小麦GRAS基因家族的全基因组鉴定与分析
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摘要
GRAS基因是一类转录因子基因,在植物的生长和发育中起关键作用。本研究利用最新的小麦基因组数据,对小麦GRAS基因进行了全基因组鉴定和分析。结果从小麦中鉴定出153个GRAS基因,这些基因不均匀分布在小麦21条染色体上。系统发育分析将这些基因分为12个亚家族,片段复制和串联重复是导致该基因家族扩张的主要原因。蛋白质序列分析发现不同亚家族间氨基酸数目、分子量存在一定差异;二级结构预测表明,小麦GRAS基因的氨基酸序列均以α-螺旋、随机卷曲为主要组成部分。通过对小麦GRAS基因在不同组织和不同逆境胁迫下的表达分析发现,GRAS基因在不同组织和逆境胁迫下存在明显的差异表达,表明GRAS基因具有组织或器官表达特异性,且可能在对逆境胁迫的响应中起重要作用。这些结果为进一步研究小麦GRAS基因的功能奠定了基础。
The GRAS gene is a kind of transcription regulator family that plays a key role in plant growth and development. The present study identified and characterized the GRAS gene family in bread wheat using the latest wheat genome data. The results showed that 153 GRAS genes were identified and they are unevenly distributed on 21 chromosomes of wheat. Phylogenetic analysis showed that the GRAS genes can be divided into at least 12 subfamilies, and fragment duplication and tandem repeats are the main expansion ways of this gene family. Protein sequences analysis found that there are different number of amino acid residues and different molecular weight among different subfamilies, and their secondary structures mainly compose of α-helix and random coils. The expression analysis of wheat GRAS genes showed that they differentially expressed in different tissues and under different stresses, indicating that wheat GRAS genes specifically expressed in different tissues and responded to different stresses. These results lay a foundation for further study on the function of GRAS genes in wheat.
The GRAS gene is a kind of transcription regulator family that plays a key role in plant growth and development. The present study identified and characterized the GRAS gene family in bread wheat using the latest wheat genome data. The results showed that 153 GRAS genes were identified and they are unevenly distributed on 21 chromosomes of wheat. Phylogenetic analysis showed that the GRAS genes can be divided into at least 12 subfamilies, and fragment duplication and tandem repeats are the main expansion ways of this gene family. Protein sequences analysis found that there are different number of amino acid residues and different molecular weight among different subfamilies, and their secondary structures mainly compose of α-helix and random coils. The expression analysis of wheat GRAS genes showed that they differentially expressed in different tissues and under different stresses, indicating that wheat GRAS genes specifically expressed in different tissues and responded to different stresses. These results lay a foundation for further study on the function of GRAS genes in wheat.
引文
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[2]ZHANG D,IYER L M,ARAVIND L.Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms [J].Bioinformatics,2012,28(19):2407.
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[15]TORRESGAL P,HIRTREITER B,BOLLE C.Two GRAS proteins,SCARECROW-LIKE21 and PHYTOCHROME A SIGNAL TRANSDUCTION1,function cooperatively in phytochrome A signal transduction [J].Plant Physiology,2013,161(1):291.
[16]MA H S.The salt- and drought-inducible poplar GRAS protein SCL7 confers salt and drought tolerance in Arabidopsis thaliana [J].Journal of Experimental Botany,2010,61(14):4011.
[17]FODE B,SIEMSEN T,THUROW C,et al.The Arabidopsis GRAS protein SCL14 interacts with class II TGA transcription factors and is essential for the activation of stress-inducible promoters [J].Plant Cell,2008,20(11):3122.
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[19]邢光伟,王梦醒,马小飞,等.小麦LBD基因家族的全基因组鉴定、表达特性及调控网络分析[J].麦类作物学报,2017,37(07):855.XING G H,WANG M X,MA X F,et al.Genome-wide analysis,expression characteristics and regulatory network of LBD gene family in bread wheat(Triticum aestivum L.)[J].Journal of Triticeae Crops,2017,37(07):855.
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[21]LI Y,XIAO J,WU J et al.A tandem segmental duplication(TSD) in green revolution gene Rht-D1b region underlies plant height variation [J].New Phytol,2012,196(1):282.
[22]CANNON S B,MITRA A,BAUMGARTEN A,et al.The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana [J].BMC Plant Biology,2004,4(1):10.
[23]WANG D,ZHANG Y,ZHANG Z,et al.KaKs_Calculator 2.0:A toolkit incorporating gamma-series methods and sliding window strategies [J].Genomics,Proteomics & Bioinformatics,2010,8(1):77.
[24]LAN T,YANG Z L,YANG X,et al.Extensive functional diversification of the Populus glutathione S-transferase supergene family [J].Plant Cell,2009,21(12):3749.
[25]SUN X,XUE B,JONES W T,et al.A functionally required unfoldome from the plant kingdom:Intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development [J].Plant Molecular Biology,2011,77(3):205.
[26]TIAN C,WAN P,SUN S,et al.Genome-wide analysis of the GRAS gene family in rice and Arabidopsis [J].Plant Molecular Biology,2004,54(4):519.
[27]HANADA K,ZOU C,LEHTISHIU M D,et al.Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli [J].Plant Physiology,2008,148(2):993.
[28]JIANG S Y,MA Z,RAMACHANDRAN S.Evolutionary history and stress regulation of the lectin superfamily in higher plants [J].BMC Evolutionary Biology,2010,10(1):79.
[29]JAIN M,KHURANA P,TYAGI A K,et al.Genome-wide analysis of intronless genes in rice and Arabidopsis [J].Functional & Integrative Genomics,2008,8(1):69.
[30]ZOU M,GUO B,HE S.The roles and evolutionary patterns of intronless genes in deuterostomes [J].Comparative & Functional Genomics,2011,2011(4):680673.
[31]KONG F,WANG J,CHENG L,et al.Genome-wide analysis of the mitogen-activated protein kinase gene family in Solanum lycopersicum [J].Gene,2012,499(1):108.
[32]PENG J R,CAROL P,RICHARDS D E,et al.The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses [J].Genes & Development,1998,11(23):3194.
[2]ZHANG D,IYER L M,ARAVIND L.Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms [J].Bioinformatics,2012,28(19):2407.
[3]PYSH L D,WYSOCKA-DILLER J W,CAMILLERI C,et al.The GRAS gene family in Arabidopsis:Sequence characterization and basic expression analysis of the SCARECROW-LIKE genes [J].Plant Journal for Cell & Molecular Biology,1999,18(1):111.
[4]BOLLE C.The role of GRAS proteins in plant signal transduction and development [J].Planta,2004,218(5):683.
[5]SUN X,XUE B,JONES W T,et al.A functionally required unfoldome from the plant kingdom:Intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development [J].Plant Molecular Biology,2011,77(3):205.
[6]PENG J,CAROL P,RICHARDS D E,et al.The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses [J].Genes & Development,1997,11(23):3194.
[7]GREB T,CLARENZ O,SCHAFER E,et al.Molecular analysis of the LATERAL SUPPRESSOR gene in Arabidopsis reveals a conserved control mechanism for axillary meristem formation [J].Genes & Development,2003,17(9):1175.
[8]SCHUMACHER K,SCHMITT T,ROSSBERG M,et al.The Lateral suppressor(Ls) gene of tomato encodes a new member of the VHIID protein family [J].Proceedings of the National Academy of Sciences of the United States of America,1999,96(1):290.
[9]LI X,QIAN Q,FU Z,et al.Control of tillering in rice [J].Nature,2003,422(6932):618.
[10]TORRES-GALEA P,HUANG L F,CHUA N H,et al.The GRAS protein SCL13 is a positive regulator of phytochrome-dependent red light signaling,but can also modulate phytochrome A responses [J].Molecular Genetics & Genomics,2006,276(1):13.
[11]SCHULZE S,SCHAFER B N,PARIZOTTO E A,et al.LOST MERISTEMS genes regulate cell differentiation of central zone descendants in Arabidopsis shoot meristems [J].Plant Journal,2010,64(4):668.
[12]WANG L,MAI Y X,ZHANG Y C,et al.MicroRNA171c-targeted SCL6-II, SCL6-III,and SCL6-IV genes regulate shoot branching in Arabidopsis [J].Molecular Plant,2010,3(5):794.
[13]ENGSTROM E M,ANDERSEN C M,GUMULAKSMITH J,et al.Arabidopsis homologs of the Petunia HAIRY MERISTEM gene are required for maintenance of shoot and root indeterminacy [J].Plant Physiology,2011,155(6):735.
[14]BOLLE C,KONCZ C,CHUA N H.PAT1,a new member of the GRAS family,is involved in phytochrome A signal transduction [J].Genes & Development,2000,14(10):1269.
[15]TORRESGAL P,HIRTREITER B,BOLLE C.Two GRAS proteins,SCARECROW-LIKE21 and PHYTOCHROME A SIGNAL TRANSDUCTION1,function cooperatively in phytochrome A signal transduction [J].Plant Physiology,2013,161(1):291.
[16]MA H S.The salt- and drought-inducible poplar GRAS protein SCL7 confers salt and drought tolerance in Arabidopsis thaliana [J].Journal of Experimental Botany,2010,61(14):4011.
[17]FODE B,SIEMSEN T,THUROW C,et al.The Arabidopsis GRAS protein SCL14 interacts with class II TGA transcription factors and is essential for the activation of stress-inducible promoters [J].Plant Cell,2008,20(11):3122.
[18]HUANG W,XIAN Z Q,XIA K,et al.Genome-wide identification,phylogeny and expression analysis of GRAS gene family in tomato [J].BMC Plant Biology,2015,15(1):209.
[19]邢光伟,王梦醒,马小飞,等.小麦LBD基因家族的全基因组鉴定、表达特性及调控网络分析[J].麦类作物学报,2017,37(07):855.XING G H,WANG M X,MA X F,et al.Genome-wide analysis,expression characteristics and regulatory network of LBD gene family in bread wheat(Triticum aestivum L.)[J].Journal of Triticeae Crops,2017,37(07):855.
[20]YU C S,CHEN Y C,LU C H,et al.Prediction of protein subcellular localization[J].Proteins Structure Function & Bioinformatics,2006,64(3):643.
[21]LI Y,XIAO J,WU J et al.A tandem segmental duplication(TSD) in green revolution gene Rht-D1b region underlies plant height variation [J].New Phytol,2012,196(1):282.
[22]CANNON S B,MITRA A,BAUMGARTEN A,et al.The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana [J].BMC Plant Biology,2004,4(1):10.
[23]WANG D,ZHANG Y,ZHANG Z,et al.KaKs_Calculator 2.0:A toolkit incorporating gamma-series methods and sliding window strategies [J].Genomics,Proteomics & Bioinformatics,2010,8(1):77.
[24]LAN T,YANG Z L,YANG X,et al.Extensive functional diversification of the Populus glutathione S-transferase supergene family [J].Plant Cell,2009,21(12):3749.
[25]SUN X,XUE B,JONES W T,et al.A functionally required unfoldome from the plant kingdom:Intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development [J].Plant Molecular Biology,2011,77(3):205.
[26]TIAN C,WAN P,SUN S,et al.Genome-wide analysis of the GRAS gene family in rice and Arabidopsis [J].Plant Molecular Biology,2004,54(4):519.
[27]HANADA K,ZOU C,LEHTISHIU M D,et al.Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli [J].Plant Physiology,2008,148(2):993.
[28]JIANG S Y,MA Z,RAMACHANDRAN S.Evolutionary history and stress regulation of the lectin superfamily in higher plants [J].BMC Evolutionary Biology,2010,10(1):79.
[29]JAIN M,KHURANA P,TYAGI A K,et al.Genome-wide analysis of intronless genes in rice and Arabidopsis [J].Functional & Integrative Genomics,2008,8(1):69.
[30]ZOU M,GUO B,HE S.The roles and evolutionary patterns of intronless genes in deuterostomes [J].Comparative & Functional Genomics,2011,2011(4):680673.
[31]KONG F,WANG J,CHENG L,et al.Genome-wide analysis of the mitogen-activated protein kinase gene family in Solanum lycopersicum [J].Gene,2012,499(1):108.
[32]PENG J R,CAROL P,RICHARDS D E,et al.The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses [J].Genes & Development,1998,11(23):3194.
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