Identification and Analysis of WRKY Gene Family in Rheum palmatum L.

doi:10.13560/j.cnki.biotech.bull.1985.2023-0326

Abstract

Abstract:

【Objective】This study provides a basis for the functional verification of WRKY genes, and then provide a scientific basis for the transcriptional regulation mechanism research into rhubarb quality formation. 【Method】In this study, we identified WRKY gene family members in R. palmatum L. based on full-length transcriptome data, and performed a series of bioinformatics analysis, including physicochemical properties, protein domains and phylogenetic tree. RNA-seq was used for gene tissue expression analysis, along with expression profile in response to MeJA treatment. 【Result】53 gene members in RpWRKYs family with complete ORFs, and the numbers of amino acids encoding the protein ranged from 192 to 748 bp, all were hydrophilic proteins, and the predicted localization was all in the nucleus. RpWRKYs combined with A. thaliana WRKYs were clustered into three groups, i.e., subgroup I, II and III, and group II with the highest number of WRKYs, accounting for 58.49%. The RNA-seq analysis revealed that RpWRKYs were differentially expressed in the roots, rhizomes and leaves of R. palmatum L., seven of them genes were highly expressed in the roots and rhizomes. Twelve RpWRKY genes showed differential expressions in the response to MeJA treatment, ten of them were significantly induced by MeJA. The expression profile of RpWRKY5, RpWRKY6, RpWRKY9 and RpWRKY33 verified by qPCR was almost consistent with the transcriptome results. RpWRKY2, RpWRKY16, RpWRKY20, RpWRKY22 and RpWRKY23 interacted with chalcone synthase (CHS) gene. 【Conclusion】Expression profiles of 53 R. palmatum L. WRKY genes, bioinformatics, tissues and response to MeJA were obtained, five of which may be related to the synthesis of rhubarb anthraquinones.

Key words: Rheum palmatum L., RpWRKY, transcription factor, gene expression, MeJA

WU Zhen, ZHANG Ming-Ying, YAN Feng, LI Yi-min, GAO Jing, YAN Yong-Gang, ZHANG Gang. Identification and Analysis of WRKY Gene Family in Rheum palmatum L.[J]. Biotechnology Bulletin, 2024, 40(1): 250-261.

Figures/Tables 7

References 35

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基因名称 Gene name	基因ID Gene ID	ORF protein length/aa	分子量 Molecular weight/Da	等电点pI	平均亲水性GRAVY	不稳定指数 Instability index	脂肪族指数 Fatty coefficient	α螺旋 Alpha helix/%	延伸链 Extended strand/%	β转角 Beta turn/%	无规则卷曲Random coil/%
RpWRKY1	Isoform0001571	748	80746.12	6.04	-0.769	49.13	53.33	11.36	12.03	3.34	73.26
RpWRKY2	Isoform0003671	447	48784.58	9.50	-0.870	53.90	55.91	14.99	10.74	4.25	70.02
RpWRKY3	Isoform0006840	593	64111.13	7.00	-0.697	52.67	63.86	9.11	12.98	4.55	73.36
RpWRKY4	Isoform0008260	593	64180.24	7.29	-0.704	52.40	63.86	7.42	13.15	3.54	75.89
RpWRKY5	Isoform0009274	365	40613.68	9.80	-0.808	49.36	65.18	25.48	11.78	3.56	59.18
RpWRKY6	Isoform0009783	573	62231.07	6.82	-0.742	48.96	59.53	35.25	9.42	5.06	50.26
RpWRKY7	Isoform0011464	529	58326.20	6.78	-0.896	61.71	49.43	8.13	10.59	2.46	78.83
RpWRKY8	Isoform0012393	524	56149.15	8.41	-0.686	55.34	56.89	13.36	11.07	3.82	71.76
RpWRKY9	Isoform0012409	573	62259.08	6.67	-0.747	48.55	59.53	29.67	10.47	4.19	55.67
RpWRKY10	Isoform0012828	462	50368.00	7.65	-0.843	57.61	52.79	10.17	14.50	3.68	71.65
RpWRKY11	Isoform0013026	356	39690.82	9.74	-0.757	60.45	65.73	29.49	10.39	4.49	55.62
RpWRKY12	Isoform0013337	467	49772.44	5.79	-0.474	51.76	69.27	29.34	9.21	4.50	56.96
RpWRKY13	Isoform0013415	593	64079.13	7.29	-0.693	52.41	63.69	9.11	13.83	4.55	72.51
RpWRKY14	Isoform0014093	528	58141.02	6.78	-0.881	61.08	49.72	11.36	10.80	2.46	75.38
RpWRKY15	Isoform0014770	430	47143.58	8.09	-0.781	62.66	53.33	11.86	16.28	3.95	67.91
RpWRKY16	Isoform0015753	447	48783.59	9.53	-0.870	53.28	55.91	13.42	9.84	4.03	72.71
RpWRKY17	Isoform0016089	469	51423.94	9.54	-0.914	47.95	53.90	18.12	9.59	2.56	69.72
RpWRKY18	Isoform0017473	363	40238.24	9.82	-0.794	48.16	67.41	25.07	15.43	4.13	55.37
RpWRKY19	Isoform0017935	354	37886.60	9.76	-0.593	53.26	65.59	25.14	8.76	2.82	63.28
RpWRKY20	Isoform0018079	403	44088.79	9.61	-0.797	47.37	62.68	15.38	9.93	4.96	69.73
RpWRKY21	Isoform0019116	354	39353.73	5.77	-0.675	58.55	57.32	19.49	10.73	2.54	67.23
RpWRKY22	Isoform0019859	400	43677.20	9.57	-0.792	48.03	62.17	14.25	11.25	5.00	69.50
RpWRKY23	Isoform0020026	405	44263.85	9.52	-0.800	49.44	62.12	18.27	10.12	4.44	67.16
RpWRKY24	Isoform0022186	368	40007.26	9.81	-0.559	49.52	71.03	23.37	8.15	2.45	66.03
RpWRKY25	Isoform0022399	367	40538.83	7.22	-1.110	42.20	53.32	10.63	14.17	4.36	70.84
RpWRKY26	Isoform0022472	361	39893.02	5.53	-0.730	49.58	55.76	17.17	9.97	3.60	69.25
RpWRKY27	Isoform0022957	365	39711.87	9.81	-0.583	49.20	69.75	22.19	6.58	2.47	68.77
RpWRKY28	Isoform0025514	380	41348.08	8.77	-0.664	48.10	65.71	27.89	10.00	1.32	60.79
RpWRKY29	Isoform0026001	365	39697.85	9.81	-0.583	48.68	69.75	21.64	9.04	4.11	65.21
RpWRKY30	Isoform0026136	350	38801.02	5.77	-0.695	58.71	55.49	21.43	9.71	2.57	66.29
RpWRKY31	Isoform0027649	358	39591.84	5.40	-0.680	51.80	57.32	21.79	11.45	4.47	62.29
RpWRKY32	Isoform0029123	356	39336.52	5.40	-0.687	53.11	56.54	21.63	10.39	3.93	64.04
RpWRKY33	Isoform0030474	366	40147.73	8.32	-0.673	57.27	67.73	27.87	13.11	1.37	57.65
RpWRKY34	Isoform0032219	318	35220.09	6.59	-0.797	48.71	55.85	25.47	5.97	3.46	65.09
RpWRKY35	Isoform0032765	365	39961.51	8.05	-0.656	55.83	68.19	28.22	14.79	2.47	54.52
RpWRKY36	Isoform0033018	261	28842.33	8.14	-0.762	47.36	54.21	22.61	11.11	4.21	62.07
RpWRKY37	Isoform0033501	325	35397.04	9.51	-0.606	55.12	55.88	18.77	8.62	2.77	69.85
RpWRKY38	Isoform0033604	354	38650.30	7.54	-0.656	52.50	64.49	30.79	11.58	2.26	55.37
RpWRKY39	Isoform0033810	332	36096.34	9.53	-0.688	49.50	60.57	18.67	9.64	6.33	65.36
RpWRKY40	Isoform0033814	325	35361.21	9.64	-0.474	43.40	64.28	20.62	9.85	2.77	66.77
RpWRKY41	Isoform0033861	342	36989.05	9.92	-0.557	52.91	65.06	19.30	11.70	2.34	66.67
RpWRKY42	Isoform0034281	354	39281.63	5.77	-0.681	58.85	56.78	21.75	10.73	4.24	63.28
RpWRKY43	Isoform0034386	354	38564.15	7.56	-0.655	54.20	64.49	31.64	12.43	2.26	53.67
RpWRKY44	Isoform0035302	274	30915.54	8.98	-0.833	38.54	56.53	22.99	19.71	6.93	50.36
RpWRKY45	Isoform0035609	354	37872.57	9.76	-0.593	52.47	65.59	24.29	9.60	2.54	63.56
RpWRKY46	Isoform0037309	376	40878.63	8.78	-0.633	50.94	65.11	23.67	14.36	2.13	59.84
RpWRKY47	Isoform0038096	289	30430.81	5.77	-0.515	56.60	58.10	17.65	7.96	2.42	71.97
RpWRKY48	Isoform0040944	354	37890.60	9.71	-0.597	52.91	64.77	24.58	8.47	2.82	64.12
RpWRKY49	Isoform0008291	321	34800.48	6.32	-0.681	57.15	55.02	17.45	9.35	3.43	69.78
RpWRKY50	Isoform0034529	319	35145.27	7.20	-0.642	58.22	58.71	26.96	8.15	4.08	60.82
RpWRKY51	Isoform0038659	325	35383.01	9.51	-0.606	55.12	55.88	19.69	10.46	2.77	67.08
RpWRKY52	Isoform0049163	227	25433.89	7.08	-0.605	41.64	73.92	37.00	12.78	2.64	47.58
RpWRKY53	Isoform0054945	192	21184.13	6.10	-0.850	36.72	41.61	18.75	23.96	7.29	50.00

基因名称 Gene name	基因ID Gene ID	ORF protein length/aa	分子量 Molecular weight/Da	等电点pI	平均亲水性GRAVY	不稳定指数 Instability index	脂肪族指数 Fatty coefficient	α螺旋 Alpha helix/%	延伸链 Extended strand/%	β转角 Beta turn/%	无规则卷曲Random coil/%
RpWRKY1	Isoform0001571	748	80746.12	6.04	-0.769	49.13	53.33	11.36	12.03	3.34	73.26
RpWRKY2	Isoform0003671	447	48784.58	9.50	-0.870	53.90	55.91	14.99	10.74	4.25	70.02
RpWRKY3	Isoform0006840	593	64111.13	7.00	-0.697	52.67	63.86	9.11	12.98	4.55	73.36
RpWRKY4	Isoform0008260	593	64180.24	7.29	-0.704	52.40	63.86	7.42	13.15	3.54	75.89
RpWRKY5	Isoform0009274	365	40613.68	9.80	-0.808	49.36	65.18	25.48	11.78	3.56	59.18
RpWRKY6	Isoform0009783	573	62231.07	6.82	-0.742	48.96	59.53	35.25	9.42	5.06	50.26
RpWRKY7	Isoform0011464	529	58326.20	6.78	-0.896	61.71	49.43	8.13	10.59	2.46	78.83
RpWRKY8	Isoform0012393	524	56149.15	8.41	-0.686	55.34	56.89	13.36	11.07	3.82	71.76
RpWRKY9	Isoform0012409	573	62259.08	6.67	-0.747	48.55	59.53	29.67	10.47	4.19	55.67
RpWRKY10	Isoform0012828	462	50368.00	7.65	-0.843	57.61	52.79	10.17	14.50	3.68	71.65
RpWRKY11	Isoform0013026	356	39690.82	9.74	-0.757	60.45	65.73	29.49	10.39	4.49	55.62
RpWRKY12	Isoform0013337	467	49772.44	5.79	-0.474	51.76	69.27	29.34	9.21	4.50	56.96
RpWRKY13	Isoform0013415	593	64079.13	7.29	-0.693	52.41	63.69	9.11	13.83	4.55	72.51
RpWRKY14	Isoform0014093	528	58141.02	6.78	-0.881	61.08	49.72	11.36	10.80	2.46	75.38
RpWRKY15	Isoform0014770	430	47143.58	8.09	-0.781	62.66	53.33	11.86	16.28	3.95	67.91
RpWRKY16	Isoform0015753	447	48783.59	9.53	-0.870	53.28	55.91	13.42	9.84	4.03	72.71
RpWRKY17	Isoform0016089	469	51423.94	9.54	-0.914	47.95	53.90	18.12	9.59	2.56	69.72
RpWRKY18	Isoform0017473	363	40238.24	9.82	-0.794	48.16	67.41	25.07	15.43	4.13	55.37
RpWRKY19	Isoform0017935	354	37886.60	9.76	-0.593	53.26	65.59	25.14	8.76	2.82	63.28
RpWRKY20	Isoform0018079	403	44088.79	9.61	-0.797	47.37	62.68	15.38	9.93	4.96	69.73
RpWRKY21	Isoform0019116	354	39353.73	5.77	-0.675	58.55	57.32	19.49	10.73	2.54	67.23
RpWRKY22	Isoform0019859	400	43677.20	9.57	-0.792	48.03	62.17	14.25	11.25	5.00	69.50
RpWRKY23	Isoform0020026	405	44263.85	9.52	-0.800	49.44	62.12	18.27	10.12	4.44	67.16
RpWRKY24	Isoform0022186	368	40007.26	9.81	-0.559	49.52	71.03	23.37	8.15	2.45	66.03
RpWRKY25	Isoform0022399	367	40538.83	7.22	-1.110	42.20	53.32	10.63	14.17	4.36	70.84
RpWRKY26	Isoform0022472	361	39893.02	5.53	-0.730	49.58	55.76	17.17	9.97	3.60	69.25
RpWRKY27	Isoform0022957	365	39711.87	9.81	-0.583	49.20	69.75	22.19	6.58	2.47	68.77
RpWRKY28	Isoform0025514	380	41348.08	8.77	-0.664	48.10	65.71	27.89	10.00	1.32	60.79
RpWRKY29	Isoform0026001	365	39697.85	9.81	-0.583	48.68	69.75	21.64	9.04	4.11	65.21
RpWRKY30	Isoform0026136	350	38801.02	5.77	-0.695	58.71	55.49	21.43	9.71	2.57	66.29
RpWRKY31	Isoform0027649	358	39591.84	5.40	-0.680	51.80	57.32	21.79	11.45	4.47	62.29
RpWRKY32	Isoform0029123	356	39336.52	5.40	-0.687	53.11	56.54	21.63	10.39	3.93	64.04
RpWRKY33	Isoform0030474	366	40147.73	8.32	-0.673	57.27	67.73	27.87	13.11	1.37	57.65
RpWRKY34	Isoform0032219	318	35220.09	6.59	-0.797	48.71	55.85	25.47	5.97	3.46	65.09
RpWRKY35	Isoform0032765	365	39961.51	8.05	-0.656	55.83	68.19	28.22	14.79	2.47	54.52
RpWRKY36	Isoform0033018	261	28842.33	8.14	-0.762	47.36	54.21	22.61	11.11	4.21	62.07
RpWRKY37	Isoform0033501	325	35397.04	9.51	-0.606	55.12	55.88	18.77	8.62	2.77	69.85
RpWRKY38	Isoform0033604	354	38650.30	7.54	-0.656	52.50	64.49	30.79	11.58	2.26	55.37
RpWRKY39	Isoform0033810	332	36096.34	9.53	-0.688	49.50	60.57	18.67	9.64	6.33	65.36
RpWRKY40	Isoform0033814	325	35361.21	9.64	-0.474	43.40	64.28	20.62	9.85	2.77	66.77
RpWRKY41	Isoform0033861	342	36989.05	9.92	-0.557	52.91	65.06	19.30	11.70	2.34	66.67
RpWRKY42	Isoform0034281	354	39281.63	5.77	-0.681	58.85	56.78	21.75	10.73	4.24	63.28
RpWRKY43	Isoform0034386	354	38564.15	7.56	-0.655	54.20	64.49	31.64	12.43	2.26	53.67
RpWRKY44	Isoform0035302	274	30915.54	8.98	-0.833	38.54	56.53	22.99	19.71	6.93	50.36
RpWRKY45	Isoform0035609	354	37872.57	9.76	-0.593	52.47	65.59	24.29	9.60	2.54	63.56
RpWRKY46	Isoform0037309	376	40878.63	8.78	-0.633	50.94	65.11	23.67	14.36	2.13	59.84
RpWRKY47	Isoform0038096	289	30430.81	5.77	-0.515	56.60	58.10	17.65	7.96	2.42	71.97
RpWRKY48	Isoform0040944	354	37890.60	9.71	-0.597	52.91	64.77	24.58	8.47	2.82	64.12
RpWRKY49	Isoform0008291	321	34800.48	6.32	-0.681	57.15	55.02	17.45	9.35	3.43	69.78
RpWRKY50	Isoform0034529	319	35145.27	7.20	-0.642	58.22	58.71	26.96	8.15	4.08	60.82
RpWRKY51	Isoform0038659	325	35383.01	9.51	-0.606	55.12	55.88	19.69	10.46	2.77	67.08
RpWRKY52	Isoform0049163	227	25433.89	7.08	-0.605	41.64	73.92	37.00	12.78	2.64	47.58
RpWRKY53	Isoform0054945	192	21184.13	6.10	-0.850	36.72	41.61	18.75	23.96	7.29	50.00