甜菜MADS-box家族基因的全基因组鉴定及进化分析

doi:10.7668/hbnxb.2018.01.014

摘要/Abstract

摘要： 为了进一步了解MADS-box家族基因的功能，利用生物信息学的手段，首次对甜菜MADS-box基因进行了全基因组的鉴定，并对其染色体定位、系统发生关系、基因结构、保守元件、表达模式以及蛋白功能联系进行预测和分析。结果表明，甜菜MADS-box基因共34个成员，其中，type Ⅰ成员7个和type Ⅱ成员27个，type Ⅰ进一步分为Mα（3）、Mβ（1）、Mγ（3）3个组；type Ⅱ进一步分为MIKC^C（22）和MIKC^*（5）2个组，MIKC^C组可进一步分为AG （2）、AGL12（2）、AP3-PI （4）、Bs （2）、SOC1（1）、SVP （1）、SEP （3）、AGL17（5）、AP1-FUL （1）和FLC （1）10个亚组。MADS-box家族基因在染色体上呈不均匀分布，同一染色体上的基因簇状分布，其中，第6号染色体上分布最多，在第7号染色体上没有分布。甜菜MADS-box家族基因虽然基因结构差别较大，但蛋白序列相对保守。基因表达谱显示，大部分MADS-box基因优势表达于分生组织，部分MADS-box基因在种子、直根、幼叶等组织亦有较高表达。部分MADS-box基因响应盐、热胁迫轻微上调，可能参与甜菜逆境生理调控。

关键词: 甜菜, MADS-box, 全基因组, 家族基因

Abstract: To further understand the function of MADS-box family gene,the genome-wide of beet MADS-box genes were first identified by bioinformatics,and chromosomal localization,phylogenetic relationship,gene structure,conserved domain,expression pattern and proteins function connections were predicted and analyzed.The results showed that there were 34 MADS-box genes in beet,among which 7 members belong to type Ⅰ and 27 members belong to type Ⅱ.Type Ⅰ was further divided into three class:Mα (3),Mβ (1) and Mγ (3),type Ⅱ was further divided into two class:MIKC^C (22) and MIKC^* (5),and MIKC^C class were further divided into ten subclass:AG (2),AGL12 (2),AP3-PI (4),Bs (2),SOC1 (1),SVP (1),SEP (3),AGL17 (5),AP1-FUL (1) and FLC (1).The MADS-box genes showed uneven distribution on the chromosome,and genes cluster distribution on one chromosome.The most distributed was on chromosome 6,none on chromosome 7.The structure of the MADS-box genes was different,but the protein sequences were conserved relatively.The expression profile showed that most MADS-box genes were expressed highly in meristem,and some MADS-box genes were expressed advantageously in seeds,roots,young leaves,and so on.Some MADS-box genes are slightly up-regulated in response to salt or heat stress and may be involved in the physiological regulation under stress.

Key words: Beta vulgaris L., MADS-box, Genome-wide, Family gene

中图分类号:

Q78
S566.03

孔维龙, 张康达, 吴俊池, 张丽平, 潘辉, 唐嘉蔚, 傅小鹏. 甜菜MADS-box家族基因的全基因组鉴定及进化分析[J]. 华北农学报, 2018, 33(1): 86-95. doi: 10.7668/hbnxb.2018.01.014.

KONG Weilong, ZHANG Kangda, WU Junchi, ZHANG Liping, PAN Hui, TANG Jiawei, FU Xiaopeng. Genome-wide Identification and Phylogenetic Analysis of MADS-box Family Gene in Beta vulgaris[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2018, 33(1): 86-95. doi: 10.7668/hbnxb.2018.01.014.

http://www.hbnxb.net/CN/Y2018/V33/I1/86

参考文献

[1] Alvarezbuylla E R,Liljegren S J,Pelaz S,et al.MADS-box gene evolution beyond flowers:expression in pollen,endosperm,guard cells,roots and trichomes[J].Plant Journal,2000,24(4):457-466.
[2] Becker A,Theissen G.The major clades of MADS-box genes and their role in the development and evolution of flowering plants[J].Molecular Phylogenetics and Evolution,2003,29(3):464-489.
[3] Kaufmann K,Melzer R,Theissen G.MIKC-type MADS-domain proteins:structural modularity,protein interactions and network evolution in land plants[J].Gene,2005,347(2):183-198.
[4] Tian Y,Dong Q,Ji Z,et al.Genome-wide identification and analysis of the MADS-box gene family in apple[J].Gene,2015,555(2):277-290.
[5] Saha G,Park J I,Jung H J,et al.Genome-wide identification and characterization of MADS-box family genes related to organ development and stress resistance in Brassica rapa[J].BMC Genomics,2015,16(1):178.
[6] Li C,Wang Y,Xu L,et al.Genome-Wide characterization of the MADS-box gene family in radish (Raphanus sativus L.) and assessment of its roles in flowering and floral organogenesis[J].Frontiers in Plant Science,2016,7:1390.
[7] 邱文明,徐育海,何秀娟.板栗雌雄花发育相关的MADS-box基因发掘与表达分析[J].园艺学报,2016,43(8):1593-1604.
[8] Bemer M,Gordon J,Weterings K,et al.Divergence of recently duplicated Mγ-type MADS-box genes in Petunia[J].Molecular Biology & Evolution,2010,27(2):481-495.
[9] Parenicová L,De Folter S,Kieffer M,et al.Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis:new openings to the MADS world[J].The Plant Cell,2003,15(7):1538-1551.
[10] Xu Z,Zhang Q,Sun L,et al.Genome-wide identification,characterisation and expression analysis of the MADS-box gene family in Prunus mume[J].Molecular Genetics and Genomics,2014,289(5):903-920.
[11] De Bodt S,Theissen G,Van De Peer Y.Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting[J].Molecular Biology and Evolution,2006,23(6):1293-1303.
[12] Martinez-Castilla L P,Alvarez-buylla E R.Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny[J].Proceedings of the National Academy of Sciences of United States in America,2003,100(23):13407-13412.
[13] Kater M M,Dreni L,Colombo L.Functional conservation of MADS-box factors controlling floral organ identity in rice and Arabidopsis[J].Journal of Experimental Botany,2006,57(13):3433-3444.
[14] Leseberg C H,Li A,Kang H,et al.Genome-wide analysis of the MADS-box gene family in Populus trichocarpa[J].Gene,2006,378(1):84-94.
[15] Arora R,Agarwal P,Ray S,et al.MADS-box gene family in rice:genome-wide identification,organization and expression profiling during reproductive development and stress[J].BMC Genomics,2007,8(1):242.
[16] Díaz-Riquelme J,Lijavetzky D,Martínez-Zapater J M,et al.Genome-wide analysis of MIKCC-type MADS box genes in grapevine[J].Plant Physiology,2009,149(1):354-369.
[17] Zhang L,Xu Y,Cloning M M,et al.And chromosomal localization of two MADS-box genes in peach(Prunus persica)[J].Journal of Genetics and Genomics,2008,35(6):365-372.
[18] Martel C,Vrebalov J,Tafelmeyer P A.The tomato MADS-box transcription factor RIPENING INHIBITOR interacts with promoters involved in numerous ripening processes in a COLORLESS NONRIPENING-Dependent manner[J].Plant Physiology,2011,157(3):1568-1579.
[19] Ma H.Molecular genetic analyses of microsporogenesis and microgametogenesis in flowering plants[J].Annual Review of Plant Biology,2005,56(1):393-434.
[20] Mara C D,Irish V F.Two GATA transcription factors are downstream effectors of floral homeotic gene action in Arabidopsis[J].Plant Physiology,2008,147(2):707-718.
[21] Kaufmann K,Muino J M,Jauregui R,et al.Target genes of the MADS transcription factor SEPALLATA3:integration of developmental and hormonal pathways in the Arabidopsis flower[J].PLoS Biology,2009,7(4):854-875.
[22] 陈璟,李名扬,闫明旭,等.矮牵牛PMADS9 基因的结构特征和mRNA的表达分析[J].园艺学报,2011,38(1):108-116.
[23] 梁芳,许申平,蒋素华,等.菊花MADS-box基因的克隆与表达载体构建[J].华北农学报,2016,31(3):25-31.
[24] 周云涛,王茂林,胡远辉,等.甘蓝型油菜MADS-box基因家族APETALA3 基因编码区的克隆与序列分析[J].四川大学学报:自然科学版,2004,41(5):1091-1093.
[25] Dohm J C,Minoche A E,Holtgraewe D A,et al.The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)[J].Nature,2014,505(7484):546.
[26] Minoche A E,Dohm J C,Schneider J A,et al.Exploiting single-molecule transcript sequencing for eukaryotic gene prediction[J].Genome Biology,2015,16(1):1-13.
[27] Stracke R,Holtgraewe D,Schneider J,et al.Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet (Beta vulgaris)[J].BMC Plant Biology,2014,14(1):1-17.
[28] 孔维龙,胡瑞,包满珠,等.香石竹水孔蛋白基因的克隆及表达分析[J].园艺学报,2017,44(3):515-527.
[29] 陈鸿飞,邵红霞,樊胜,等.苹果全基因组多聚半乳糖醛酸酶基因家族的鉴定及进化分析[J].园艺学报,2016,43(10):1863-1877.
[30] 宋春晖,张东,马娟娟,等.苹果生长素运输基因MdABCB19 的克隆及其在矮化砧木中的表达分析[J].园艺学报,2017,44(3):409-421.
[31] 林雯.TPR基序——一种介导蛋白质相互作用的结构域[J].国外医学:分子生物学分册,2000,22(5):289-293.
[32] 张霞,唐维,刘嘉,等.过量表达水稻OsP5CS1 和OsP5CS2 基因提高烟草脯氨酸的生物合成及其非生物胁迫抗性[J].应用与环境生物学报,2014,20(4):717-722.
[33] 韩兴杰,徐玲玲,廖亮,等.茶树LEAFY 基因的克隆和表达分析[J].园艺学报,2015,42(8):1606-1616.
[34] Weigel D,Meyerowitz E M.Activation of floral homeotic genes in Arabidopsis[J].Science,1993,261(5129):1723-1726.
[35] Moyroud E,Tichtinsky G,Parcy F.The LEAFY floral regulators in angiosperms:conserved proteins with diverse roles[J].Journal of Plant Biology,2009,52(3):177-185.
[36] Song C P,Galbraith D W.AtSAP18,an orthologue of human SAP18,is involved in the regulation of salt stress and mediates transcriptional repression in Arabidopsis[J].Plant Molecular Biology,2006,60(2):241-257.
[37] 张蕊芬,刘会,周李杰,等.苹果组蛋白脱乙酰化酶基因HDA19 的生物信息学分析与胁迫响应研究[J].园艺学报,2016,43(4):613-622.
[38] Yi J M,Huang T,Huang Y,et al.Phylogenetic analysis of MADS-box gene family in physcomitrella patens[J].Plant Physiology Journal,2015,51(2):197-206.
[39] Barker E I,Ashton N W.A parsimonious model of lineage-specific expansion of MADS-box genes in Physcomitrella patens[J].Plant Cell Reports,2013,32(8):1161-1177.
[40] Kwantes M,Liebsch D,Verelst W.How MIKC*MADS-box genes originated and evidence for their conserved function throughout the evolution of vascular plant gametophytes[J].Molecular Biology & Evolution,2011,29(1):293-302.
[41] Guo X H,Chen G P,Cui B L,et al. Solanum lycopersicum agamous-like MADS-box protein AGL15-like gene, SlMBP11,confers salt stress tolerance[J].Molecular Breeding,2016,36(9):125.
[42] Duan W K,Song X M,Liu T K,et al.Genome-wide analysis of the MADS-box gene family in Brassica rapa (Chinese cabbage)[J].Molecular Genetics and Genomics,2015,290(1):239-255.
[43] Gimenez E,Dominguez E,Pineda B,et al.Transcriptional activity of the MADS box ARLEQUIN/TOMATO AGAMOUS-LIKE1 gene is required for cuticle development of tomato fruit[J].Plant Physiology,2015,168(3):1036.
[44] Wang L,Yin X J,Cheng C X,et al.Evolutionary and expression analysis of a MADS-box gene superfamily involved in ovule development of seeded and seedless grapevines[J].Molecular Genetics and Genomics,2015,290(3):825-846.
[45] Liu J H,Liu L,Li Y J,et al.Role for the banana AGAMOUS-like gene MaMADS7 in regulation of fruit ripening and quality[J].Physiologia Plantarum,2015,155(3):217-231.
[46] Saito T,Bai S L,Imai T,et al.Histone modification and signalling cascade of the dormancy-associated MADS-box gene, PpMADS13-1,in Japanese pear (Pyrus pyrifolia) during endodormancy[J].Plant Cell and Environment,2015,38(6):1157-1166.

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