睡莲转录因子bZIP家族的分子进化以及功能分析

doi:10.3864/j.issn.0578-1752.2021.21.018

摘要/Abstract

摘要：

【目的】基于睡莲基因组鉴定睡莲bZIP（basic leucine zipper）家族成员,并对其进行分析,以揭示睡莲bZIP家族的分子进化和功能。【方法】从Waterlily Pond数据库获取睡莲基因组序列,利用HMMER3.0程序识别睡莲的bZIP家族成员,并使用CDD程序进一步确认其含有的保守bZIP结构域,使用IQ-tree软件构建系统进化树。利用ExPASy和SOPMA在线网站进行蛋白质结构分析,通过MEME程序进行保守基序分析,使用MCScan和Circos软件对基因复制事件进行分析以及可视化展示。从NCBI下载睡莲转录组数据（SRA Study：SRP222853）,用R软件对睡莲bZIP家族成员表达数据的Pearson相关系数（PCC）进行计算和可视化分析,使用Cytoscape软件对NcbZIP成员之间的表达数据关系进行分析。【结果】从睡莲基因组中共鉴定出46个bZIP家族成员,按成员在染色体上的分布命名为NcbZIP01—NcbZIP46。根据系统进化分析可以将睡莲bZIP家族成员分为A、B、C、D、E、G、H、I、J和S共10个亚家族,其中A亚家族所含成员最多（11个）,相同亚家族成员具有相似的保守结构域和基因结构。理化性质分析表明,睡莲bZIP家族成员蛋白质长度介于101—1 898 aa,分子量大小介于12.04—214.64 kD。染色体定位分析发现,睡莲共有14条染色体,46个bZIP家族成员不均匀地分布在其中的10条染色体上,其中1号染色体上分布最多。睡莲bZIP基因家族发生10个复制事件,其中9个片段复制事件,1个串联复制事件,A亚家族所含基因复制事件最多（3次）。对NcbZIP成员在不同组织下的表达进行分析,根据表达情况分为Ⅰ、Ⅱ和Ⅲ组,Ⅰ组成员在所有组织中均高度表达,Ⅱ组成员几乎在所有组织中均不表达,Ⅲ组成员在不同组织中表达水平各不相同,其中C、D和G亚家族的大部分成员集中在Ⅲ组。通过睡莲bZIP成员表达量的Pearson相关系数分析,发现NcbZIP45与所有NcbZIP成员之间的相关性最高。【结论】在睡莲基因组中鉴定出46个bZIP成员,分为10个亚家族,不均匀地分布在14条染色体上,结构进化保守,组织表达模式多样。

关键词: 睡莲, bZIP家族, 分子进化, 表达谱, 功能分析

Abstract:

【Objective】The genome-wide analysis of the bZIP family in Nymphaea colorata was used to identify the bZIP (basic leucine zipper) family members in waterlily, and then which were further analyzed. This study revealed molecular evolution and function of the bZIP family in waterlily.【Method】The genome sequence of N. colorata was downloaded from Waterlily Pond database. The bZIP members in waterlily were identified by using HMMER 3.0 program, and the conserved bZIP domain was verified by using CDD program. The phylogenetic tree was constructed by the IQ-tree software. The ExPASy and SOPMA online website were performed to analyze protein structure characters. The conserved motifs were identified by using MEME program. The gene duplication events were found and visualized by the MCScan and Circos software. Transcriptome data of NcbZIP members were obtained from the NCBI website (SRA Study: SRP222853). The Pearson Correlation Coefficient (PCC) about the expression levels of the NcbZIP family members was calculated by using R software, and the network of the expression levels in the NcbZIP family was analyzed by using Cytoscape software.【Result】46 bZIP members were identified in N. colorata, and were named from NcbZIP01 to NcbZIP46 according to their chromosome distributions. The A subfamily contained the most NcbZIP members (11 NcbZIPs). There were 10 subfamilies (A, B, C, D, E, G, H, I, J and S) according to the phylogenetic analysis. The protein length in the NcbZIP family was from 101 aa to 1 898 aa, and the molecular weight ranged from 12.04 kD to 214.64 kD. The NcbZIP members from same subfamily had the similar distributions of the conserved motifs and gene structures. Waterlily had 14 chromosomes, and 46 NcbZIP members were unevenly distributed across 10 chromosomes. Chromosome 1 had the highest number of NcbZIP members. There were 10 gene duplication events in the NcbZIP family, including nine segmental duplication events and one tandem duplication event. The A subfamily had the most number of the gene duplication events (three). Based on the expression patterns in different tissues, the NcbZIP family could be divided into three groups (I, II and III). The NcbZIP members in Group I were highly expressed in all tissues, while the NcbZIP members in group II were not expressed in almost all tissues. The NcbZIP members in group III had tissue-specific expression profiles, and most of NcbZIP members in C, D and E subfamilies belonged to group III. The PPC analysis about the expression levels of NcbZIP members indicated NcbZIP45 had the highest connection with other members.【Conclusion】46 NcbZIP members were identified in Nymphaea colorata, and were unevenly distributed in 14 chromosomes. The NcbZIP family could be divided into 10 subfamilies with conserved motifs distributions and diverse expression levels. The current study could lay the foundation on the functional analysis of the bZIP family in N. colorata.

Key words: Nymphaea colorata, bZIP family, molecular evolution, expression profile, function analysis

叶方婷,潘鑫峰,毛志君,李兆伟,范凯. 睡莲转录因子bZIP家族的分子进化以及功能分析[J]. 中国农业科学, 2021, 54(21): 4694-4708.

YE FangTing,PAN XinFeng,MAO ZhiJun,LI ZhaoWei,FAN Kai. Molecular Evolution and Function Analysis of bZIP Family in Nymphaea colorata[J]. Scientia Agricultura Sinica, 2021, 54(21): 4694-4708.

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https://www.chinaagrisci.com/CN/Y2021/V54/I21/4694

图/表 10

图1

表1

本研究中NcbZIP成员的鉴定及结构分析"

名称 Name	位点名称 Locus name	亚家族 Subfamily	蛋白质长度 Protein length (aa)	分子量 Molecular weight (kD)	理论pI Theoretical pI	α-螺旋 α -helix	延伸链 Extended strand	β-折叠 β -turn	无规则卷曲 Random coil
NcbZIP01	GWHPAAYW000832	D	418	46.54	6.09	215	19	9	175
NcbZIP02	GWHPAAYW000931	G	537	59.56	9.08	200	46	16	275
NcbZIP03	GWHPAAYW000954	A	425	45.47	9.24	155	44	25	201
NcbZIP04	GWHPAAYW000981	D	564	62.21	7.12	260	47	19	238
NcbZIP05	GWHPAAYW001299	C	415	44.86	6.11	164	6	5	240
NcbZIP06	GWHPAAYW001709	J	377	41.80	5.40	151	67	22	137
NcbZIP07	GWHPAAYW002908	A	336	37.46	7.80	115	19	5	197
NcbZIP08	GWHPAAYW002911	A	336	37.46	7.80	115	19	5	197
NcbZIP09	GWHPAAYW002993	D	461	50.44	7.20	242	30	7	182
NcbZIP10	GWHPAAYW003042	B	792	86.18	5.84	179	94	28	491
NcbZIP11	GWHPAAYW003339	E	266	29.16	6.15	107	16	10	133
NcbZIP12	GWHPAAYW011330	S	152	17.55	5.91	98	5	2	47
NcbZIP13	GWHPAAYW014950	S	1898	214.64	9.00	712	280	94	812
NcbZIP14	GWHPAAYW015527	A	167	18.44	9.48	87	22	5	53
NcbZIP15	GWHPAAYW015722	I	428	47.31	6.74	145	17	11	255
NcbZIP16	GWHPAAYW015723	I	217	23.98	9.92	72	37	9	99
NcbZIP17	GWHPAAYW019618	E	450	49.50	5.62	147	27	16	260
NcbZIP18	GWHPAAYW020485	S	160	18.11	5.48	94	6	4	56
NcbZIP19	GWHPAAYW020561	I	372	40.4	5.69	154	21	13	184
NcbZIP20	GWHPAAYW021201	H	166	18.22	9.90	76	7	0	83
NcbZIP21	GWHPAAYW021532	C	385	40.82	8.58	164	8	5	208
NcbZIP22	GWHPAAYW025680	A	310	34.00	5.30	110	24	6	170
NcbZIP23	GWHPAAYW025682	D	178	20.14	9.19	79	21	1	77
NcbZIP24	GWHPAAYW025732	A	488	51.90	9.37	141	55	17	275
NcbZIP25	GWHPAAYW025769	A	149	16.94	9.52	78	16	16	39
NcbZIP26	GWHPAAYW026086	D	429	46.68	7.70	211	30	15	173
NcbZIP27	GWHPAAYW026335	S	195	22.17	5.82	105	10	2	78
NcbZIP28	GWHPAAYW026612	G	371	39.05	8.48	118	27	9	217
NcbZIP29	GWHPAAYW026862	B	755	82.16	5.57	147	90	21	497
NcbZIP30	GWHPAAYW027461	G	298	30.89	4.79	94	19	6	179
NcbZIP31	GWHPAAYW027688	I	541	59.03	6.30	183	22	12	324
NcbZIP32	GWHPAAYW028327	A	268	30.70	6.11	132	30	5	101
NcbZIP33	GWHPAAYW004093	A	462	49.89	7.11	124	55	14	269
NcbZIP34	GWHPAAYW004840	A	362	40.15	6.13	143	24	10	185
NcbZIP35	GWHPAAYW004844	D	364	40.64	7.00	227	21	8	108
NcbZIP36	GWHPAAYW004881	G	283	32.04	8.68	147	54	24	58
NcbZIP37	GWHPAAYW005079	H	168	18.92	6.64	78	7	6	77
NcbZIP38	GWHPAAYW005229	E	452	49.64	5.71	162	33	9	248
NcbZIP39	GWHPAAYW005452	S	169	18.77	5.53	103	5	2	59
NcbZIP40	GWHPAAYW005509	I	355	38.40	5.68	145	28	11	171
NcbZIP41	GWHPAAYW005714	G	545	60.52	8.75	175	66	22	282
NcbZIP42	GWHPAAYW005783	C	410	44.35	5.67	153	36	17	204
NcbZIP43	GWHPAAYW005814	A	101	12.04	8.96	81	4	0	16
NcbZIP44	GWHPAAYW005854	D	511	56.99	7.75	245	23	19	224
NcbZIP45	GWHPAAYW009588	I	334	36.76	7.01	137	19	13	165
NcbZIP46	GWHPAAYW028567	C	264	28.72	6.13	119	10	7	128

表1

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图3

图4

表2

图5

图6

图7

图8

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复制基因1 Duplicated gene 1	复制基因2 Duplicated gene 2	亚家族 Subfamily	Ka Ka	Ks Ks	Ka/Ks Ka/Ks	纯化选择 Purifying selection	复制类型 Duplicated type
GWHPAAYW001299	GWHPAAYW021532	C	0.32	1.24	0.26	Yes	Segmental duplication 片段复制
GWHPAAYW000931	GWHPAAYW005714	G	0.36	0.95	0.38	Yes	Segmental duplication 片段复制
GWHPAAYW000954	GWHPAAYW005814	A	0.53	2.19	0.24	Yes	Segmental duplication 片段复制
GWHPAAYW000981	GWHPAAYW005854	D	0.11	0.78	0.15	Yes	Segmental duplication 片段复制
GWHPAAYW015527	GWHPAAYW025769	A	0.61	1.84	0.33	Yes	Segmental duplication 片段复制
GWHPAAYW020485	GWHPAAYW005452	S	0.09	1.29	0.07	Yes	Segmental duplication 片段复制
GWHPAAYW020561	GWHPAAYW005509	I	0.20	1.04	0.19	Yes	Segmental duplication 片段复制
GWHPAAYW019618	GWHPAAYW005229	E	0.22	1.29	0.17	Yes	Segmental duplication 片段复制
GWHPAAYW025680	GWHPAAYW004840	A	0.22	1.61	0.14	Yes	Segmental duplication 片段复制
GWHPAAYW015722	GWHPAAYW015723	I	0.28	0.96	0.30	Yes	Tandem duplication 串联复制