Crops ›› 2022, Vol. 38 ›› Issue (4): 37-45.doi: 10.16035/j.issn.1001-7283.2022.04.006

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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 E-mail:jysong@126.com;hmj007@126.com

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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

Table 1

Statistics of transcriptome assembly in ginger"

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

Fig.1

Phylogenetic relationships of WRKY transcription factors in Zingiber and Arabidopsis “*”represent the AtWRKY transcription factor"

Fig.2

The sequence tags (a) and three-dimensional structural model (b) of the WRKY conserved domain in ZoWRKY proteins A sequence tag consists of a stack of letters at each position, the relative sizes of the letters indicate their frequency in the sequences, the total height of the letters depicts the information content of the position, in bits"

Fig.3

Sequence analysis of the WRKY conserved domain in ZoWRKY proteins Colors indicate the sequence simility and a darker color had a higher conservatism"

Table 2

Physicochemical analysis of amino acid in ZoWRKY transcription factors"

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

Fig.4

Expression analysis of ZoWRKY gene under stress conditions (a) Gene ZoWRKY responses to soil moistures. (b) Gene ZoWRKY responses to infection of R. solanacearum. LUN: low soil moisture (WFPS: 10%); HUN: high soil moisture (WFPS: 40%); HI: high soil moisture (WFPS: 40%) and infection of R. solanacearum; log2FC value was calculated pairwise based on the expression level for each ZoWRKY gene, DEGs were identified between each two groups by edgeR with thresholds of log2FC ≥1 and FDR < 0.05; color scale increases from left to right with values -1.0 to 1.0; red arrow indicates up-regulated expression, green arrow indicates down-regulated expression"

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