Identification of a WRKY gene family based on full-length transcriptome sequences and analysis of response patterns under salt stress in Halogeton glomeratus

doi:10.11686/cyxb2021478

Abstract

Abstract:

WRKY is a plant-specific transcription factor that plays an important role in plant growth， plant development and plant stress responses. This research aimed to identify members of the WRKY gene family in Halogeton glomeratus， explore their evolutionary relationships and elucidate the expression response pattern of HgWRKY genes under salt stress. From the full-length transcriptome data of H. glomeratus， the WRKY gene family members were identified and analyzed by bioinformatics methods， and their relative expression levels under salt stress were detected by qRT-PCR. A total of 31 HgWRKY genes were identified from H. glomeratus，with the coded amino acid number of identified HgWRKYs ranging from 220 to 611. All HgWRKY proteins had complete conserved WRKYGQK sequences at the N-terminal. Subcellularly， all HgWRKYs were located in the nucleus， and HgWRKY20 and HgWRKY21 were also located in mitochondria. Based on phylogenetic analysis， the 31 detected HgWRKYs can be divided into three groups： Ⅰ （8 members）， Ⅱ （22 members）， Ⅲ （1 member）. Group Ⅱ contained five subgroups： Ⅱ-a （1 member）， Ⅱ-b （2 members）， Ⅱ-c （1 member）， Ⅱ-d （15 members） and Ⅱ-e （3 members）. Motif 1 and Motif 2 were the characteristic motifs of the HgWRKYs family， and these were found to be relatively conserved in the evolutionary process. The qRT-PCR results indicated that HgWRKYs were mainly expressed in roots with tissue specificity， and the expression levels of HgWRKY19， HgWRKY23 and HgWRKY27 genes were the highest at 24 h. These three were therefore selected as candidate genes for salt stress response， in order to provide a basis for further study of the molecular mechanisms of HgWRKY genes in response to salt stress.

Key words: Halogeton glomeratus, WRKY gene family, salt stress, bioinformatics analysis

Qian CHEN, Xiao-yun XU, Jun-cheng WANG, Li-rong YAO, Er-jing SI, Ke YANG, Xiao-ling WEI, Xiao-le MA, Bao-chun LI, Xun-wu SHANG, Ya-xiong MENG, Hua-jun WANG. Identification of a WRKY gene family based on full-length transcriptome sequences and analysis of response patterns under salt stress in Halogeton glomeratus[J]. Acta Prataculturae Sinica, 2022, 31(12): 146-157.

Figures/Tables 6

References 38

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基因Gene	产物长度Product length （bp）	上游引物Forward primer （5′-3′）	下游引物Reverse primer （5′-3′）
HgWRKY1	108	CGCATCCAAATTGTCCAACGA	TACCAGGCTGAGGCTTAGGA
HgWRKY2	193	GCAAGGCACTCAAACCCAAC	CGGTGGTGTCTGACCTTCAT
HgWRKY3	164	TCGTCGATTTCGGTTGCTGA	ACTACTCTTGGCTCCCTCACT
HgWRKY4	136	CCGCAAGCAAGCAACATGAA	TCCCAACATCACCCACTTCC
HgWRKY5	108	CGCATCCAAATTGTCCAACGA	TACCAGGCTGAGGCTTAGGA
HgWRKY6	164	TCGTCGATTTCGGTTGCTGA	ACTACTCTTGGCTCCCTCACT
HgWRKY7	174	TCCCAGTTGGCTAGGACTGT	CCAGCGGTACCCATCATCAA
HgWRKY8	120	CACAACCACGATGTTCCTGC	ACTGAGAGGCCTTAGACCGA
HgWRKY9	116	CCATCATCAGGTGGCTCGAA	GCGTTGGTCACGTAGGACTT
HgWRKY10	162	TGCCCTCAATGGCTATAAGGC	GCCCAGGGTTTTGTAGCATC
HgWRKY11	164	TCGTCGATTTCGGTTGCTGA	ACTACTCTTGGCTCCCTCACT
HgWRKY12	197	TCCGATGAAAGAGCCTGGTG	TGGGATGCGGAGTTCCTTTG
HgWRKY13	102	TGGATGGAAGTGTGGCGAAT	CGGAGCACCTCTTCCTATGC
HgWRKY14	193	TGGATCTTCTGGTCGTTGCC	TCCCCGTACGCTACTACACT
HgWRKY15	175	GGGATGGTATCGTCGGTTGG	TCGCGCTTATTGCTGGTACT
HgWRKY16	113	GTATCGTCGGTTGGGAGACC	GAACAGTGACAGCGACCAGA
HgWRKY17	117	CATTGCTCCTCGTCAAAGCG	GCCGTATTTGCGCCATGAAT
HgWRKY18	142	TCTCTTCGTTGAGCGTGGAT	TTGACACTCCCATCTTCGCC
HgWRKY19	169	CCGACAGTGTTCAACCGTCT	TGGCAACGACCAGAAGATCC
HgWRKY20	195	CGTTGACTGGTGAGACGGAT	GTCTCCCAACCGACGATACC
HgWRKY21	119	GGATGGTATCGTCGGTTGGG	AGAACAGTGACAGCGACCAG
HgWRKY22	155	CTTACCCGCACACAAGTCCA	AGACGGTTGAACACTGTCGG
HgWRKY23	117	CATTGCTCCTCGTCAAAGCG	GCCGTATTTGCGCCATGAAT
HgWRKY24	102	TGGATGGAAGTGTGGCGAAT	CGGAGCACCTCTTCCTATGC
HgWRKY25	117	CATTGCTCCTCGTCAAAGCG	GCCGTATTTGCGCCATGAAT
HgWRKY26	191	GGCGGTGGTGGATCTATGTT	TTACGCTTTGACGAGGAGCA
HgWRKY27	155	CTTACCCGCACACAAGTCCA	AGACGGTTGAACACTGTCGG
HgWRKY28	185	TACTACCGGTGCACGAACAG	GGCATTGGAGGAGCAAAACG
HgWRKY29	129	AGTTACTACCGTTGCACCACT	ACGTGGGAGGACAGTACAAG
HgWRKY30	163	ATGGGCAAAAAGCCGTCAAG	AATGTAGCCGGAACTGGGTG
HgWRKY31	137	ACAGATGCACCCATCGTCATT	GGGCTGTGAGAAATGGGCTT

基因Gene	产物长度Product length （bp）	上游引物Forward primer （5′-3′）	下游引物Reverse primer （5′-3′）
HgWRKY1	108	CGCATCCAAATTGTCCAACGA	TACCAGGCTGAGGCTTAGGA
HgWRKY2	193	GCAAGGCACTCAAACCCAAC	CGGTGGTGTCTGACCTTCAT
HgWRKY3	164	TCGTCGATTTCGGTTGCTGA	ACTACTCTTGGCTCCCTCACT
HgWRKY4	136	CCGCAAGCAAGCAACATGAA	TCCCAACATCACCCACTTCC
HgWRKY5	108	CGCATCCAAATTGTCCAACGA	TACCAGGCTGAGGCTTAGGA
HgWRKY6	164	TCGTCGATTTCGGTTGCTGA	ACTACTCTTGGCTCCCTCACT
HgWRKY7	174	TCCCAGTTGGCTAGGACTGT	CCAGCGGTACCCATCATCAA
HgWRKY8	120	CACAACCACGATGTTCCTGC	ACTGAGAGGCCTTAGACCGA
HgWRKY9	116	CCATCATCAGGTGGCTCGAA	GCGTTGGTCACGTAGGACTT
HgWRKY10	162	TGCCCTCAATGGCTATAAGGC	GCCCAGGGTTTTGTAGCATC
HgWRKY11	164	TCGTCGATTTCGGTTGCTGA	ACTACTCTTGGCTCCCTCACT
HgWRKY12	197	TCCGATGAAAGAGCCTGGTG	TGGGATGCGGAGTTCCTTTG
HgWRKY13	102	TGGATGGAAGTGTGGCGAAT	CGGAGCACCTCTTCCTATGC
HgWRKY14	193	TGGATCTTCTGGTCGTTGCC	TCCCCGTACGCTACTACACT
HgWRKY15	175	GGGATGGTATCGTCGGTTGG	TCGCGCTTATTGCTGGTACT
HgWRKY16	113	GTATCGTCGGTTGGGAGACC	GAACAGTGACAGCGACCAGA
HgWRKY17	117	CATTGCTCCTCGTCAAAGCG	GCCGTATTTGCGCCATGAAT
HgWRKY18	142	TCTCTTCGTTGAGCGTGGAT	TTGACACTCCCATCTTCGCC
HgWRKY19	169	CCGACAGTGTTCAACCGTCT	TGGCAACGACCAGAAGATCC
HgWRKY20	195	CGTTGACTGGTGAGACGGAT	GTCTCCCAACCGACGATACC
HgWRKY21	119	GGATGGTATCGTCGGTTGGG	AGAACAGTGACAGCGACCAG
HgWRKY22	155	CTTACCCGCACACAAGTCCA	AGACGGTTGAACACTGTCGG
HgWRKY23	117	CATTGCTCCTCGTCAAAGCG	GCCGTATTTGCGCCATGAAT
HgWRKY24	102	TGGATGGAAGTGTGGCGAAT	CGGAGCACCTCTTCCTATGC
HgWRKY25	117	CATTGCTCCTCGTCAAAGCG	GCCGTATTTGCGCCATGAAT
HgWRKY26	191	GGCGGTGGTGGATCTATGTT	TTACGCTTTGACGAGGAGCA
HgWRKY27	155	CTTACCCGCACACAAGTCCA	AGACGGTTGAACACTGTCGG
HgWRKY28	185	TACTACCGGTGCACGAACAG	GGCATTGGAGGAGCAAAACG
HgWRKY29	129	AGTTACTACCGTTGCACCACT	ACGTGGGAGGACAGTACAAG
HgWRKY30	163	ATGGGCAAAAAGCCGTCAAG	AATGTAGCCGGAACTGGGTG
HgWRKY31	137	ACAGATGCACCCATCGTCATT	GGGCTGTGAGAAATGGGCTT

基因编号 Genetic code	基因号 Gene ID	分子量 Molecular weight （Da）	氨基酸数 Amino acid quantity （aa）	长度 Length （bp）	等电点 Isoelectric point （PI）	亚细胞定位 Subcellular localization	α螺旋 Alpha-helix （%）	β转角 Beta-turn （%）	延长链 Extended strand （%）	无规则卷曲 Random coil （%）
HgWRKY1	Hg32527	39020.8	348	1047	8.63	Nucleus	10.63	5.17	12.93	71.26
HgWRKY2	Hg33422	65872.3	611	1836	6.29	Nucleus	9.66	3.93	13.58	72.83
HgWRKY3	Hg33512	64774.9	592	1779	6.48	Nucleus	10.81	3.38	8.78	77.03
HgWRKY4	Hg33871	58072.5	525	1578	6.22	Nucleus	11.24	2.67	13.52	72.57
HgWRKY5	Hg35093	64054.2	578	1737	6.03	Nucleus	11.42	2.77	10.38	75.43
HgWRKY6	Hg41718	48852.7	439	1320	7.61	Nucleus	10.48	3.87	8.43	77.22
HgWRKY7	Hg42748	54482.6	503	1512	6.07	Nucleus	9.74	3.98	12.92	73.36
HgWRKY8	Hg47058	42592.6	380	1143	8.76	Nucleus	11.58	2.89	13.68	71.84
HgWRKY9	Hg44248	40456.7	367	1104	8.43	Nucleus	27.25	2.18	15.80	54.77
HgWRKY10	Hg52691	35453.2	326	981	7.14	Nucleus	14.72	3.07	11.66	70.55
HgWRKY11	Hg32535	35453.2	326	981	7.14	Nucleus	14.72	3.07	11.66	70.55
HgWRKY12	Hg33409	30814.3	283	852	6.80	Nucleus	20.85	2.47	13.43	63.25
HgWRKY13	Hg34478	41789.8	378	1137	9.67	Nucleus	27.25	5.56	12.17	55.03
HgWRKY14	Hg34900	42129.2	389	1170	9.56	Nucleus	23.39	4.88	10.28	61.44
HgWRKY15	Hg40923	42243.2	387	1164	9.54	Nucleus	17.31	3.62	11.11	67.96
HgWRKY16	Hg42453	42243.2	387	1164	9.54	Nucleus	17.31	3.62	11.11	67.96
HgWRKY17	Hg42552	40884.7	378	1137	9.60	Nucleus	17.20	10.10	19.58	53.17
HgWRKY18	Hg43510	41710.6	377	1134	9.67	Nucleus	28.91	4.77	10.08	56.23
HgWRKY19	Hg44563	42129.4	389	1170	9.56	Nucleus	23.39	4.88	10.28	61.44
HgWRKY20	Hg45217	42243.2	387	1164	9.54	Nucleus， Mitochondria	17.31	3.62	11.11	67.96
HgWRKY21	Hg46151	42243.2	387	1164	9.54	Nucleus， Mitochondria	17.31	3.62	11.11	67.96
HgWRKY22	Hg46356	39330.3	361	1086	9.70	Nucleus	16.62	4.43	12.19	66.76
HgWRKY23	Hg46711	40884.7	378	1137	9.60	Nucleus	17.20	10.10	19.58	53.17
HgWRKY24	Hg47922	41789.8	378	1137	9.67	Nucleus	27.25	5.56	12.17	55.03
HgWRKY25	Hg49441	40065.7	369	1110	9.56	Nucleus	18.70	7.32	18.43	55.56
HgWRKY26	Hg50014	40610.4	375	1128	9.60	Nucleus	17.60	8.53	19.47	54.40
HgWRKY27	Hg51207	42129.4	389	1170	9.56	Nucleus	23.39	4.88	10.28	61.44
HgWRKY28	Hg49431	24463.3	220	663	9.77	Nucleus	9.55	4.09	13.18	73.18
HgWRKY29	Hg41342	45534.9	414	1245	6.19	Nucleus	27.78	5.07	16.91	50.24
HgWRKY30	Hg50291	39304.0	359	1080	6.15	Nucleus	28.97	5.57	12.53	52.92
HgWRKY31	Hg45674	30599.6	272	819	9.26	Nucleus	24.26	3.31	12.87	59.56

基因编号 Genetic code	基因号 Gene ID	分子量 Molecular weight （Da）	氨基酸数 Amino acid quantity （aa）	长度 Length （bp）	等电点 Isoelectric point （PI）	亚细胞定位 Subcellular localization	α螺旋 Alpha-helix （%）	β转角 Beta-turn （%）	延长链 Extended strand （%）	无规则卷曲 Random coil （%）
HgWRKY1	Hg32527	39020.8	348	1047	8.63	Nucleus	10.63	5.17	12.93	71.26
HgWRKY2	Hg33422	65872.3	611	1836	6.29	Nucleus	9.66	3.93	13.58	72.83
HgWRKY3	Hg33512	64774.9	592	1779	6.48	Nucleus	10.81	3.38	8.78	77.03
HgWRKY4	Hg33871	58072.5	525	1578	6.22	Nucleus	11.24	2.67	13.52	72.57
HgWRKY5	Hg35093	64054.2	578	1737	6.03	Nucleus	11.42	2.77	10.38	75.43
HgWRKY6	Hg41718	48852.7	439	1320	7.61	Nucleus	10.48	3.87	8.43	77.22
HgWRKY7	Hg42748	54482.6	503	1512	6.07	Nucleus	9.74	3.98	12.92	73.36
HgWRKY8	Hg47058	42592.6	380	1143	8.76	Nucleus	11.58	2.89	13.68	71.84
HgWRKY9	Hg44248	40456.7	367	1104	8.43	Nucleus	27.25	2.18	15.80	54.77
HgWRKY10	Hg52691	35453.2	326	981	7.14	Nucleus	14.72	3.07	11.66	70.55
HgWRKY11	Hg32535	35453.2	326	981	7.14	Nucleus	14.72	3.07	11.66	70.55
HgWRKY12	Hg33409	30814.3	283	852	6.80	Nucleus	20.85	2.47	13.43	63.25
HgWRKY13	Hg34478	41789.8	378	1137	9.67	Nucleus	27.25	5.56	12.17	55.03
HgWRKY14	Hg34900	42129.2	389	1170	9.56	Nucleus	23.39	4.88	10.28	61.44
HgWRKY15	Hg40923	42243.2	387	1164	9.54	Nucleus	17.31	3.62	11.11	67.96
HgWRKY16	Hg42453	42243.2	387	1164	9.54	Nucleus	17.31	3.62	11.11	67.96
HgWRKY17	Hg42552	40884.7	378	1137	9.60	Nucleus	17.20	10.10	19.58	53.17
HgWRKY18	Hg43510	41710.6	377	1134	9.67	Nucleus	28.91	4.77	10.08	56.23
HgWRKY19	Hg44563	42129.4	389	1170	9.56	Nucleus	23.39	4.88	10.28	61.44
HgWRKY20	Hg45217	42243.2	387	1164	9.54	Nucleus， Mitochondria	17.31	3.62	11.11	67.96
HgWRKY21	Hg46151	42243.2	387	1164	9.54	Nucleus， Mitochondria	17.31	3.62	11.11	67.96
HgWRKY22	Hg46356	39330.3	361	1086	9.70	Nucleus	16.62	4.43	12.19	66.76
HgWRKY23	Hg46711	40884.7	378	1137	9.60	Nucleus	17.20	10.10	19.58	53.17
HgWRKY24	Hg47922	41789.8	378	1137	9.67	Nucleus	27.25	5.56	12.17	55.03
HgWRKY25	Hg49441	40065.7	369	1110	9.56	Nucleus	18.70	7.32	18.43	55.56
HgWRKY26	Hg50014	40610.4	375	1128	9.60	Nucleus	17.60	8.53	19.47	54.40
HgWRKY27	Hg51207	42129.4	389	1170	9.56	Nucleus	23.39	4.88	10.28	61.44
HgWRKY28	Hg49431	24463.3	220	663	9.77	Nucleus	9.55	4.09	13.18	73.18
HgWRKY29	Hg41342	45534.9	414	1245	6.19	Nucleus	27.78	5.07	16.91	50.24
HgWRKY30	Hg50291	39304.0	359	1080	6.15	Nucleus	28.97	5.57	12.53	52.92
HgWRKY31	Hg45674	30599.6	272	819	9.26	Nucleus	24.26	3.31	12.87	59.56

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