黄花蒿R2R3-MYB转录因子全基因组鉴定及生物信息学分析

doi:10.13560/j.cnki.biotech.bull.1985.2021-0173

摘要/Abstract

摘要：

MYB家族转录因子广泛参与植物的各种生物过程,其中R2R3-MYB数量最多、功能最广泛,有研究表明黄花蒿R2R3-MYB转录因子能调控分泌性腺毛的发育及青蒿素的生物合成,但相关研究还较少。以黄花蒿基因组数据为基础,通过本地BLAST和HMMsearch的方法,获得黄花蒿R2R3-MYB转录因子序列132条,并对其保守结构域进行分析,同时构建了与拟南芥R2R3-MYB转录因子的系统进化树,结合BLAST2GO软件的注释结果进行功能预测;此外,本研究还通过转录组数据库分析了R2R3-MYB基因在不同组织的表达模式。综合以上生物信息学分析数据获得了可能参与青蒿素生物合成的R2R3-MYB转录因子基因,同时为参与关键生物过程的R2R3-MYB转录因子基因的筛选提供依据。

关键词: 黄花蒿, R2R3-MYB转录因子, 基因组, 转录组, 生物信息学

Abstract:

The transcription factors in MYB family are widely involved in a variety of plant biological processes,among which R2R3-MYB is the most abundant type and has the most extensive functions. Previous studies have shown that some R2R3-MYB transcription factors can regulate the development of glandular secretory trichomes and the biosynthesis of artemisinin in Artemisia annua,however,the relevant studies are still little. Based on the genome data of A. annua,132 sequences of R2R3-MYB transcription factors were identified by local BLAST and HMMsearch,and their conserved domains were analyzed. Meanwhile,a phylogenetic tree of R2R3-MYB transcription factors between A. annua and Arabidopsis thaliana was constructed,and the functions of R2R3-MYB transcription factors were predicted with BLAST2GO. In addition,the expression patterns of R2R3-MYB genes in different tissues were analyzed based on transcriptome databases. Synthesizing the above bioinformatics analysis data,the genes of R2R3-MYB transcription factor that may participate in artemisinin biosynthesis are obtained,which provides the evidences for screening the genes of R2R3-MYB transcription factors involved in key biological processes.

Key words: Artemisia annua L., R2R3-MYB transcription factors, genome, transcriptome, bioinformatics

李琦, 王怡超, 刘畅, 谭何新. 黄花蒿R2R3-MYB转录因子全基因组鉴定及生物信息学分析[J]. 生物技术通报, 2021, 37(8): 65-74.

LI Qi, WANG Yi-chao, LIU Chang, TAN He-xin. Genome-wide Identification and Bioinformatics Analysis of R2R3-MYB Transcription Factors in Artemisia annua[J]. Biotechnology Bulletin, 2021, 37(8): 65-74.

图/表 6

参考文献 29

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Protein code	MYB name	Protein code	MYB name	Protein code	MYB name
PWA71644.1	AaMYB2R1	PWA99792.1	AaMYB2R45	PWA38419.1	AaMYB2R89
PWA43204.1	AaMYB2R2	PWA41205.1	AaMYB2R46	PWA56935.1	AaMYB2R90
PWA86000.1	AaMYB2R3	PWA96412.1	AaMYB2R47	PWA35205.1	AaMYB2R91
PWA65390.1	AaMYB2R4	PWA50143.1	AaMYB2R48	PWA76413.1	AaMYB2R92
PWA47067.1	AaMYB2R5	PWA95387.1	AaMYB2R49	PWA61358.1	AaMYB2R93
PWA39356.1	AaMYB2R6	PWA87312.1	AaMYB2R50	PWA68967.1	AaMYB2R94
PWA75916.1	AaMYB2R7	PWA72501.1	AaMYB2R51	PWA70735.1	AaMYB2R95
PWA43649.1	AaMYB2R8	PWA88612.1	AaMYB2R52	PWA65469.1	AaMYB2R96
PWA51649.1	AaMYB2R9	PWA71899.1	AaMYB2R53	PWA73667.1	AaMYB2R97
PWA64888.1	AaMYB2R10	PWA60948.1	AaMYB2R54	PWA60339.1	AaMYB2R98
PWA67214.1	AaMYB2R11	PWA66225.1	AaMYB2R55	PWA47768.1	AaMYB2R99
PWA89491.1	AaMYB2R12	PWA35659.1	AaMYB2R56	PWA65296.1	AaMYB2R100
PWA46461.1	AaMYB2R13	PWA98977.1	AaMYB2R57	PWA93717.1	AaMYB2R101
PWA78544.1	AaMYB2R14	PWA87993.1	AaMYB2R58	PWA99549.1	AaMYB2R102
PWA71245.1	AaMYB2R15	PWA63153.1	AaMYB2R59	PWA44719.1	AaMYB2R103
PWA96367.1	AaMYB2R16	PWA70731.1	AaMYB2R60	PWA74420.1	AaMYB2R104
PWA52706.1	AaMYB2R17	PWA90922.1	AaMYB2R61	PWA74110.1	AaMYB2R105
PWA64358.1	AaMYB2R18	PWA56311.1	AaMYB2R62	PWA66731.1	AaMYB2R106
PWA52104.1	AaMYB2R19	PWA81663.1	AaMYB2R63	PWA46401.1	AaMYB2R107
PWA34289.1	AaMYB2R20	PWA75167.1	AaMYB2R64	PWA60446.1	AaMYB2R108
PWA45135.1	AaMYB2R21	PWA64917.1	AaMYB2R65	PWA50364.1	AaMYB2R109
PWA46713.1	AaMYB2R22	PWA54615.1	AaMYB2R66	PWA81967.1	AaMYB2R110
PWA60682.1	AaMYB2R23	PWA50450.1	AaMYB2R67	PWA55616.1	AaMYB2R111
PWA52704.1	AaMYB2R24	PWA55247.1	AaMYB2R68	PWA39801.1	AaMYB2R112
PWA86815.1	AaMYB2R25	PWA78936.1	AaMYB2R69	PWA65860.1	AaMYB2R113
PWA52975.1	AaMYB2R26	PWA48003.1	AaMYB2R70	PWA93789.1	AaMYB2R114
PWA84715.1	AaMYB2R27	PWA84612.1	AaMYB2R71	PWA70975.1	AaMYB2R115
PWA47058.1	AaMYB2R28	PWA98963.1	AaMYB2R72	PWA63331.1	AaMYB2R116
PWA48985.1	AaMYB2R29	PWA85713.1	AaMYB2R73	PWA37853.1	AaMYB2R117
PWA71307.1	AaMYB2R30	PWA67086.1	AaMYB2R74	PWA78715.1	AaMYB2R118
PWA66224.1	AaMYB2R31	PWA47522.1	AaMYB2R75	PWA87301.1	AaMYB2R119
PWA66489.1	AaMYB2R32	PWA96303.1	AaMYB2R76	PWA62998.1	AaMYB2R120
PWA88884.1	AaMYB2R33	PWA74168.1	AaMYB2R77	PWA94056.1	AaMYB2R121
PWA60694.1	AaMYB2R34	PWA80451.1	AaMYB2R78	PWA35582.1	AaMYB2R122
PWA96157.1	AaMYB2R35	PWA60300.1	AaMYB2R79	PWA92852.1	AaMYB2R123
PWA60193.1	AaMYB2R36	PWA72588.1	AaMYB2R80	PWA56697.1	AaMYB2R124
PWA89756.1	AaMYB2R37	PWA60276.1	AaMYB2R81	PWA93922.1	AaMYB2R125
PWA89743.1	AaMYB2R38	PWA77673.1	AaMYB2R82	PWA82717.1	AaMYB2R126
PWA59700.1	AaMYB2R39	PWA70733.1	AaMYB2R83	PWA38555.1	AaMYB2R127
PWA72169.1	AaMYB2R40	PWA56370.1	AaMYB2R84	PWA43034.1	AaMYB2R128
PWA34017.1	AaMYB2R41	PWA50987.1	AaMYB2R85	PWA70165.1	AaMYB2R129
PWA87210.1	AaMYB2R42	PWA88000.1	AaMYB2R86	PWA95682.1	AaMYB2R130
PWA71841.1	AaMYB2R43	PWA85391.1	AaMYB2R87	PWA89358.1	AaMYB2R131
PWA79178.1	AaMYB2R44	PWA71534.1	AaMYB2R88	PWA90842.1	AaMYB2R132

Protein code	MYB name	Protein code	MYB name	Protein code	MYB name
PWA71644.1	AaMYB2R1	PWA99792.1	AaMYB2R45	PWA38419.1	AaMYB2R89
PWA43204.1	AaMYB2R2	PWA41205.1	AaMYB2R46	PWA56935.1	AaMYB2R90
PWA86000.1	AaMYB2R3	PWA96412.1	AaMYB2R47	PWA35205.1	AaMYB2R91
PWA65390.1	AaMYB2R4	PWA50143.1	AaMYB2R48	PWA76413.1	AaMYB2R92
PWA47067.1	AaMYB2R5	PWA95387.1	AaMYB2R49	PWA61358.1	AaMYB2R93
PWA39356.1	AaMYB2R6	PWA87312.1	AaMYB2R50	PWA68967.1	AaMYB2R94
PWA75916.1	AaMYB2R7	PWA72501.1	AaMYB2R51	PWA70735.1	AaMYB2R95
PWA43649.1	AaMYB2R8	PWA88612.1	AaMYB2R52	PWA65469.1	AaMYB2R96
PWA51649.1	AaMYB2R9	PWA71899.1	AaMYB2R53	PWA73667.1	AaMYB2R97
PWA64888.1	AaMYB2R10	PWA60948.1	AaMYB2R54	PWA60339.1	AaMYB2R98
PWA67214.1	AaMYB2R11	PWA66225.1	AaMYB2R55	PWA47768.1	AaMYB2R99
PWA89491.1	AaMYB2R12	PWA35659.1	AaMYB2R56	PWA65296.1	AaMYB2R100
PWA46461.1	AaMYB2R13	PWA98977.1	AaMYB2R57	PWA93717.1	AaMYB2R101
PWA78544.1	AaMYB2R14	PWA87993.1	AaMYB2R58	PWA99549.1	AaMYB2R102
PWA71245.1	AaMYB2R15	PWA63153.1	AaMYB2R59	PWA44719.1	AaMYB2R103
PWA96367.1	AaMYB2R16	PWA70731.1	AaMYB2R60	PWA74420.1	AaMYB2R104
PWA52706.1	AaMYB2R17	PWA90922.1	AaMYB2R61	PWA74110.1	AaMYB2R105
PWA64358.1	AaMYB2R18	PWA56311.1	AaMYB2R62	PWA66731.1	AaMYB2R106
PWA52104.1	AaMYB2R19	PWA81663.1	AaMYB2R63	PWA46401.1	AaMYB2R107
PWA34289.1	AaMYB2R20	PWA75167.1	AaMYB2R64	PWA60446.1	AaMYB2R108
PWA45135.1	AaMYB2R21	PWA64917.1	AaMYB2R65	PWA50364.1	AaMYB2R109
PWA46713.1	AaMYB2R22	PWA54615.1	AaMYB2R66	PWA81967.1	AaMYB2R110
PWA60682.1	AaMYB2R23	PWA50450.1	AaMYB2R67	PWA55616.1	AaMYB2R111
PWA52704.1	AaMYB2R24	PWA55247.1	AaMYB2R68	PWA39801.1	AaMYB2R112
PWA86815.1	AaMYB2R25	PWA78936.1	AaMYB2R69	PWA65860.1	AaMYB2R113
PWA52975.1	AaMYB2R26	PWA48003.1	AaMYB2R70	PWA93789.1	AaMYB2R114
PWA84715.1	AaMYB2R27	PWA84612.1	AaMYB2R71	PWA70975.1	AaMYB2R115
PWA47058.1	AaMYB2R28	PWA98963.1	AaMYB2R72	PWA63331.1	AaMYB2R116
PWA48985.1	AaMYB2R29	PWA85713.1	AaMYB2R73	PWA37853.1	AaMYB2R117
PWA71307.1	AaMYB2R30	PWA67086.1	AaMYB2R74	PWA78715.1	AaMYB2R118
PWA66224.1	AaMYB2R31	PWA47522.1	AaMYB2R75	PWA87301.1	AaMYB2R119
PWA66489.1	AaMYB2R32	PWA96303.1	AaMYB2R76	PWA62998.1	AaMYB2R120
PWA88884.1	AaMYB2R33	PWA74168.1	AaMYB2R77	PWA94056.1	AaMYB2R121
PWA60694.1	AaMYB2R34	PWA80451.1	AaMYB2R78	PWA35582.1	AaMYB2R122
PWA96157.1	AaMYB2R35	PWA60300.1	AaMYB2R79	PWA92852.1	AaMYB2R123
PWA60193.1	AaMYB2R36	PWA72588.1	AaMYB2R80	PWA56697.1	AaMYB2R124
PWA89756.1	AaMYB2R37	PWA60276.1	AaMYB2R81	PWA93922.1	AaMYB2R125
PWA89743.1	AaMYB2R38	PWA77673.1	AaMYB2R82	PWA82717.1	AaMYB2R126
PWA59700.1	AaMYB2R39	PWA70733.1	AaMYB2R83	PWA38555.1	AaMYB2R127
PWA72169.1	AaMYB2R40	PWA56370.1	AaMYB2R84	PWA43034.1	AaMYB2R128
PWA34017.1	AaMYB2R41	PWA50987.1	AaMYB2R85	PWA70165.1	AaMYB2R129
PWA87210.1	AaMYB2R42	PWA88000.1	AaMYB2R86	PWA95682.1	AaMYB2R130
PWA71841.1	AaMYB2R43	PWA85391.1	AaMYB2R87	PWA89358.1	AaMYB2R131
PWA79178.1	AaMYB2R44	PWA71534.1	AaMYB2R88	PWA90842.1	AaMYB2R132

Motif	Top scoring sequence	E-value	Site
1	AGLQRCGKSCRLRWTNYLRPDJKRGNFTEEEEELIJQLHALLGNRWSAIA	1.3e-4561	125
2	HLPGRTDNEIKNYWNTHLKKK	1.3e-1932	126
3	KKGPWTPEEDQKLINYIZKHGHGN	3.0e-1621	127
4	MGRAPCCDKNG	8.1e-356	60
5	LLKMGIDPVTHKPK	2.80E-228	37
6	TNLSHMAQWENARLEAEARLVRQSRVVS	6.00E-132	12
7	WRSLPK	3.00E-129	110
8	INKSSVSSLLVPQPLCFDVLKAWQGJTLSKLSSL	7.90E-35	5
9	TMSKGQWERRLQTDIHMAKQALCDALSIDNKSI	2.00E-32	4
10	LDLSDLSSJLNSAIENLSNLLNLQSLVNP	1.10E-30	7
11	EFVDVMQEMIAKEVRNYI	2.70E-29	7
12	QLKCDVNSKQFKDTMRYLWMPRLLEKIZA	4.40E-28	5
13	SDLTDCYYPISESQNQNFLQINNTVGDEFDCPIISPTIYFNREMDFEGQM	2.60E-27	3
14	PLGLVNDLISQASCQDMIMDDDLLWSTJD	2.80E-25	8
15	NVVESVEPQTLKGMSTEYHMN	9.10E-19	4
16	KEEATQHTLEVNDMIYQDNYLAEAFTNHLVNDANCHGHLED	6.80E-22	4
17	YASSAENIARLLPNWMKSSSKSSQTSS	8.70E-17	5
18	PPSSYEPAGNFWTEPFLVDN	5.90E-16	10
19	FNSWDECATWLLDCQDFGIHDFGLDCFGZVEM	1.50E-09	2
20	KQKLGTKDSEPLQQHAKVSVIKPQPQTFSRIQNC	6.40E-10	3
21	DSIFSTPISSPTPLNSSSTLINSSSTEDERESYC	2.20E-09	4
22	TMWPCKLNPIQEKJMQNLQLLNESSNPLMMQHFSPSTPQKIEYY	2.40E-19	3
23	CSSMTNEEFNDFAVQQPLLKRSVSDGSGVP	9.70E-13	3
24	PGTIDDLQYFWDQLCPVENLELRNNHLD	1.00E-07	3
25	MAQDVARWWDTVSEDGLWGGFLWNQENDHPNKQAIEQSFSPCF	1.30E-07	2
26	EIEGFKDMDGAKDDMTWWSBEFDANSASSNSWDSBGVLDH	1.10E-06	3
27	TDDGVNNALDIPQGLISSPIESGDKIDEYLDELFNDEENEFEGEIDWTLD	2.00E-06	2
28	NHFNEDIDGKIKVEEVVGFENHWPGENFKIGEWDFEGFLANIPSJPYLDF	2.10E-06	2
29	FKFEIPESLEFDDFM	5.70E-06	6
30	DYFLRVWHSEVGESFR	7.50E-05	4
31	SSSETSSSSLSGSDYVVPSDV	1.70E-04	7
32	KRRVGRVSRRVAKKYNKDRV	2.40E-04	3
33	GMFMSMHDHDJMAICME	2.90E-04	2
34	FTKRKCRSKWPKPSPILQNYIKSLNLPRG	4.80E-04	2
35	ELQQFLAFQAEIDEFLS	3.00E-05	3
36	PFIDFLGVG	4.90E-05	5
37	VSVNDPPTSLSLSLPGV	4.90E-04	7
38	DSSDTQLQLFFDFPGPNDANF	6.30E-04	4
39	SGGEEDDQMNMMMD	1.60E-03	4
40	AAQVNKLPKILFADWLSLDEFH	1.70E-03	3
41	DSNYWSNILDKLGN	3.50E-03	4
42	YTRDNSSNTAVSPV	1.30E-02	3
43	WNMDDLWQFR	4.20E-02	4
44	FHLPDEVMWDF	9.90E-02	3
45	YDHGHHHHHHN	4.50E-02	3

Motif	Top scoring sequence	E-value	Site
1	AGLQRCGKSCRLRWTNYLRPDJKRGNFTEEEEELIJQLHALLGNRWSAIA	1.3e-4561	125
2	HLPGRTDNEIKNYWNTHLKKK	1.3e-1932	126
3	KKGPWTPEEDQKLINYIZKHGHGN	3.0e-1621	127
4	MGRAPCCDKNG	8.1e-356	60
5	LLKMGIDPVTHKPK	2.80E-228	37
6	TNLSHMAQWENARLEAEARLVRQSRVVS	6.00E-132	12
7	WRSLPK	3.00E-129	110
8	INKSSVSSLLVPQPLCFDVLKAWQGJTLSKLSSL	7.90E-35	5
9	TMSKGQWERRLQTDIHMAKQALCDALSIDNKSI	2.00E-32	4
10	LDLSDLSSJLNSAIENLSNLLNLQSLVNP	1.10E-30	7
11	EFVDVMQEMIAKEVRNYI	2.70E-29	7
12	QLKCDVNSKQFKDTMRYLWMPRLLEKIZA	4.40E-28	5
13	SDLTDCYYPISESQNQNFLQINNTVGDEFDCPIISPTIYFNREMDFEGQM	2.60E-27	3
14	PLGLVNDLISQASCQDMIMDDDLLWSTJD	2.80E-25	8
15	NVVESVEPQTLKGMSTEYHMN	9.10E-19	4
16	KEEATQHTLEVNDMIYQDNYLAEAFTNHLVNDANCHGHLED	6.80E-22	4
17	YASSAENIARLLPNWMKSSSKSSQTSS	8.70E-17	5
18	PPSSYEPAGNFWTEPFLVDN	5.90E-16	10
19	FNSWDECATWLLDCQDFGIHDFGLDCFGZVEM	1.50E-09	2
20	KQKLGTKDSEPLQQHAKVSVIKPQPQTFSRIQNC	6.40E-10	3
21	DSIFSTPISSPTPLNSSSTLINSSSTEDERESYC	2.20E-09	4
22	TMWPCKLNPIQEKJMQNLQLLNESSNPLMMQHFSPSTPQKIEYY	2.40E-19	3
23	CSSMTNEEFNDFAVQQPLLKRSVSDGSGVP	9.70E-13	3
24	PGTIDDLQYFWDQLCPVENLELRNNHLD	1.00E-07	3
25	MAQDVARWWDTVSEDGLWGGFLWNQENDHPNKQAIEQSFSPCF	1.30E-07	2
26	EIEGFKDMDGAKDDMTWWSBEFDANSASSNSWDSBGVLDH	1.10E-06	3
27	TDDGVNNALDIPQGLISSPIESGDKIDEYLDELFNDEENEFEGEIDWTLD	2.00E-06	2
28	NHFNEDIDGKIKVEEVVGFENHWPGENFKIGEWDFEGFLANIPSJPYLDF	2.10E-06	2
29	FKFEIPESLEFDDFM	5.70E-06	6
30	DYFLRVWHSEVGESFR	7.50E-05	4
31	SSSETSSSSLSGSDYVVPSDV	1.70E-04	7
32	KRRVGRVSRRVAKKYNKDRV	2.40E-04	3
33	GMFMSMHDHDJMAICME	2.90E-04	2
34	FTKRKCRSKWPKPSPILQNYIKSLNLPRG	4.80E-04	2
35	ELQQFLAFQAEIDEFLS	3.00E-05	3
36	PFIDFLGVG	4.90E-05	5
37	VSVNDPPTSLSLSLPGV	4.90E-04	7
38	DSSDTQLQLFFDFPGPNDANF	6.30E-04	4
39	SGGEEDDQMNMMMD	1.60E-03	4
40	AAQVNKLPKILFADWLSLDEFH	1.70E-03	3
41	DSNYWSNILDKLGN	3.50E-03	4
42	YTRDNSSNTAVSPV	1.30E-02	3
43	WNMDDLWQFR	4.20E-02	4
44	FHLPDEVMWDF	9.90E-02	3
45	YDHGHHHHHHN	4.50E-02	3

GO term	Ontology	Description	Gene number
GO：0005634	C	Nucleus	128
GO：0043565	F	Sequence-specific DNA binding	95
GO：0044212	F	Transcription regulatory region DNA binding	84
GO：0003700	F	DNA-binding transcription factor activity	83
GO：0030154	P	Cell differentiation	80
GO：0006355	P	Regulation of transcription,DNA-templated	67
GO：0003677	F	DNA binding	36
GO：0009733	P	Response to auxin	4
GO：0010119	P	Regulation of stomatal movement	3
GO：0009751	P	Response to salicylic acid	2
GO：0048658	P	Anther wall tapetum development	2
GO：0005515	F	Protein binding	1
GO：0005524	F	ATP binding	1
GO：0016021	C	Integral component of membrane	1
GO：0009739	P	Response to gibberellin	1
GO：0009753	P	Response to jasmonic acid	1
GO：0048481	P	Plant ovule development	1
GO：0090377	P	Seed trichome initiation	1
GO：0004222	F	Metalloendopeptidase activity	1
GO：0006508	P	Proteolysis	1
GO：0003824	F	Catalytic activity	1
GO：0001101	P	Response to acid chemical	1
GO：1901700	P	Response to oxygen-containing compound	1
GO：0052545	P	Callose localization	1
GO：0055046	P	Microgametogenesis	1
GO：0050789	P	Regulation of biological process	1
GO：0010090	P	Trichome morphogenesis	1
GO：0048354	P	Mucilage biosynthetic process involved in seed coat development	1
GO：0048522	P	Positive regulation of cellular process	1
GO：0048523	P	Negative regulation of cellular process	1
GO：0050793	P	Regulation of developmental process	1
GO：0044839	P	Cell cycle G2/M phase transition	1
GO：0045893	P	Positive regulation of transcription,DNA-templated	1
GO：0048235	P	Pollen sperm cell differentiation	1
GO：0048555	C	Generative cell nucleus	1
GO：0055047	P	Generative cell mitosis	1