喜马拉雅紫茉莉MYB家族的生物信息学及表达分析

doi:10.11924/j.issn.1000-6850.casb2020-0104

中国农学通报 ›› 2020, Vol. 36 ›› Issue (29): 54-61.doi: 10.11924/j.issn.1000-6850.casb2020-0104

喜马拉雅紫茉莉MYB家族的生物信息学及表达分析

刘佳佳¹(), 佘露露¹, 兰小中², 陆雅宁¹, 杨佳慧¹, 刘欢¹, 卢存福¹, 陈玉珍¹()

¹北京林业大学教育部林木花卉育种与基因工程重点实验室/生物科学与生物技术学院,北京 100083
²西藏农牧学院,西藏林芝 860000

收稿日期:2020-05-15 修回日期:2020-07-29 出版日期:2020-10-15 发布日期:2020-10-16
通讯作者: 陈玉珍
作者简介:刘佳佳,女,1994年出生,内蒙古呼和浩特人,硕士,主要从事药用植物分子生物学研究。通信地址：100083 北京林业大学生物科学与技术学院,E-mail：273602389@qq.com
基金资助:
天津市企业重点实验室开放基金“药用植物细胞系筛选及药用成分合成调控机制”(2017166);国家自然科学基金“沙冬青脱水素基因家族生物学功能研究”(31270737);北京市自然科学基金“沙冬青AmCIP基因功能研究”(6112016)

Bioinformatics and Expression Analysis of MYB Gene Family Based on Transcriptome of Cold-acclimated Mirabilis himalaica Callus

Liu Jiajia¹(), She Lulu¹, Lan Xiaozhong², Lu Yaning¹, Yang Jiahui¹, Liu Huan¹, Lu Cunfu¹, Chen Yuzhen¹()

¹The Key Laboratory of Education Ministry for Genetic Breeding and Gene Engineering of Woody and Ornamental Plants/ College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083
² Tibetan College of Agriculture and Husbandry, Linzhi Tibet 860000

Received:2020-05-15 Revised:2020-07-29 Online:2020-10-15 Published:2020-10-16
Contact: Chen Yuzhen

摘要/Abstract

摘要：

旨在筛选高山植物喜马拉雅紫茉莉调控类黄酮等次生代谢产物合成的MYB转录因子(MhMYB)基因家族。基于喜马拉雅紫茉莉愈伤组织低温转录组测序数据库,利用PlantTFDB 3.0和BLASTP等软件对MhMYB序列进行筛选与鉴定,使用Web Logo 3.0、MEGA 7.0和Mev等生物信息学软件对MhMYB转录因子进行结构域、系统进化及低温诱导表达水平分析。研究筛选出34个喜马拉雅紫茉莉MhMYB家族成员,分别为1R-MYB（2个）、R2R3-MYB（30个）和3R-MYB（2个）3类转录因子;亚细胞定位预测大多数定位于细胞核中;进化分析显示,MhMYB家族成员可分为15个亚类,基于拟南芥AtMYB家族成员的生物学功能,预测MhMYB的S2、S7、S20亚家族成员可能参与调控类黄酮等次生代谢产物合成;转录组数据分析显示,低温可诱导MhMYB6、MhMYB15、MhMYB62基因表达水平增加;共表达分析发现,MhMYB6、MhMYB15、MhMYB62对类黄酮合成途径基因起到一定调控作用。初步研究表明,MhMYB6、MhMYB15、MhMYB62可参与调控低温诱导喜马拉雅紫茉莉类黄酮的累积。

关键词: 喜马拉雅紫茉莉, 转录组, MYB基因家族, 生物信息学分析, 类黄酮

Abstract:

The paper aims to get insight into the MYB genes in Mirabilis himalaica. We used bioinformatics methods to screen the MYB genes from Mirabilis himalaica callus transcriptome data. The MYB protein sequences were identified by PlantTFDB 3.0 and BLASTP. At the same time, conserved domain was analyzed by using Web Logo 3.0 for those R2R3-MYB transcription factors with the largest proportion. Phylogenetic tree analysis was conducted by using Web MEGA 7.0 for all MhMYB. The expression levels of MhMYB under cold acclimation were analyzed by Mev. The results showed that 34 MYB genes were identified in Mirabilis himalaica, 30 of them belonged to R2R3-MYB, 2 of them belonged to 1R-MYB and 2 of them belonged to 3R-MYB. The subcellular localization prediction showed that MhMYB proteins were mostly localized in nucleus. The MhMYB proteins were divided into 15 subfamilies according to the classification method of Arabidopsis family. The homologous genes involved in flavonoids biosynthesis mainly belonged to the S2, S7 and S20 subfamilies. Gene expression analysis indicated that the expression level of MhMYB6, MhMYB15, MhMYB62 genes were up-regulated during cold-acclimation. Co-expression analysis showed that MhMYB6, MhMYB15 and MhMYB62 played a certain role in the regulation of flavonoids synthesis. This study shows that MhMYB genes play an important regulatory role in flavonoids biosynthesis and provides basic information for further exploration of the function of MhMYB genes.

Key words: Mirabilis himalaica, transcriptome, MYB gene family, bioinformatic analysis, flavonoid

中图分类号:

刘佳佳, 佘露露, 兰小中, 陆雅宁, 杨佳慧, 刘欢, 卢存福, 陈玉珍. 喜马拉雅紫茉莉MYB家族的生物信息学及表达分析[J]. 中国农学通报, 2020, 36(29): 54-61.

Liu Jiajia, She Lulu, Lan Xiaozhong, Lu Yaning, Yang Jiahui, Liu Huan, Lu Cunfu, Chen Yuzhen. Bioinformatics and Expression Analysis of MYB Gene Family Based on Transcriptome of Cold-acclimated Mirabilis himalaica Callus[J]. Chinese Agricultural Science Bulletin, 2020, 36(29): 54-61.

图/表 6

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基因ID		基因编号		MYB类型		不稳定指数	等电点		氨基酸数目		分子量		亚细胞定位			α螺旋		扩展链		β折叠		无规则卷曲
Cluster-17452.17425		MYB4		R2R3-MYB		58.58	8.63		239		27073.45		Mitochondrial			49		9		13		48
Cluster-17452.71422		MYB6		R2R3-MYB		36.38	8.51		216		24671.7		Nuclear			58		20		12		129
Cluster-17452.60445		MYB14		R2R3-MYB		40.23	5.68		283		32439.98		Nuclear			74		15		13		181
Cluster-17452.100539		MYB15		R2R3-MYB		54.37	5.57		271		31185.5		Nuclear			86		10		15		160
Cluster-17452.116547		MYB17		R2R3-MYB		51.43	5.84		294		32990.84		Nuclear			107		19		15		153
Cluster-12557.0		MYB18		R2R3-MYB		56.73	6.63		246		28269.58		Nuclear			76		7		14		149
Cluster-110.1		MYB21		R2R3-MYB		54.25	6.75		209		24412.26		Mitochondrial			66		15		8		120
Cluster-31361.2		MYB27		R2R3-MYB		68.11	5.82		260		30513.96		Nuclear			94		23		13		129
Cluster-17452.39855		MYB30		R2R3-MYB		63.82	6.79		364		75504.49		Nuclear			195		82		36		353
Cluster-17452.65292		MYB36		R2R3-MYB		57.52	6.68		302		34324.79		Nuclear			59		74				169
Cluster-17452.38918		MYB41		R2R3-MYB		51.43	5.84		294		32990.84		Nuclear			86		31				177
Cluster-17452.122836		MYB48		R2R3-MYB		65.01	9.54		179		20541.16		Nuclear			41		36				102
Cluster-17452.114977		MYB59		R2R3-MYB		52.75	6.72		207		23976.6		Nuclear			71		14		10		112
Cluster-17452.25903		MYB61		R2R3-MYB		9.87	9.87		155		17830.42		Mitochondrial			69		3		17		66
Cluster-17452.60725		MYB62		R2R3-MYB		65.54	5.31		269		30447.87		Nuclear			107		21		9		132
Cluster-3908.2		MYB63		R2R3-MYB		49.39	7.76		233		26781.79		Nuclear			83		15		18		118
Cluster-17452.86434		MYB73		R2R3-MYB		48.54	8.72		276		30146		Nuclear			72		17		7		181
Cluster-9350.0		MYB77		R2R3-MYB		57.29	5.43		242		26999.38		Nuclear			61		52				129
Cluster-17452.59151		MYB78		R2R3-MYB		36.5	5.04		204		23190.33		Nuclear			37		37				130
Cluster-17452.109149		MYB79		R2R3-MYB		47.11	8.99		255		29758.52		Nuclear			115		30		19		91
Cluster-17452.114985		MYB84		R2R3-MYB		51.09	6.18		297		33810.8		Nuclear			103		16		10		168
Cluster-17452.95774		MYB88		R2R3-MYB		56.68	7.7		434		48606.42		Nuclear			163		47		21		203
Cluster-16803.0		MYB92		R2R3-MYB		63.97	4.83		239		15317.74		Mitochondrial			50		11		13		59
Cluster-17452.52590		MYB94		R2R3-MYB		62.02	8.55		352		39486.18		Nuclear			109		26		11		206
Cluster-17452.65641		MYB97		R2R3-MYB		66.14	8.18		284		31906.24		Nuclear			86		12		11		175
Cluster-23158.1		MYB102		R2R3-MYB		54.88	8.1		309		35297.72		Mitochondrial			84		26		16		183
Cluster-31442.0		MYB106		R2R3-MYB		55.58	8.23		357		39742.16		Nuclear			106		53		21		177
Cluster-30491.5	MYB108		R2R3-MYB		65.19			6.44		283		31439.28		Nuclear	37		37				130
Cluster-17452.69681	MYB121		R2R3-MYB		52.44			9.44		285		1833.93		Nuclear	70		46		24		139
Cluster-17452.65641	MYB125		R2R3-MYB		62.82			9.74		240		27058.78		Nuclear	55		45
Cluster-3511.0	MYB1R1		MYB1R1		54.53			6.93		327		35652.31		Nuclear	62		40				225
Cluster-30491.5	MYB1R2		MYB1R3		65.19			6.44		283		31439.28		Nuclear	73		20				190
Cluster-21203.0	MYB3R1		3R-MYB		71.36			5.21		981		107388.4		Nuclear	227		126				610
Cluster-15152.9	MYB3R2		3R-MYB		70.02			5.1		987		109565.91		Nuclear	230		166				166

基因ID		基因编号		MYB类型		不稳定指数	等电点		氨基酸数目		分子量		亚细胞定位			α螺旋		扩展链		β折叠		无规则卷曲
Cluster-17452.17425		MYB4		R2R3-MYB		58.58	8.63		239		27073.45		Mitochondrial			49		9		13		48
Cluster-17452.71422		MYB6		R2R3-MYB		36.38	8.51		216		24671.7		Nuclear			58		20		12		129
Cluster-17452.60445		MYB14		R2R3-MYB		40.23	5.68		283		32439.98		Nuclear			74		15		13		181
Cluster-17452.100539		MYB15		R2R3-MYB		54.37	5.57		271		31185.5		Nuclear			86		10		15		160
Cluster-17452.116547		MYB17		R2R3-MYB		51.43	5.84		294		32990.84		Nuclear			107		19		15		153
Cluster-12557.0		MYB18		R2R3-MYB		56.73	6.63		246		28269.58		Nuclear			76		7		14		149
Cluster-110.1		MYB21		R2R3-MYB		54.25	6.75		209		24412.26		Mitochondrial			66		15		8		120
Cluster-31361.2		MYB27		R2R3-MYB		68.11	5.82		260		30513.96		Nuclear			94		23		13		129
Cluster-17452.39855		MYB30		R2R3-MYB		63.82	6.79		364		75504.49		Nuclear			195		82		36		353
Cluster-17452.65292		MYB36		R2R3-MYB		57.52	6.68		302		34324.79		Nuclear			59		74				169
Cluster-17452.38918		MYB41		R2R3-MYB		51.43	5.84		294		32990.84		Nuclear			86		31				177
Cluster-17452.122836		MYB48		R2R3-MYB		65.01	9.54		179		20541.16		Nuclear			41		36				102
Cluster-17452.114977		MYB59		R2R3-MYB		52.75	6.72		207		23976.6		Nuclear			71		14		10		112
Cluster-17452.25903		MYB61		R2R3-MYB		9.87	9.87		155		17830.42		Mitochondrial			69		3		17		66
Cluster-17452.60725		MYB62		R2R3-MYB		65.54	5.31		269		30447.87		Nuclear			107		21		9		132
Cluster-3908.2		MYB63		R2R3-MYB		49.39	7.76		233		26781.79		Nuclear			83		15		18		118
Cluster-17452.86434		MYB73		R2R3-MYB		48.54	8.72		276		30146		Nuclear			72		17		7		181
Cluster-9350.0		MYB77		R2R3-MYB		57.29	5.43		242		26999.38		Nuclear			61		52				129
Cluster-17452.59151		MYB78		R2R3-MYB		36.5	5.04		204		23190.33		Nuclear			37		37				130
Cluster-17452.109149		MYB79		R2R3-MYB		47.11	8.99		255		29758.52		Nuclear			115		30		19		91
Cluster-17452.114985		MYB84		R2R3-MYB		51.09	6.18		297		33810.8		Nuclear			103		16		10		168
Cluster-17452.95774		MYB88		R2R3-MYB		56.68	7.7		434		48606.42		Nuclear			163		47		21		203
Cluster-16803.0		MYB92		R2R3-MYB		63.97	4.83		239		15317.74		Mitochondrial			50		11		13		59
Cluster-17452.52590		MYB94		R2R3-MYB		62.02	8.55		352		39486.18		Nuclear			109		26		11		206
Cluster-17452.65641		MYB97		R2R3-MYB		66.14	8.18		284		31906.24		Nuclear			86		12		11		175
Cluster-23158.1		MYB102		R2R3-MYB		54.88	8.1		309		35297.72		Mitochondrial			84		26		16		183
Cluster-31442.0		MYB106		R2R3-MYB		55.58	8.23		357		39742.16		Nuclear			106		53		21		177
Cluster-30491.5	MYB108		R2R3-MYB		65.19			6.44		283		31439.28		Nuclear	37		37				130
Cluster-17452.69681	MYB121		R2R3-MYB		52.44			9.44		285		1833.93		Nuclear	70		46		24		139
Cluster-17452.65641	MYB125		R2R3-MYB		62.82			9.74		240		27058.78		Nuclear	55		45
Cluster-3511.0	MYB1R1		MYB1R1		54.53			6.93		327		35652.31		Nuclear	62		40				225
Cluster-30491.5	MYB1R2		MYB1R3		65.19			6.44		283		31439.28		Nuclear	73		20				190
Cluster-21203.0	MYB3R1		3R-MYB		71.36			5.21		981		107388.4		Nuclear	227		126				610
Cluster-15152.9	MYB3R2		3R-MYB		70.02			5.1		987		109565.91		Nuclear	230		166				166

基因ID	基因编号	丝氨酸Ser	苏氨酸Thr	酪氨酸Tyr	基因ID	基因编号	丝氨酸Ser	苏氨酸Thr	酪氨酸Tyr
Cluster-17452.17426	MYB4	1	2	0	Cluster-17452.86434	MYB73	17	4	0
Cluster-17452.71422	MYB6	7	4	1	Cluster-9350.0	MYB77	20	2	0
Cluster-17452.60445	MYB14	12	6	7	Cluster-17452.59151	MYB78	1	2	3
Cluster-17452.100539	MYB15	14	8	5	Cluster-17452.109149	MYB79	5	4	2
Cluster-17452.116547	MYB17	16	8	4	Cluster-17452.114985	MYB84	9	6	5
Cluster-12557.0	MYB18	8	4	3	Cluster-17452.95774	MYB88	23	7	2
Cluster-110.1	MYB21	5	4	2	Cluster-16803.0	MYB92	3	3	1
Cluster-31361.2	MYB27	9	3	7	Cluster-17452.52590	MYB94	20	6	3
Cluster-17452.39855	MYB30	38	3	8	Cluster-17452.65641	MYB97	14	2	2
Cluster-17452.65292	MYB36	11	0	7	Cluster-23158.1	MYB102	8	3	3
Cluster-17452.38918	MYB41	16	8	4	Cluster-31442.0	MYB106	18	4	2
Cluster-17452.122836	MYB48	13	0	1	Cluster-30491.5	MYB108	18	4	2
Cluster-17452.16659	MYB56	18	4	3	Cluster-17452.69681	MYB121	12	3	3
Cluster-17452.114977	MYB59	16	2	4	Cluster-3511.0	MYB1R1	21	8	1
Cluster-17452.25903	MYB61	4	4	0	Cluster-30491.5	MYB1R2	18	4	2
Cluster-17452.60725	MYB62	23	3	1	Cluster-21203.0	MYB3R1	49	18	6
Cluster-3908.2	MYB63	6	1	2	Cluster-15152.9	MYB3R2	49	18	7

基因ID	基因编号	丝氨酸Ser	苏氨酸Thr	酪氨酸Tyr	基因ID	基因编号	丝氨酸Ser	苏氨酸Thr	酪氨酸Tyr
Cluster-17452.17426	MYB4	1	2	0	Cluster-17452.86434	MYB73	17	4	0
Cluster-17452.71422	MYB6	7	4	1	Cluster-9350.0	MYB77	20	2	0
Cluster-17452.60445	MYB14	12	6	7	Cluster-17452.59151	MYB78	1	2	3
Cluster-17452.100539	MYB15	14	8	5	Cluster-17452.109149	MYB79	5	4	2
Cluster-17452.116547	MYB17	16	8	4	Cluster-17452.114985	MYB84	9	6	5
Cluster-12557.0	MYB18	8	4	3	Cluster-17452.95774	MYB88	23	7	2
Cluster-110.1	MYB21	5	4	2	Cluster-16803.0	MYB92	3	3	1
Cluster-31361.2	MYB27	9	3	7	Cluster-17452.52590	MYB94	20	6	3
Cluster-17452.39855	MYB30	38	3	8	Cluster-17452.65641	MYB97	14	2	2
Cluster-17452.65292	MYB36	11	0	7	Cluster-23158.1	MYB102	8	3	3
Cluster-17452.38918	MYB41	16	8	4	Cluster-31442.0	MYB106	18	4	2
Cluster-17452.122836	MYB48	13	0	1	Cluster-30491.5	MYB108	18	4	2
Cluster-17452.16659	MYB56	18	4	3	Cluster-17452.69681	MYB121	12	3	3
Cluster-17452.114977	MYB59	16	2	4	Cluster-3511.0	MYB1R1	21	8	1
Cluster-17452.25903	MYB61	4	4	0	Cluster-30491.5	MYB1R2	18	4	2
Cluster-17452.60725	MYB62	23	3	1	Cluster-21203.0	MYB3R1	49	18	6
Cluster-3908.2	MYB63	6	1	2	Cluster-15152.9	MYB3R2	49	18	7

喜马拉雅紫茉莉MYB家族的生物信息学及表达分析

Bioinformatics and Expression Analysis of MYB Gene Family Based on Transcriptome of Cold-acclimated Mirabilis himalaica Callus

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