香石竹WRKY家族全基因组鉴定及其表达分析

doi:10.16420/j.issn.0513-353x.2019-0986

摘要/Abstract

摘要：

以拟南芥WRKY蛋白序列及保守结构域种子文件（PF03106）检索香石竹（Dianthus caryophyllus L.）基因组数据库,共鉴定出香石竹WRKY家族基因DcaWRKY 53个,分别编码161 ~ 747个氨基酸,蛋白质平均分子量在18.27 ~ 82.58 kD之间,等电点在5.07 ~ 10.25之间,内含子数1 ~ 5。系统发育分析显示,DcaWRKY可分为3组,其中groupⅡ又可进一步分为5个亚组。DcaWRKY结构域具有高度保守性,皆为WRKYGQK七肽结构域,偶有变型。DcaWRKY20的N端WRKYGQK七肽结构域出现缺失,形成了WRK的缺失变型;DcaWRKY39的C端WRKYGQK七肽结构域中的K突变成了N,形成了WRNYGQK七肽结构域;DcaWRKY48为WRKYGKK七肽结构域。DcaWRKY蛋白序列中至少存在10个保守基序,同源关系较近的成员具有相似的保守基序。启动子区的顺式作用元件分析显示DcaWRKY启动子区含有大量与光信号、植物激素、胁迫和分生组织等相关的功能域。转录组数据分析结果显示,有20个DcaWRKY在不定根形成过程中表现出不同程度地上调或下调,推测其可能在香石竹插穗不定根形成过程中发挥重要作用。定量分析结果表明DcaWRKY11、DcaWRKY13、DcaWRKY15、DcaWRKY22、DcaWRKY23、DcaWRKY31及DcaWRKY39的表达模式与转录组结果基本一致,且在香石竹不定根生长过程中表现出多样性。此外,DcaWRKY在生长素处理组和对照组中的表达水平无显著差异性,说明DcaWRKY对生长素不敏感。

关键词: 香石竹, WRKY, 基因, 不定根形成, 表达

Abstract:

The WRKY genes of carnation（DcaWRKY）were identified from Dianthus caryophyllus genomic database based on the WRKY protein sequences of Arabidopsis thaliana and the conserved domain sequence of WRKY proteins（PF03106）. In total,53 DcaWRKY members were identified in the carnation genome,with the amino acid size,molecular weight of protein（average）,isoelectric point and the gene intron numbers varying from 161-747 aa,18.27-82.58 kD,5.10-10.52 and 1-5 respectively. According to phylogenetic analysis,DcaWRKYs can be divided into three groups and groupⅡcan be further divided into five subgroups. DcaWRKY conserved domain analysis revealed three mutations in the WRKY domain,the WRKYGQK heptapeptide domain in N terminal of DcaWRKY20 were lack of ‘YGQK’and formatted the missing variant WRK,and the K in the heptapeptide domain of WRKYGQK at the C terminal of DcaWRKY39 is mutated to N,forming the heptapeptide domain of WRNYGQK and DcaWRKY48 is the WRKYGKK heptapeptide domain. In addition,Conserved motifs analysis showed that there were at least 10 motifs in DcaWRKY members and they have similar conserved motifs when they are in a closer phylogenetic relationship. Cis-acting element analysis in the promoter region showed that DcaWRKYs contained a large number of functional domains related to light signal,plant hormone,stress and meristem. Based on the transcriptomic data analysis,there were 20 DcaWRKY gene family members up-regulated or down-regulated during adventitious root formation,and we speculated that these genes may play an important role in the formation of adventitious roots in carnations cuttings. And the qRT-PCR analysis revealed that the mRNA expression patterns of DcaWRKY11,DcaWRKY13,DcaWRKY15,DcaWRKY22,DcaWRKY23,DcaWRKY31 and DcaWRKY39 showed a fairly good match to the RNA-seq analysis and showed diversity in the growth process of adventitious roots. In addition,there was no significant difference in the expression of DcaWRKYs between auxin group and control group,indicating that the DcaWRKYs is not sensitive to auxin.

Key words: Dianthus caryophyllus, WRKY, gene, adventitious root formation, expression

中图分类号:

S681.5

林胜男, 刘杰玮, 张晓妮, 包满珠, 傅小鹏. 香石竹WRKY家族全基因组鉴定及其表达分析[J]. 园艺学报, 2021, 48(9): 1768-1784.

LIN Shengnan, LIU Jiewei, ZHANG Xiaoni, BAO Manzhu, FU Xiaopeng. Genome-wide Identification and Expression Analysis of WRKY Gene Family in Dianthus caryophyllus[J]. Acta Horticulturae Sinica, 2021, 48(9): 1768-1784.

图/表 8

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基因 Gene	组 Group	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reverse primer
DcaWRKY11	Ⅱ-d	CCCGACCCTATACAGCAAGTC	CCATCTCCCTCTTCATCCCC
DcaWRKY13	Ⅱ-e	CGTTGTCGTTGTCGCAGTTT	TGATTCAACAGGTTTGAGGGGA
DcaWRKY15	Ⅱ-a	AGATTACTCGTGTCGCTGTTCG	TCTGTGTTCTCTACTCCGATCAA
DcaWRKY22	Ⅲ	CAAGGGACCCAAGGACACAT	AGAATGGGCAAAATGGGAATGA
DcaWRKY23	Ⅱ-b	ACCCGGCCTTTGCTGATACC	GCCGCCGTGAAATTAGGGTC
DcaWRKY31	Ⅱ-c	TACAAAGACAAGGGCGCGAA	TGCAAAAGACCGTCATCCCT
DcaWRKY39	Ⅰ	CCTAGACCGTTTGTGTCGCT	ACCCGCTTCAGTGATGTCTT
DcaGAPDH	—	CGGAAAGTTGACTGGTATGGC	CATCCTCGGTGTAGCCCAAAAT

基因 Gene	组 Group	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reverse primer
DcaWRKY11	Ⅱ-d	CCCGACCCTATACAGCAAGTC	CCATCTCCCTCTTCATCCCC
DcaWRKY13	Ⅱ-e	CGTTGTCGTTGTCGCAGTTT	TGATTCAACAGGTTTGAGGGGA
DcaWRKY15	Ⅱ-a	AGATTACTCGTGTCGCTGTTCG	TCTGTGTTCTCTACTCCGATCAA
DcaWRKY22	Ⅲ	CAAGGGACCCAAGGACACAT	AGAATGGGCAAAATGGGAATGA
DcaWRKY23	Ⅱ-b	ACCCGGCCTTTGCTGATACC	GCCGCCGTGAAATTAGGGTC
DcaWRKY31	Ⅱ-c	TACAAAGACAAGGGCGCGAA	TGCAAAAGACCGTCATCCCT
DcaWRKY39	Ⅰ	CCTAGACCGTTTGTGTCGCT	ACCCGCTTCAGTGATGTCTT
DcaGAPDH	—	CGGAAAGTTGACTGGTATGGC	CATCCTCGGTGTAGCCCAAAAT

元件名称 Element name	保守序列 Consensus sequence	生物学功能 Biological function	基因名称 Gene name	来源 Source
A-box	CCGTCC	顺式作用调节元件 cis-acting regulatory element	DcaWRKY16,33,35,39,41,42,48	香芹 Petroselinum crispum
CAAT-box	CCAAT	启动子和增强子区常见的顺式作用元件 Common cis-acting element in promoter and enhancer regions	DcaWRKY1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,53	拟南芥 Arabidopsis thaliana
G-box	TACGTG	参与光响应的顺式调控元件 cis-acting regulatory element involved in light responsiveness	DcaWRKY1,3,10,12,13,15,17,18,20,21,26,30,32,33,41,42,43,44,49,50	拟南芥 Arabidopsis thaliana
ABRE	ACGTG	参与脱落酸反应的顺式作用元件 cis-acting element involved in the abscisic acid responsiveness	DcWRKY1,2,3,8,9,10,12,13,15,17,18,20,21,22,24,26,27,29,30,32,34,36,43,44,46,49,50,53	拟南芥 Arabidopsis thaliana
LTR	CCGAAA	参与低温反应的顺式作用元件 cis-acting element involved in low-temperature responsiveness	DcaWRKY1,3,5,8,9,10,11,12,14,15,16,17,19, 22,25,27,32,36,39,40,43,44,47,49,51	大麦 Hordeum vulgare
ARE	AAACCA	厌氧诱导所必需的顺式作用调节元件 cis-acting regulatory element essential for the anaerobic induction	DcaWRKY1,2,3,5,6,7,8,9,10,12,13,14,17,18,19,21,23,25,27,31,32,35,36,37,38,42,43,44,45,46,47,48,49,50	玉米 Zea mays
TC-rich repeats	GTTTTCTTAC	参与防御和应激反应的顺式作用元件 cis-acting element involved in defense and stress responsiveness	DcaWRKY1,7,15,17,19,22,23,29,32,33,40,45,49	烟草 Nicotiana tabacum
GCN4_ motif	TGAGTCA	参与胚乳表达的顺式调控元件 cis-regulatory element involved in endosperm expression	DcaWRKY4,6,11,15,17,21,30,36,38,48,49	水稻 Oryza sativa
CGTCA- motif	CGTCA	参与MeJA反应的顺式调控元件 cis-acting regulatory element involved in the MeJA-responsiveness	DcaWRKY3,5,6,7,8,9,10,11,14,15,16,17,18,19,20,22,24,26,27,29,30,34,35,38,39,40,41,45,46,48,49,51,53	大麦 Hordeum vulgare
WUN- motif	AAATTTCCT	损伤反应元件 Wound-responsive element	DcaWRKY18,28	芸薹 Brassica oleracea
TCA- element	CCATCTTTTT	参与水杨酸反应的顺式作用元件 cis-acting element involved in salicylic acid responsiveness	DcaWRKY3,4,12,13,15,16,18,25,28,32,40,41,43,48,51	烟草 Nicotiana tabacum
RY-element	CATGCATG	参与种子特异性调控的顺式调控元件 cis-acting regulatory element involved in seed-specific regulation	DcaWRKY43	向日葵 Helianthus annuus
AuxRR- core	GGTCCAT	参与生长素反应的顺式调控元件 cis-acting regulatory element involved in auxin responsiveness	DcaWRKY12,13,15,16,23,24,39,40,51,53	烟草 Nicotiana tabacum
MSA-like	TCCAACGGT	参与细胞周期调控的顺式作用元件 cis-acting element involved in cell cycle regulation	DcaWRKY6,17,49	长春花 Catharanthus roseus

元件名称 Element name	保守序列 Consensus sequence	生物学功能 Biological function	基因名称 Gene name	来源 Source
A-box	CCGTCC	顺式作用调节元件 cis-acting regulatory element	DcaWRKY16,33,35,39,41,42,48	香芹 Petroselinum crispum
CAAT-box	CCAAT	启动子和增强子区常见的顺式作用元件 Common cis-acting element in promoter and enhancer regions	DcaWRKY1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,53	拟南芥 Arabidopsis thaliana
G-box	TACGTG	参与光响应的顺式调控元件 cis-acting regulatory element involved in light responsiveness	DcaWRKY1,3,10,12,13,15,17,18,20,21,26,30,32,33,41,42,43,44,49,50	拟南芥 Arabidopsis thaliana
ABRE	ACGTG	参与脱落酸反应的顺式作用元件 cis-acting element involved in the abscisic acid responsiveness	DcWRKY1,2,3,8,9,10,12,13,15,17,18,20,21,22,24,26,27,29,30,32,34,36,43,44,46,49,50,53	拟南芥 Arabidopsis thaliana
LTR	CCGAAA	参与低温反应的顺式作用元件 cis-acting element involved in low-temperature responsiveness	DcaWRKY1,3,5,8,9,10,11,12,14,15,16,17,19, 22,25,27,32,36,39,40,43,44,47,49,51	大麦 Hordeum vulgare
ARE	AAACCA	厌氧诱导所必需的顺式作用调节元件 cis-acting regulatory element essential for the anaerobic induction	DcaWRKY1,2,3,5,6,7,8,9,10,12,13,14,17,18,19,21,23,25,27,31,32,35,36,37,38,42,43,44,45,46,47,48,49,50	玉米 Zea mays
TC-rich repeats	GTTTTCTTAC	参与防御和应激反应的顺式作用元件 cis-acting element involved in defense and stress responsiveness	DcaWRKY1,7,15,17,19,22,23,29,32,33,40,45,49	烟草 Nicotiana tabacum
GCN4_ motif	TGAGTCA	参与胚乳表达的顺式调控元件 cis-regulatory element involved in endosperm expression	DcaWRKY4,6,11,15,17,21,30,36,38,48,49	水稻 Oryza sativa
CGTCA- motif	CGTCA	参与MeJA反应的顺式调控元件 cis-acting regulatory element involved in the MeJA-responsiveness	DcaWRKY3,5,6,7,8,9,10,11,14,15,16,17,18,19,20,22,24,26,27,29,30,34,35,38,39,40,41,45,46,48,49,51,53	大麦 Hordeum vulgare
WUN- motif	AAATTTCCT	损伤反应元件 Wound-responsive element	DcaWRKY18,28	芸薹 Brassica oleracea
TCA- element	CCATCTTTTT	参与水杨酸反应的顺式作用元件 cis-acting element involved in salicylic acid responsiveness	DcaWRKY3,4,12,13,15,16,18,25,28,32,40,41,43,48,51	烟草 Nicotiana tabacum
RY-element	CATGCATG	参与种子特异性调控的顺式调控元件 cis-acting regulatory element involved in seed-specific regulation	DcaWRKY43	向日葵 Helianthus annuus
AuxRR- core	GGTCCAT	参与生长素反应的顺式调控元件 cis-acting regulatory element involved in auxin responsiveness	DcaWRKY12,13,15,16,23,24,39,40,51,53	烟草 Nicotiana tabacum
MSA-like	TCCAACGGT	参与细胞周期调控的顺式作用元件 cis-acting element involved in cell cycle regulation	DcaWRKY6,17,49	长春花 Catharanthus roseus