辣椒HD-Zip基因家族鉴定、系统进化及表达分析

doi:10.3864/j.issn.0578-1752.2020.05.012

摘要/Abstract

摘要：

【目的】鉴定辣椒HD-Zip基因家族,并利用生物信息学方法系统分析其在基因组中的分布、基因结构、进化分化特征及在不同组织中的时空表达特异性,解析该家族的进化特征及生物学功能。【方法】根据已报道及PlantTFDB数据库中的拟南芥HD-Zip序列,利用本地BLAST工具在我国辣椒测序品种‘遵辣1号’基因组中比对,并利用Pfam、SMART工具进一步验证。采用EMBOSS Programs、MEGA、GSDS、MEME、MCScanX、OrthoMCL、Circos等软件预测辣椒HD-Zip基因家族成员蛋白理化性质,构建系统进化树,定位染色体,分析基因结构、基因复制类型及直系、旁系同源基因。基于GEO数据库,运用R软件、本地perl语言及Cytoscape分析辣椒HD-Zip组织表达差异并绘制共表达网络。【结果】本研究在‘遵辣1号’基因组中鉴定获得42条辣椒HD-Zip,命名为CaHDZ01—CaHDZ42。CaHDZs长度跨度较大,70% CaHDZ蛋白的pI小于7.0。除CaHDZ42,其余基因不均匀地分布在12条染色体上,部分基因为片段复制。该基因家族可分为4个亚族,分别含有18、9、5、10个HD-Zip,基因结构及蛋白结构域差别显著。辣椒、番茄和拟南芥3个物种中的直系同源基因对数目大体相同,但同为茄科的辣椒和番茄之间的稍多;辣椒中的旁系同源基因少于番茄和拟南芥,说明辣椒基因组的倍增事件并没有使CaHDZs明显扩增。对无油樟、水稻、玉米、番茄、马铃薯、辣椒‘CM334’、辣椒‘Zunla-1’、毛果杨、葡萄以及拟南芥9个代表物种的HD-Zip进化特征分析结果表明,从被子植物开始,HD-Zip基因家族就稳定存在4个亚族。推测在形成4个亚族前,HD-Zip分为两组,其中一组分化成I和II亚族,而另一组则分化成为III和IV亚族。CaHDZs在根、茎、叶、花芽、花和果实不同发育时期的表达模式分析结果显示,4个亚族具有不同程度的表达趋势。其中I亚族基因在辣椒不同组织中的表达量均较高,且不同成员间表达模式不同,CaHDZ22在茎中的表达最高,表明该基因可能对辣椒茎的生长有重要作用。II、III和IV亚族基因在不同组织中的表达量相对较低,但部分基因在特定组织中具有较大的表达量。如CaHDZ34在辣椒果实成熟后期具有较大高的表达量,CaHDZ02和CaHDZ28在果实膨大时表达较高,CaHDZ04在果实成熟前期具有较高的表达量。CaHDZs表达网络中有33对基因表达趋势的相关系数（PCC）大于0.8,6对大于0.9,表明CaHDZs协同调控了辣椒的生长发育,不同亚族之间也具有协同性。【结论】在‘遵辣1号’基因组中鉴定获得42条CaHDZs,可分为4个亚族,不同亚族的基因结构、蛋白保守结构域及表达模式不同。在进化过程中,辣椒HD-Zip保守性高,数目没有明显扩增,I和II亚族、III和IV亚族关系更近。CaHDZs具有组织表达差异性,协同调控了辣椒的生长发育。

关键词: 辣椒, HD-Zip基因家族, 系统进化, 表达分析

Abstract:

【Objective】The objectives of this research were to identify the Homeodomain-Leucine Zipper (HD-Zip) family genes from pepper (Capsicum annuum) genome, to know the profile of HD-Zip family such as gene number, gene distribution, gene structure, evolutionary process and expression patterns in different tissues, and to provide theoretical basis for exploring what roles the HD-Zips play in pepper. 【Method】HD-Zip genes in pepper genome were identified by BLAST software based on HD-Zip from Arabidopsis, and verified by Pfam and SMART software. EMBOSS Programs, MEGA, GSDS, MEME, MCScanX, OrthoMCL and Circos softwares were used for bioinformatics analysis of HD-Zip protein and gene sequences. Expression patterns and gene co-regulatory network were analyzed by R and Cytoscape software. 【Result】Total of 42 HD-Zip genes were identified from ‘Zunla-1’ pepper genome, named as CaHDZ01-CaHDZ42. The length of their coding sequences ranged from 459 to 2 529 bps, and the isoelectric point of 70% CaHDZs was less than 7.0. The analysis of the gene’s location on the chromosome revealed that CaHDZs were unevenly distributed on 12 chromosomes of the pepper, except for CaHDZ42. The gene family could be divided into four subgroups, containing 18, 9, 5 and 10 CaHDZ genes, respectively. There were significant differences in gene structure and protein conserved domains among the subgroups. The number of orthologs among pepper, tomato and Arabidopsis was almost the same, but there were a little more orthologs between pepper and tomato. While the number of paralogs in Arabidopsis was significantly more than that in tomato and pepper, and the least in pepper, suggesting that the number of CaHDZ genes did not increase significantly along with genomic replication. To further understand the evolutionary history of CaHDZs in plant, HD-Zip homologous genes in Arabidopsis and 8 other plant species were analyzed. The results showed that all the major subgroups of HD-Zips existed in angiosperms. It was inferred that HD-Zip genes were divided into two groups initially. Then, one group differentiated into subgroup I and II, and the other differentiated into subgroups III and IV. The results of expression patterns analysis showed that the expression trends of four subgroups were different. Most of subgroup I genes expressed highly in pepper, such as CaHDZ22, and the expression of which was highest in stem, suggesting that this gene might play an important role in the growth of pepper stem. The expressions of subgroups II, III and IV CaHDZs were relatively low, but some of them expressed highly in specific tissues. For example, the expression of CaHDZ34 was high in late ripening stage of pepper fruits, CaHDZ02 and CaHDZ28 expressed highly in fruit enlargement stage, and CaHDZ04 expressed highly in early ripening stage of pepper fruits. In the coregulatory networks of CaHDZs, the Pearson correlation coefficients (PCCs) of 33 pairs of CaHDZs were greater than 0.8, and 6 pairs were greater than 0.9, suggesting that the CaHDZs coordinated the growth and development in pepper, and there were cooperative interactions among subgroups. 【Conclusion】All of 42 HD-Zip gene family members were identified from the ‘Zunla-1’ pepper genome, which could be divided into four subgroups. During the evolutionary history, CaHDZs were highly conservative and expanded slowly. Subgroup I and subgroup II had a closer relationship, so did subgroup III and subgroup IV. CaHDZ genes expressed specifically in different tissues and coordinately regulated the growth and development of pepper.

Key words: Capsicum annuum, HD-Zip gene family, systematic evolution, gene expression analyses

邵晨冰,黄志楠,白雪滢,王云鹏,段伟科. 辣椒HD-Zip基因家族鉴定、系统进化及表达分析[J]. 中国农业科学, 2020, 53(5): 1004-1017.

SHAO ChenBing,HUANG ZhiNan,BAI XueYing,WANG YunPeng,DUAN WeiKe. Identification, Systematic Evolution and Expression Analysis of HD-Zip Gene Family in Capsicum annuum[J]. Scientia Agricultura Sinica, 2020, 53(5): 1004-1017.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2020.05.012

https://www.chinaagrisci.com/CN/Y2020/V53/I5/1004

图/表 9

表1

辣椒HD-Zip基因家族信息"

基因名称 Gene name	亚族 Group	基因组登录号 Gene accession No.	大小 Size (aa)	长度 Length (bp)	染色体位置 Chromosome location	分子量 Molecular weight (kD)	等电点 pI	拟南芥同源蛋白 Arabidopsis homologous	E值 E-value
CaHDZ01	I	Capana01g000046	211	636	Chr01:803719..804778	24.44	4.83	ATHB7	1.00E-31
CaHDZ02	II	Capana01g000658	282	849	Chr01:12827760..12830218	31.94	7.26	ATHB2	2.00E-102
CaHDZ03	IV	Capana01g001104	842	2529	Chr01:30759598..30765550	93.61	4.98	HDG5	0
CaHDZ04	IV	Capana01g001442	764	2295	Chr01:45982654..45987435	83.76	6.31	ANL2	0
CaHDZ05	II	Capana01g002526	392	1179	Chr01:165755875..165758134	42.42	7.36	HAT14	1.00E-64
CaHDZ06	II	Capana01g003482	300	903	Chr01:227843358..227845842	33.34	6.76	HAT3	9.00E-65
CaHDZ07	I	Capana02g000407	219	660	Chr02:53806313..53809076	25.62	6.28	ATHB40	2.00E-70
CaHDZ08	II	Capana02g000632	241	726	Chr02:79582528..79585428	27.00	9.36	HAT22	3.00E-73
CaHDZ09	I	Capana02g000916	273	822	Chr02:102327531..102329744	31.10	5.87	ATHB3	9.00E-51
CaHDZ10	III	Capana02g001374	830	2493	Chr02:123107922..123114705	91.73	6.17	ATHB14	0
CaHDZ11	IV	Capana02g002164	708	2127	Chr02:141118184..141122121	77.85	5.97	PDF2	0
CaHDZ12	I	Capana02g002657	215	648	Chr02:148700184..148702221	25.03	5.26	ATHB40	1.00E-64
CaHDZ13	II	Capana02g002922	272	819	Chr02:152663803..152665091	30.28	8.15	HAT22	4.00E-96
CaHDZ14	I	Capana02g003384	245	738	Chr02:160009225..160010619	28.01	5.39	ATHB13	3.00E-61
CaHDZ15	I	Capana02g003485	215	648	Chr02:161300767..161302593	24.09	4.51	ATHB1	2.00E-55
CaHDZ16	III	Capana03g000260	838	2517	Chr03:3882950..3890673	92.06	6.46	ATHB15	0
CaHDZ17	IV	Capana03g000292	772	2319	Chr03:4166533..4174964	86.44	6.80	GL2	0
CaHDZ18	I	Capana03g001081	322	969	Chr03:18412063..18413771	37.09	4.78	ATHB1	7.00E-42
CaHDZ19	IV	Capana03g001526	720	2163	Chr03:28572926..28576191	79.49	6.64	HDG11	0
CaHDZ20	I	Capana03g001926	220	663	Chr03:39229362..39230232	25.76	6.11	ATHB7	1.00E-39
CaHDZ21	IV	Capana03g002346	800	2403	Chr03:61310140..61314456	86.93	6.27	ANL2	0
CaHDZ22	I	Capana03g002675	178	537	Chr03:99390829..99391365	20.60	8.16	ATHB52	6.00E-29
CaHDZ23	I	Capana04g000966	294	885	Chr04:23370253..23371908	33.69	4.77	ATHB16	4.00E-41
CaHDZ24	I	Capana04g002305	211	636	Chr04:195248401..195250017	25.13	6.98	ATHB40	7.00E-55
CaHDZ25	I	Capana05g001458	222	669	Chr05:129767576..129768389	25.69	4.92	ATHB7	3.00E-34
CaHDZ26	I	Capana05g001741	284	855	Chr05:172400277..172401713	32.24	4.26	ATHB16	1.00E-51
CaHDZ27	IV	Capana06g000834	734	2205	Chr06:13187448..13191074	80.88	6.50	HDG11	0
CaHDZ28	II	Capana06g001620	286	861	Chr06:41280020..41282406	32.52	8.17	ATHB2	2.00E-93
CaHDZ29	IV	Capana07g001455	777	2334	Chr07:184550371..184557526	85.90	5.52	HDG2	0
CaHDZ30	I	Capana07g002156	177	534	Chr07:215423716..215424249	20.70	5.84	ATHB52	9.00E-25
CaHDZ31	III	Capana08g000475	553	1662	Chr08:73848414..73853082	61.12	7.73	ATHB8	0
CaHDZ32	I	Capana09g002322	245	738	Chr09:236366842..236370358	28.43	8.01	ATHB51	5.00E-56
CaHDZ33	IV	Capana10g000585	731	2196	Chr10:26552568..26561787	80.57	5.67	PDF2	0
CaHDZ34	II	Capana10g002189	333	1002	Chr10:200359705..200363261	37.16	8.65	HAT14	5.00E-69
CaHDZ35	III	Capana11g000079	841	2526	Chr11:2280596..2286141	92.17	6.15	IFL1	0
CaHDZ36	I	Capana11g001580	278	837	Chr11:181752291..181754489	32.10	4.54	ATHB1	4.00E-49
CaHDZ37	I	Capana11g001647	311	936	Chr11:187454288..187456636	35.61	6.00	ATHB13	2.00E-126
CaHDZ38	II	Capana11g002379	152	459	Chr11:219730688..219733084	18.09	8.51	ATHB17	6.00E-62
CaHDZ39	III	Capana12g001248	486	1461	Chr12:64777481..64784271	53.89	8.48	ATHB15	0
CaHDZ40	I	Capana12g002675	354	1065	Chr12:225304884..225307563	39.57	4.20	ATHB6	1.00E-68
CaHDZ41	IV	Capana12g002821	634	1905	Chr12:228410133..228419272	71.59	6.36	HDG8	2.00E-113
CaHDZ42	II	Capana00g004586	211	636	Chr00:656715560..656716427	24.26	10.00	HAT22	2.00E-46

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参考文献 36

[1]	ARIEL F D, MANAVELLA P A, DEZAR C A, CHAN R L . The true story of the HD-Zip family. Trends in Plant Science, 2007,12(9):419-426.
[2]	李俐, 王义, 王康宇, 赵明珠, 孙春玉, 林彦萍, 张美萍 . HD-Zip基因家族的结构、功能与表达模式. 分子植物育种, 2018,16(3):781-790.
	LI L, WANG Y, WANG K Y, ZHAO M Z, SUN C Y, LIN Y P, ZHANG M P . The structure, function and expression pattern of HD-Zip gene family. Molecular Plant Breeding, 2018,16(3):781-790. (in Chinese)
[3]	NAKASHIMA K, ITO Y, YAMAGUCHI-SHINOZAKI K . Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant Physiology, 2009,149(1):88-95.
[4]	HENRIKSSON E, OLSSON A S, JOHANNESSON H, JOHANSSON H, HANSON J, ENGSTROM P, SODERMAN E . Homeodomain leucine zipper class I genes in Arabidopsis. Expression patterns and phylogenetic relationships. Plant Physiology, 2005,139(1):509-518.
[5]	WANG Y, HENRIKSSON E, SODERMAN E, HENRIKSSON K N, SUNDBERG E, ENGSTROM P . The Arabidopsis homeobox gene, ATHB16, regulates leaf development and the sensitivity to photoperiod in Arabidopsis. Developmental Biology, 2003,264(1):228-239.
[6]	CIARBELLI A R, CIOLFI A, SALVUCCI S, RUZZA V, POSSENTI M, CARABELLI M, FRUSCALZO A, SESSA G, MORELLI G, RUBERTI I . The Arabidopsis homeodomain-leucine zipper II gene family: Diversity and redundancy. Plant Molecular Biology, 2008,68(4/5):465-478.
[7]	HARRIS J C, HRMOVA M, LOPATO S, LANGRIDGE P . Modulation of plant growth by HD-Zip class I and II transcription factors in response to environmental stimuli. The New Phytologist, 2011,190(4):823-837.
[8]	PRIGGE M J, OTSUGA D, ALONSO J M, ECKER J R, DREWS G N, CLARK S E . Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development. The Plant Cell, 2005,17(1):61-76.
[9]	BRANDT R, SALLA-MARTRET M, BOU-TORRENT J, MUSIELAK T, STAHL M, LANZ C, OTT F, SCHMID M, GREB T, SCHWARZ M, CHOI S B, BARTON M K, REINHART B J, LIU T, QUINT M, PALAUQUI J C, MARTINEZ-GARCIA J F, WENKEL S. Genome-wide binding-site analysis of REVOLUTA reveals a link between leaf patterning and light-mediated growth responses. The Plant Journal, 2012,72(1):31-42.
[10]	OTSUGA D, DEGUZMAN B, PRIGGE M J, DREWS G N, CLARK S E . REVOLUTA regulates meristem initiation at lateral positions. The Plant Journal, 2001,25(2):223-236.
[11]	OCHANDO I, GONZALEZ-REIG S, RIPOLL J J, VERA A, MARTINEZ-LABORDA A . Alteration of the shoot radial pattern in Arabidopsis thaliana by a gain-of-function allele of the class III HD-Zip gene INCURVATA4. International Journal of Developmental Biology, 2004,52(7):953-961.
[12]	NAKAMURA M, KATSUMATA H, ABE M, YABE N, KOMEDA Y, YAMAMOTO K T, TAKAHASHI T . Characterization of the class IV homeodomain-Leucine Zipper gene family in Arabidopsis. Plant Physiology, 2006,141(4):1363-1375.
[13]	PETERSON K M, SHYU C, BURR C A, HORST R J, KANAOKA M M, OMAE M, SATO Y, TORII K U . Arabidopsis homeodomain- leucine zipper IV proteins promote stomatal development and ectopically induce stomata beyond the epidermis. Development, 2013,140(9):1924-1935.
[14]	WEI Q, KUAI B K, HU P, DING Y L . Ectopic-overexpression of an HD-Zip IV transcription factor from Ammopiptanthus mongolicus (Leguminosae) promoted upward leaf curvature and non-dehiscent anthers in Arabidopsis thaliana. Plant Cell Tissue & Organ Culture, 2012,110(2):299-306.
[15]	KUBO H, PEETERS A J, AARTS M G, PEREIRA A, KOORNNEEF M . ANTHOCYANINLESS2, a homeobox gene affecting anthocyanin distribution and root development in Arabidopsis. The Plant Cell, 1999,11(7):1217-1226.
[16]	OOI S E, RAMLI Z, SYED ALWEE S S R, KULAVEERASINGAM H, ONG-ABDULLAH M . EgHOX1, a HD-Zip II gene, is highly expressed during early oil palm (Elaeis guineensis Jacq.) somatic embryogenesis. Plant Gene, 2016,8:16-25.
[17]	GAO Y N, GAO S H, XIONG C, YU G, CHANG J, YE Z B, YANG C X . Comprehensive analysis and expression profile of the homeodomain leucine zipper IV transcription factor family in tomato. Plant Physiology and Biochemistry, 2015,96:141-153.
[18]	LI Z Q, ZHANG C, GUO Y R, NIU W L, WANG Y J, XU Y . Evolution and expression analysis reveal the potential role of the HD-Zip gene family in regulation of embryo abortion in grapes (Vitis vinifera L.). BMC Genomics, 2017,18(1):744.
[19]	ZHAO Y, ZHOU Y Q, JIANG H Y, LI X Y, GAN D F, PENG X J, ZHU S W, CHENG B J . Systematic analysis of sequences and expression patterns of drought-responsive members of the HD-Zip gene family in maize. PLoS ONE, 2011,6(12):e28488.
[20]	KIM S, PARK M, YEOM S I, KIM Y M, LEE J M, LEE H A, SEO E, CHOI J, CHEONG K, KIM K T, JUNG K, LEE G W, OH S K, BAE C, KIM S B, LEE H Y, KIM S Y, KIM M S, KANG B C, JO Y D , et al. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nature Genetics, 2014,46(3):270-278.
[21]	QIN C, YU C S, SHEN Y O, FANG X D, CHEN L, MIN J M, CHENG J W, ZHAO S C, XU M, LUO Y, YANG Y L, WU Z M, MAO L K, WU H Y, LING-HU C Y, ZHOU H K, LIN H J, GONZALEZ-MORALES S, TREJO-SAAVEDRA D L, TIAN H, et al. Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proceedings of the National Academy of Sciences of the United States of America, 2014,111(14):5135-5140.
[22]	陈国梁, 高瑜, 张昊, 王亚洁, 王睿, 王延峰 . 辣椒HD-ZIP转录因子家族鉴定与生物信息学分析. 分子植物育种, 2019. http://kns. cnki.net/kcms/detail/46.1068.s.20190603.1114.010.html
	CHEN G L, GAO Y, ZHANG H, WANG Y J, WANG R, WANG Y F. Identification and bioinformatics analysis of Hd-Zip transcription factor family in Capsicum annuum. Molecular Plant Breeding, 2019.http://kns.cnki.net/kcms/detail/46.1068.s.20190603.1114.010.html. (in Chinese)
[23]	THOMPSON J D, GIBSON T J, HIGGINS D G . Multiple sequence alignment using ClustalW and ClustalX. Current Protocols in Bioinformatics, 2002. doi: 10.1002/0471250953.bi0203s00.
[24]	TAMURA K, STECHER G, PETERSON D, FILIPSKI A, KUMAR S . MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 2013,30(12):2725-2729.
[25]	CHEN C J, XIA R, CHEN H, HE Y H . TBtools, a Toolkit for Biologists integrating various biological data handling tools with a user-friendly interface. BioRxiv, 2018. doi: https://doi.org/10.1101/ 289660.
[26]	WANG Y P, TANG H B, DEBARRY J D, TAN X, LI J P, WANG X Y, LEE T H, JIN H Z, MARLER B, GUO H, KISSINGER J C, PATERSON A H . MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research, 2012,40(7):e49.
[27]	LI W, DONG J Y, CAO M X, GAO X X, WANG D D, LIU B L, CHEN Q . Genome-wide identification and characterization of HD-ZIP genes in potato. Gene, 2019,697:103-117.
[28]	HU R B, CHI X Y, CHAI G H, KONG Y Z, HE G, WANG X Y, SHI D C, ZHANG D Y, ZHOU G K . Genome-wide identification, evolutionary expansion, and expression profile of homeodomain- leucine zipper gene family in poplar (Populus trichocarpa). PLoS ONE, 2012,7(2):e31149.
[29]	FORCE A, LYNCH M, PICKETT F B, AMORES A, YAN Y L, POSTLETHWAIT J . Preservation of duplicate genes by complementary, degenerative mutations. Genetics, 1999,151(4):1531-1545.
[30]	SULTAN S E . Plant developmental responses to the environment: Eco-devo insights. Current Opinion in Plant Biology, 2010,13(1):96-101.
[31]	DES MARAIS D L, RAUSHER M D . Escape from adaptive conflict after duplication in an anthocyanin pathway gene. Nature, 2008,454(7205):762-765.
[32]	LIU W, FU R, LI Q, LI J, WANG L N, REN Z H . Genome-wide identification and expression profile of homeodomain-leucine zipper Class I gene family in Cucumis sativus. Gene, 2013,531(2):279-287.
[33]	RE D A, DEZAR C A, CHAN R L, BALDWIN I T, BONAVENTURE G . Nicotiana attenuata NaHD20 plays a role in leaf ABA accumulation during water stress, benzylacetone emission from flowers, and the timing of bolting and flower transitions. Journal of Experimental Botany, 2011,62(1):155-166.
[34]	ARIEL F, DIET A, VERDENAUD M, GRUBER V, FRUGIER F, CHAN R, CRESPI M . Environmental regulation of lateral root emergence in Medicago truncatula requires the HD-Zip I transcription factor HB1. The Plant Cell, 2010,22(7):2171-2183.
[35]	AOYAMA T, DONG C H, WU Y, CARABELLI M, SESSA G, RUBERTI I, MORELLI G, CHUA N H . Ectopic expression of the Arabidopsis transcriptional activator Athb-1 alters leaf cell fate in tobacco. The Plant Cell, 1995,7(11):1773-1785.
[36]	KIM Y K, SON O, KIM M R, NAM K H, KIM G T, LEE M S, CHOI S Y, CHEON C I . ATHB23, an Arabidopsis class I homeodomain- leucine zipper gene, is expressed in the adaxial region of young leaves. Plant Cell Reports, 2007,26(8):1179-1185.