were mainly distributed inⅠ,Ⅱ-a, and Ⅱ-c, which speculated that ZoWRKY has important function in stress responses. These results provide valuable information for further research of WRKY transcription factors in ginger, and can promote the resistance breeding and the yield increase of ginger.

Key words: Ginger, WRKY, Transcription factor, Stress response

表1

生姜转录组组装统计

项目Item 数值
Numerial number
双末端读长数PE read number 27 645 008
基因数Unigenes number 381 871
长度≥10 000bp的基因 Unigenes≥10 000bp 47
长度≥2000bp的基因 Unigenes≥2000bp 19 182
长度≥1000bp的基因 Unigenes≥1000bp 61 387
平均长度Average length (bp) 891
最大长度Maximum length (bp) 16 953
N50长度N50 length (bp) 1260
总长度Total length (bp) 340 247 061

图1

生姜与拟南芥WRKY转录因子家族成员系统进化关系 “*”表示拟南芥AtWRKY转录因子

图2

ZoWRKY蛋白保守结构域序列标签(a)及三维结构模型(b) 序列标签由每个位置的字母组成,字母相对大小表明它们在序列中的频率,字母总高度表示位置的信息内容,以位为单位

图3

ZoWRKY转录因子保守结构域分析 颜色表示序列保守性差异,颜色越深表示保守性越高

表2

ZoWRKY转录因子氨基酸理化分析

序号
Number		 序列ID
Sequence ID		 类型
Type		 理论等电点
PI		 相对分子质量
MW (kDa)		 氨基酸长度
Amino acid length		 α-螺旋
α-helix (%)		 β-折叠
β-fold (%)		 其他
Others (%)
1 Zoff119209 Ⅰ 10.02 18 952.62 174 1.72 17.24 81.03
2 Zoff146524 Ⅰ 6.05 47 740.90 433 1.15 15.70 83.14
3 Zoff199075 Ⅰ 5.50 58 838.27 540 1.67 14.81 83.52
4 Zoff210606 Ⅰ 7.36 49 275.37 451 2.22 15.96 81.82
5 Zoff227889 Ⅰ 9.61 31 473.00 281 3.56 20.64 75.80
6 Zoff232809 Ⅰ 5.19 43 100.82 391 2.05 9.97 87.98
7 Zoff238069 Ⅰ 6.63 52 133.52 479 2.92 16.28 80.79
8 Zoff238668 Ⅰ 5.59 60 829.58 537 2.79 16.01 81.19
9 Zoff239268 Ⅰ 6.08 68 096.41 629 2.07 11.76 86.17
10 Zoff244943 Ⅰ 5.93 53 600.22 492 4.27 14.02 81.71
11 Zoff253493 Ⅰ 8.78 59 842.01 551 1.63 12.89 85.48
12 Zoff258147 Ⅰ 6.26 78 055.61 718 3.48 11.56 84.96
13 Zoff284143 Ⅰ 6.70 53 481.19 491 4.07 15.07 80.86
14 Zoff295642 Ⅰ 5.41 75 059.16 690 3.19 11.01 85.80
15 Zoff193573 Ⅱ-a 7.66 17 444.56 151 27.15 12.58 60.26
16 Zoff197334 Ⅱ-a 9.74 32 649.05 307 7.82 13.68 78.50
17 Zoff202059 Ⅱ-a 8.77 23 689.98 208 22.12 16.83 61.06
18 Zoff204548 Ⅱ-a 9.33 24 747.76 218 20.64 14.22 65.14
19 Zoff224514 Ⅱ-a 9.18 22 334.06 198 16.67 13.64 69.70
20 Zoff224526 Ⅱ-a 6.72 22 023.94 199 21.11 16.58 62.31
序号
Number		 序列ID
Sequence ID		 类型
Type		 理论等电点
PI		 相对分子质量
MW (kDa)		 氨基酸长度
Amino acid length		 α-螺旋
α-helix (%)		 β-折叠
β-fold (%)		 其他
Others (%)
21 Zoff224527 Ⅱ-a 8.64 12 187.19 107 0.00 28.04 71.96
22 Zoff237180 Ⅱ-a 9.26 23 765.91 206 21.36 13.11 65.53
23 Zoff296350 Ⅱ-a 8.76 33 220.01 303 14.52 18.48 67.00
24 Zoff600680 Ⅱ-a 8.61 22 434.71 200 0.00 18.50 81.50
25 Zoff025802 Ⅱ-b 8.49 34 543.18 310 11.29 13.87 74.84
26 Zoff192125 Ⅱ-b 8.78 25 559.49 242 11.16 14.88 73.97
27 Zoff199392 Ⅱ-b 8.74 40 995.52 370 15.95 16.22 67.84
28 Zoff211883 Ⅱ-b 8.69 30 587.88 279 3.23 14.34 82.44
29 Zoff228302 Ⅱ-b 7.79 39 532.76 353 18.98 8.78 72.24
30 Zoff229635 Ⅱ-b 6.97 42 701.98 392 8.42 11.48 80.10
31 Zoff237181 Ⅱ-b 8.14 39 597.65 367 16.62 11.72 71.66
32 Zoff244550 Ⅱ-b 9.31 49 121.07 456 18.20 10.96 70.83
33 Zoff255712 Ⅱ-b 5.85 44 598.95 418 16.51 13.64 69.86
34 Zoff275612 Ⅱ-b 8.28 23 926.18 210 20.95 9.05 70.00
35 Zoff290487 Ⅱ-b 8.99 13 316.46 122 0.82 13.11 86.07
36 Zoff290491 Ⅱ-b 6.07 35 980.81 324 15.43 9.88 74.69
37 Zoff129734 Ⅱ-c 9.79 17 944.08 164 6.71 18.29 75.00
38 Zoff147627 Ⅱ-c 10.04 24 896.67 223 5.38 16.59 78.03
39 Zoff165467 Ⅱ-c 6.65 21 534.40 190 6.32 19.47 74.21
40 Zoff173677 Ⅱ-c 9.20 33 840.50 317 6.62 14.83 78.55
41 Zoff186957 Ⅱ-c 9.60 21 486.76 187 0.00 19.79 80.21
42 Zoff226774 Ⅱ-c 5.96 40 489.58 368 2.45 11.41 86.14
43 Zoff239221 Ⅱ-c 9.51 21 050.93 191 2.62 19.37 78.01
44 Zoff242316 Ⅱ-c 9.51 16 605.34 149 0.00 22.82 77.18
45 Zoff253853 Ⅱ-c 6.01 30 576.87 262 0.00 15.27 84.73
46 Zoff290286 Ⅱ-c 9.93 19 356.01 171 4.09 21.64 74.27
47 Zoff614319 Ⅱ-c 10.14 12 362.28 109 0.00 33.94 66.06
48 Zoff150646 Ⅱ-d 9.87 29 012.97 269 7.06 15.24 77.70
49 Zoff170651 Ⅱ-d 10.12 34 732.26 321 22.12 10.59 67.29
50 Zoff185798 Ⅱ-d 9.98 27 468.14 252 23.41 15.08 61.51
51 Zoff186024 Ⅱ-d 9.55 41 308.75 372 14.78 11.56 73.66
52 Zoff188265 Ⅱ-d 9.75 39 505.83 352 12.78 12.22 75.00
53 Zoff192006 Ⅱ-d 10.18 33 047.28 308 10.71 14.29 75.00
54 Zoff199154 Ⅱ-d 9.85 38 393.36 346 12.43 12.14 75.43
55 Zoff204858 Ⅱ-d 9.77 35 680.37 324 16.98 12.65 70.37
56 Zoff208722 Ⅱ-d 10.15 12 913.60 116 0.00 33.62 66.38
57 Zoff209584 Ⅱ-d 9.95 35 415.23 328 15.85 11.89 72.26
58 Zoff238579 Ⅱ-d 9.63 38 150.32 344 12.50 11.92 75.58
59 Zoff238581 Ⅱ-d 9.71 38 594.60 345 12.75 12.17 75.07
60 Zoff305561 Ⅱ-d 9.90 28 447.66 271 19.93 7.01 73.06
61 Zoff407487 Ⅱ-d 10.13 14 806.36 136 0.00 15.44 84.56
62 Zoff066597 Ⅱ-e 10.86 12 246.39 108 0.93 30.56 68.52
63 Zoff178498 Ⅱ-e 9.69 26 402.19 236 2.54 17.37 80.08
64 Zoff186238 Ⅱ-e 8.34 23 262.53 212 3.77 18.40 77.83
65 Zoff223289 Ⅱ-e 9.23 23 531.70 214 6.54 22.43 71.03
66 Zoff288806 Ⅱ-e 7.00 17 884.78 160 3.75 15.00 81.25
67 Zoff288813 Ⅱ-e 5.39 41 512.52 384 0.78 12.24 86.98
68 Zoff311150 Ⅱ-e 5.77 35 150.65 326 7.98 11.66 80.37
69 Zoff536230 Ⅱ-e 9.41 16 935.56 148 6.08 14.86 79.05
70 Zoff109660 Ⅲ 7.71 29 460.72 261 21.46 9.96 68.58
71 Zoff160883 Ⅲ 9.23 12 035.04 102 21.57 34.31 44.12
72 Zoff184272 Ⅲ 9.35 24 075.94 215 26.51 16.28 57.21
73 Zoff188162 Ⅲ 9.89 27 125.18 243 21.81 10.29 67.90
74 Zoff196199 Ⅲ 5.96 39 530.50 355 16.90 9.86 73.24
75 Zoff217771 Ⅲ 6.23 32 122.87 290 13.45 13.79 72.76
76 Zoff254593 Ⅲ 8.79 20 719.11 183 3.28 19.13 77.60
77 Zoff301103 Ⅲ 5.68 24 958.96 224 4.91 15.18 79.91
78 Zoff554263 Ⅲ 9.79 11 591.13 104 30.77 8.65 60.58

图4

ZoWRKY基因对逆境的响应分析 (a) ZoWRKY基因对土壤湿度的响应。(b) ZoWRKY基因对青枯菌侵染的响应。LUN：低土壤湿度（WFPS：10%）,HUN：高土壤湿度（WFPS：40%）,HI：高土壤湿度（WFPS：40%）且感染青枯菌;根据每个ZoWRKY基因的表达水平分组计算log2FC,通过edgeR对2组样本间的差异基因进行识别,阈值为log2FC≥1和FDR < 0.05;色阶标尺从左-1.0到右1.0逐渐增大;右侧红色箭头表示上调表达,绿色箭头表示下调表达

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