Genome-wide Identification and Expression Analysis of WRKY Gene Family in Dianthus caryophyllus

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

Acta Horticulturae Sinica ›› 2021, Vol. 48 ›› Issue (9): 1768-1784.doi: 10.16420/j.issn.0513-353x.2019-0986

• Research Papers • Previous Articles Next Articles

Genome-wide Identification and Expression Analysis of WRKY Gene Family in Dianthus caryophyllus

LIN Shengnan, LIU Jiewei, ZHANG Xiaoni, BAO Manzhu, FU Xiaopeng^*()

College of Horticulture and Forestry Science,Huazhong Agricultural University,Wuhan 430070,China

Received:2021-04-09 Revised:2021-05-26 Online:2021-09-25 Published:2021-09-30
Contact: FU Xiaopeng E-mail:fuxiaopeng@mail.hzau.edu.cn

Abstract

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

CLC Number:

S681.5

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.

Figures/Tables 8

References 33

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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

Genome-wide Identification and Expression Analysis of WRKY Gene Family in Dianthus caryophyllus

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