Bioinformatics and Expression Analysis of 11 BpSPLs in Betula platyphylla Suk.

NING Kun; YANG Yang; MA Shu-shan; LI Hui-yu

Volume 29 Issue 5

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Bioinformatics and Expression Analysis of 11 BpSPLs in Betula platyphylla Suk.

1.
Key Laboratory of Tree Genetic Improvement and Biotechnology, Northeast Forestry University, Harbin 150040, Heilongjiang, China

Received Date: 2015-08-26

Abstract

[Objective] To analyze the sequence features and gene expression rules in different tissues and periods of SPL transcription factor from Betula platyphylla Suk. [Method] Based on 45 transcriptome databases of Birch, 12 BpSPL genes were obtained and named as BpSPL1-BpSPL12, of which 11 genes were analyzed. [Result] Bioinformatics analysis showed that all the 11 BpSPLs contained a highly conserved SBP domain, their lengths exhibited a high diversity and owned 210 numbers of exon in genetic sequences. Phylogenetic analysis showed that the 11 Birch SPL proteins belonged to six major categories. The qRT-PCR results suggested that the expression levels of the 11 BpSPL genes changed significantly in different periods and different tissues (leaves, terminal buds, stems, male inflorescences). In terminal buds, most BpSPL genes were up-regulated on July 5 and August 20 to September 20. In male inflorescences, with the exception of BpSPL1 which was down-regulated or unchanged, all the other BpSPL genes exhibited a gradual increasing pattern from June to September (the growth stage). [Conclusion] This study suggested that these BpSPL genes may be involved in the growth and development of birch terminal buds and male inflorescences.
- Betula platyphylla Suk.,
- BpSPL gene family,
- bioinformatics,
- gene expression

References

[1]	Cardon G H,H hmann S,Nettesheim K,et al. Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3:A novel gene involved in the floral transition[J].The Plant Journal, 1997,12(2):367-377.
[2]	Unte U S,Sorensen A M,Pesaresi P,et al. SPL8,an SBP-box gene that affects pollen sac development in Arabidopsis[J]. The Plant Cell Online,2003,15(4):1009-1019.
[3]	Stone JM,Liang X,Nekl ER,et al. Arabidopsis AtSPL14,a plant-specific SBP-domain transcription factor,participates in plant development and sensitivity to fumonisin B1[J].The Plant Journal,2005,41(5):744-754.
[4]	Nonogaki H. MicroRNA gene regulation cascades during early stages of plant development[J]. Plant and Cell Physiology, 2010,51(11):1840-1846.
[5]	Wang J W,Park M Y,Wang L J,et al. miRNA control of vegetative phase change in trees[J]. PLoS Genetics,2011,7(2):e1002012.
[6]	Gou J Y,Felippes F F,Liu C J,et al.Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor[J].The Plant Cell Online, 2011,23(4):1512-1522.
[7]	Wang J W,Czech B,Weigel D. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana[J]. Cell,2009,138(4):738-749.
[8]	Wu G,Poethig RS.Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3[J]. Development 2006, 133(18):3539-3547.
[9]	Gandikota M,Birkenbihl RP,Hhmann S,et al.The miRNA156/157 recognition element in the 3'UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings[J]. The Plant Journa,2007, 49(4):683-693.
[10]	Rhoades M W,Reinhart B J,Lim L P,et al.Prediction of plant microRNA targets[J]. cell,2002,110(4):513-520.
[11]	Schwab R,Palatnik JF,Riester M,et al. Specific effects of microRNAs on the plant transcriptome[J]. Developmental cell,2005, 8(4):517-527.
[12]	Klein J,Saedler H,Huijser P. A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA[J].Molecular and General Genetics MGG 1996,250(1):7-16.
[13]	Manning KM,Poole M,Hong Y,et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening[J]. Nature genetics,2006,38(8):948-952.
[14]	Zhang Y,Schwarz S,Saedler H,et al.SPL8,a local regulator in a subset of gibberellin-mediated developmental processes in Arabidopsis[J]. Plant molecular biology,2007, 63(3):429-439.
[15]	Becraft PW,Bongard-Pierce DK,Sylvester AW,et al.The liguleless-1 gene acts tissue specifically in maize leaf development[J]. Developmental biology,1990,141(1):220-232.
[16]	Yang J H,Fang Z M,Yu J Q. Relationship between cytoplasmic male sterility and SPL-like gene expression in stem mustard[J]. Physiol Plantarum,2008,133:426-434.
[17]	刘雪梅,杨传平.白桦雌雄花发育周期的时序特征[J].林业科学,2006,(12):28-32.
[18]	官民晓,刘雪梅,张妍,等.白桦SPL8转录因子基因的分离及转录表达分析[J].南京林业大学学报:自然科学版, 2013,37(3):17-22.
[19]	Salinas M,Xing S,Hhmann S,et al.Genomic organization,phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato[J].Planta, 2012,235(6):1171-1184.
[20]	Tamura K,Dudley J,Nei M,et al.MEGA4:molecular evolutionary genetics analysis (MEGA) software version 4.0[J].Molecular biology and evolution,2007,24(8):1596-1599.
[21]	Wang LQ,Qin LP,Liu WJ,et al.A novel ethylene-responsive factor from Tamarix hispida, ThERF1,is a GCC-box and DRE-motif binding protein that negatively modulates abiotic stress tolerance in Arabidopsis[J].Physiologia Plantarum,2014,152:84-97.
[22]	Li HY,Ning K,Song X,et al.Molecular Cloning and Expression Analysis of Nine ThTrx Genes in Tamarix hispida[J].Plant Mol Biol Rep,2013,31:917-924.
[23]	Yamasaki K,Kigawa T,Inoue M,et al.A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors[J].Journal of Molecular Biology,2004,337(1):49-63.
[24]	Guo AY,Zhu QH,Gu XC,et al.Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family[J].Gene,2008,418,1-8.
[25]	李明,李长生,赵传志,等. 植物SPL 转录因子研究进展[J]. 植物学报,2013,48(001):107-116.
[26]	Xing S,Salinas M,Hhmann S,et al.miR156-targeted and nontargeted SBP-box transcription factors act in concert to secure male fertility in Arabidopsis[J].The Plant Cell Online,2010, 22(12):3935-3950.
[27]	李玉岭,周厚君,林二培,等.光皮桦BpSPL1 转录因子基因的克隆,表达及单核苷酸多态性分析[J].林业科学,2013,49(9):52-61.
[28]	肖政,李纪元,范正琪,等.荔波连蕊茶GA2ox1基因的克隆及表达分析[J].林业科学研究,2016,29(1):41-47.
[29]	宋长年,钱剑林,房经贵,等.枳SPL9和SPL13全长cDNA克隆、亚细胞定位和表达分析[J].中国农业科学,2010,43(10):2105-2114.
[30]	李洁,范术丽,宋美珍,等.陆地棉GhSPL3基因的克隆、亚细胞定位及表达分析[J]. 棉花学报,2012,24(5):414-419.

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通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

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Bioinformatics and Expression Analysis of 11 BpSPLs in Betula platyphylla Suk.

1. Key Laboratory of Tree Genetic Improvement and Biotechnology, Northeast Forestry University, Harbin 150040, Heilongjiang, China

Received Date: 2015-08-26

Abstract: [Objective] To analyze the sequence features and gene expression rules in different tissues and periods of SPL transcription factor from Betula platyphylla Suk. [Method] Based on 45 transcriptome databases of Birch, 12 BpSPL genes were obtained and named as BpSPL1-BpSPL12, of which 11 genes were analyzed. [Result] Bioinformatics analysis showed that all the 11 BpSPLs contained a highly conserved SBP domain, their lengths exhibited a high diversity and owned 210 numbers of exon in genetic sequences. Phylogenetic analysis showed that the 11 Birch SPL proteins belonged to six major categories. The qRT-PCR results suggested that the expression levels of the 11 BpSPL genes changed significantly in different periods and different tissues (leaves, terminal buds, stems, male inflorescences). In terminal buds, most BpSPL genes were up-regulated on July 5 and August 20 to September 20. In male inflorescences, with the exception of BpSPL1 which was down-regulated or unchanged, all the other BpSPL genes exhibited a gradual increasing pattern from June to September (the growth stage). [Conclusion] This study suggested that these BpSPL genes may be involved in the growth and development of birch terminal buds and male inflorescences.

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[1]	Cardon G H,H hmann S,Nettesheim K,et al. Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3:A novel gene involved in the floral transition[J].The Plant Journal, 1997,12(2):367-377.
[2]	Unte U S,Sorensen A M,Pesaresi P,et al. SPL8,an SBP-box gene that affects pollen sac development in Arabidopsis[J]. The Plant Cell Online,2003,15(4):1009-1019.
[3]	Stone JM,Liang X,Nekl ER,et al. Arabidopsis AtSPL14,a plant-specific SBP-domain transcription factor,participates in plant development and sensitivity to fumonisin B1[J].The Plant Journal,2005,41(5):744-754.
[4]	Nonogaki H. MicroRNA gene regulation cascades during early stages of plant development[J]. Plant and Cell Physiology, 2010,51(11):1840-1846.
[5]	Wang J W,Park M Y,Wang L J,et al. miRNA control of vegetative phase change in trees[J]. PLoS Genetics,2011,7(2):e1002012.
[6]	Gou J Y,Felippes F F,Liu C J,et al.Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor[J].The Plant Cell Online, 2011,23(4):1512-1522.
[7]	Wang J W,Czech B,Weigel D. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana[J]. Cell,2009,138(4):738-749.
[8]	Wu G,Poethig RS.Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3[J]. Development 2006, 133(18):3539-3547.
[9]	Gandikota M,Birkenbihl RP,Hhmann S,et al.The miRNA156/157 recognition element in the 3'UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings[J]. The Plant Journa,2007, 49(4):683-693.
[10]	Rhoades M W,Reinhart B J,Lim L P,et al.Prediction of plant microRNA targets[J]. cell,2002,110(4):513-520.
[11]	Schwab R,Palatnik JF,Riester M,et al. Specific effects of microRNAs on the plant transcriptome[J]. Developmental cell,2005, 8(4):517-527.
[12]	Klein J,Saedler H,Huijser P. A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA[J].Molecular and General Genetics MGG 1996,250(1):7-16.
[13]	Manning KM,Poole M,Hong Y,et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening[J]. Nature genetics,2006,38(8):948-952.
[14]	Zhang Y,Schwarz S,Saedler H,et al.SPL8,a local regulator in a subset of gibberellin-mediated developmental processes in Arabidopsis[J]. Plant molecular biology,2007, 63(3):429-439.
[15]	Becraft PW,Bongard-Pierce DK,Sylvester AW,et al.The liguleless-1 gene acts tissue specifically in maize leaf development[J]. Developmental biology,1990,141(1):220-232.
[16]	Yang J H,Fang Z M,Yu J Q. Relationship between cytoplasmic male sterility and SPL-like gene expression in stem mustard[J]. Physiol Plantarum,2008,133:426-434.
[17]	刘雪梅,杨传平.白桦雌雄花发育周期的时序特征[J].林业科学,2006,(12):28-32.
[18]	官民晓,刘雪梅,张妍,等.白桦SPL8转录因子基因的分离及转录表达分析[J].南京林业大学学报:自然科学版, 2013,37(3):17-22.
[19]	Salinas M,Xing S,Hhmann S,et al.Genomic organization,phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato[J].Planta, 2012,235(6):1171-1184.
[20]	Tamura K,Dudley J,Nei M,et al.MEGA4:molecular evolutionary genetics analysis (MEGA) software version 4.0[J].Molecular biology and evolution,2007,24(8):1596-1599.
[21]	Wang LQ,Qin LP,Liu WJ,et al.A novel ethylene-responsive factor from Tamarix hispida, ThERF1,is a GCC-box and DRE-motif binding protein that negatively modulates abiotic stress tolerance in Arabidopsis[J].Physiologia Plantarum,2014,152:84-97.
[22]	Li HY,Ning K,Song X,et al.Molecular Cloning and Expression Analysis of Nine ThTrx Genes in Tamarix hispida[J].Plant Mol Biol Rep,2013,31:917-924.
[23]	Yamasaki K,Kigawa T,Inoue M,et al.A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors[J].Journal of Molecular Biology,2004,337(1):49-63.
[24]	Guo AY,Zhu QH,Gu XC,et al.Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family[J].Gene,2008,418,1-8.
[25]	李明,李长生,赵传志,等. 植物SPL 转录因子研究进展[J]. 植物学报,2013,48(001):107-116.
[26]	Xing S,Salinas M,Hhmann S,et al.miR156-targeted and nontargeted SBP-box transcription factors act in concert to secure male fertility in Arabidopsis[J].The Plant Cell Online,2010, 22(12):3935-3950.
[27]	李玉岭,周厚君,林二培,等.光皮桦BpSPL1 转录因子基因的克隆,表达及单核苷酸多态性分析[J].林业科学,2013,49(9):52-61.
[28]	肖政,李纪元,范正琪,等.荔波连蕊茶GA2ox1基因的克隆及表达分析[J].林业科学研究,2016,29(1):41-47.
[29]	宋长年,钱剑林,房经贵,等.枳SPL9和SPL13全长cDNA克隆、亚细胞定位和表达分析[J].中国农业科学,2010,43(10):2105-2114.
[30]	李洁,范术丽,宋美珍,等.陆地棉GhSPL3基因的克隆、亚细胞定位及表达分析[J]. 棉花学报,2012,24(5):414-419.

Bioinformatics and Expression Analysis of 11 BpSPLs in Betula platyphylla Suk.

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通讯作者: 陈斌, bchen63@163.com

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Bioinformatics and Expression Analysis of 11 BpSPLs in Betula platyphylla Suk.

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