毛竹B3家族全基因组鉴定及表达模式分析
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摘要
B3家族是一类含有B3功能域的转录因子家族,在植物的生长发育过程中起重要的调控作用。本研究利用生物信息学的技术和手段共鉴定出78条毛竹(Phyllostachys edulis) B3家族基因,其在LAV(LEAFY COTYLE-DON2[LEC2]-ABSCISIC ACID INSENSITIVE3[ABI3]-VAL)、生长素应答因子(auxin response factor, ARF)、RAV(Related ABI3-VP1)和生殖分生组织(reproduction meristem, REM) 4个亚家族中均有分布。通过对毛竹7个组织材料的转录本进行分析发现78条毛竹B3家族基因表达模式可分为5类,第1类的15个基因主要在花序中大量表达,第2类的20个基因主要在根中大量表达,第3类的23个基因主要在笋中大量表达,第4类的7个基因主要在叶中大量表达,第5类的13个基因主要在竹鞭中大量表达。在4个亚家族中,每个家族挑取2个基因,通过q RT-PCR分析毛竹B3家族基因在毛竹笋中不同部位的表达模式,结果显示,在大多数节间组织中大多数B3家族成员都有较高的表达量;在节隔,只有2个基因有高水平表达;在笋箨中,有6个基因有高水平表达,其中有1个基因几乎不表达;在根中,只有1个基因有高水平的表达。本研究对毛竹B3家族全基因组进行了结构的鉴定、进化关系的研究和表达模式的分析,为毛竹B3家族基因功能的深入研究提供了良好的数据基础。
The B3 family is a family of transcription factors that contains the B3 domain, which plays an important role in the growth and development of plants. In order to analysis the structure and expression pattern of Phyllostachys edulis B3 family genes, in this study, a total of 78 P. edulis B3 family genes were identified using bioinformatics techniques and methods. These genes could be divided into 4 evolutionary branches of the families, including LEAFY COTYLE-DON2[LEC2]-ABSCISIC ACID INSENSITIVE3[ABI3]-VAL(LAV), auxin response factor(ARF), related ABI3-VP1(RAV) and reproduction meristem(REM). The transcriptome analysis of 7 materials in moso bamboo showed that the expression patterns of the78 B3 family genes of could be divided into 5 groups, and B3 family genes had different expression level in 7materials in moso bamboo. The first 15 genes were mainly expressed in panicles; 20 genes in the second groupwere mainly expressed in roots; 23 genes in the third group were mainly expressed in young shoots; 7 genes in the fourth group were mainly expressed in leaves; 13 genes in the fifth group were mainly expressed in bamboo rhizome. So, the B3 family of P. edulis plays a important role during the growth of moso bamboo.Two genes were selected from 4 subfamilies to detect the expression patterns of B3 family of P. edulis in different parts of bamboo shoots by qRT-PCR. The results showed that the P. edulis family genes were diversely expressed in different parts of bamboo shoots. Most of B3 family members had high expression in most internode tissues. For example, PH01000024 G2370, PH01000297 G0830, PH01001094 G0220,PH01000114 G0050, PH01000548 G0300 and PH01000528 G0920 had high levels of expression in the 2-4 node internode(internode 2-4). Only 2 genes(PH01000198 G0380, PH01001094 G0220) had high levels of expression in interval. There were 6 genes(PH01000297 G0830, PH01000198 G0380, PH01000114 G0050,PH01000548 G0300, PH01000528 G0920 and PH01000469 G0440) with high levels of expression in sheath,and one gene(PH01000024 G2370) was almost no expression. Only one gene(PH01000024 G2370) had a high level of expression in roots. Results suggested that the ARF family(eg PH01000114 G0050,PH01000548 G0300) played an important role in the rapid growth of bamboo shoots. According to the expression patterns of RAV family(e. g. PH01000024 G2370, PH01000297 G0830), it was presumed that the growth of shoots in roots and near roots was relatively inhibited during the rapid jointing growth of bamboo shoots. This study systematically investigated the structure, phylogenetic relationship and the expression pattern of B3 family genes of P. edulis, which provides basic data for the further study of B3 family gene function.
The B3 family is a family of transcription factors that contains the B3 domain, which plays an important role in the growth and development of plants. In order to analysis the structure and expression pattern of Phyllostachys edulis B3 family genes, in this study, a total of 78 P. edulis B3 family genes were identified using bioinformatics techniques and methods. These genes could be divided into 4 evolutionary branches of the families, including LEAFY COTYLE-DON2[LEC2]-ABSCISIC ACID INSENSITIVE3[ABI3]-VAL(LAV), auxin response factor(ARF), related ABI3-VP1(RAV) and reproduction meristem(REM). The transcriptome analysis of 7 materials in moso bamboo showed that the expression patterns of the78 B3 family genes of could be divided into 5 groups, and B3 family genes had different expression level in 7materials in moso bamboo. The first 15 genes were mainly expressed in panicles; 20 genes in the second groupwere mainly expressed in roots; 23 genes in the third group were mainly expressed in young shoots; 7 genes in the fourth group were mainly expressed in leaves; 13 genes in the fifth group were mainly expressed in bamboo rhizome. So, the B3 family of P. edulis plays a important role during the growth of moso bamboo.Two genes were selected from 4 subfamilies to detect the expression patterns of B3 family of P. edulis in different parts of bamboo shoots by qRT-PCR. The results showed that the P. edulis family genes were diversely expressed in different parts of bamboo shoots. Most of B3 family members had high expression in most internode tissues. For example, PH01000024 G2370, PH01000297 G0830, PH01001094 G0220,PH01000114 G0050, PH01000548 G0300 and PH01000528 G0920 had high levels of expression in the 2-4 node internode(internode 2-4). Only 2 genes(PH01000198 G0380, PH01001094 G0220) had high levels of expression in interval. There were 6 genes(PH01000297 G0830, PH01000198 G0380, PH01000114 G0050,PH01000548 G0300, PH01000528 G0920 and PH01000469 G0440) with high levels of expression in sheath,and one gene(PH01000024 G2370) was almost no expression. Only one gene(PH01000024 G2370) had a high level of expression in roots. Results suggested that the ARF family(eg PH01000114 G0050,PH01000548 G0300) played an important role in the rapid growth of bamboo shoots. According to the expression patterns of RAV family(e. g. PH01000024 G2370, PH01000297 G0830), it was presumed that the growth of shoots in roots and near roots was relatively inhibited during the rapid jointing growth of bamboo shoots. This study systematically investigated the structure, phylogenetic relationship and the expression pattern of B3 family genes of P. edulis, which provides basic data for the further study of B3 family gene function.
引文
陈勇兵,王燕,张海利.2015.番茄热激转录因子(Hsf)基因家族鉴定及表达分析[J].农业生物技术学报,23(4):492-501.(Chen Y B,Wang Y,Zhang H L.2015.Identification and expression analysis of heat shock factor(hsf)gene family in tomato(Solanum lycopersicum)[J].Journal of Agricultural Biotechnology,23(4):492-501.
程占超,侯丹,马艳军,等.2017.毛竹生长素反应因子基因的生物信息学分析及差异表达[J].浙江农林大学学报,34(4):574-580.(Cheng Z C,Hou D,Ma Y J,et al2017.Bioinformatic analysis and differential expression of auxin response factor(ARF)gene in Phyllostachys edulis[J].Journal of Zhejiang A&F University,34(4)574-580.)
李冬梅,张可欣,李文滨.2017.大豆Gm MP基因的功能预测及表达分析[J].大豆科学,36(1):28-32.(Li D MZhang K X,Li W B.2017.Functional prediction and expression analysis of GmMP in soybean[J].Soybean Science,36(1):28-32.)
梁超琼,孟嫣,罗来鑫,等.2015.基于复制酶基因序列的黄瓜绿斑驳花叶病毒系统进化及生物信息学分析[J].病毒学报,31(6):620-628.(Liang C Q,Meng M,Luo L X,et al.2015.Phylogenetic analysis and bioinformatics analysis of Cucumber green marker mosaic virus based on replicase gene sequences[J].Chinese Journal of Virology,31(6):620-628.)
刘颖慧,董志平.2017.植物B3转录因子的结构和功能[J].分子植物育种,(05):1868-1873.(Liu Y H,Dong Z P.2017.Structure and function of plant B3 transcription factor[J].Molecular Plant Breeding,(05):1868-1873.)
刘政.2015.柑橘珠心胚起始转录组分析及体细胞胚发生相关基因CsFUS3功能鉴定[D].博士学位论文,华中农业大学,导师:郭文武.pp.83-84.(Liu Z.2015.Analysis of CsFUS3 function of citrus bead embryo initiation transcriptome and somatic embryogenesis related gene[D].Thesis for Ph.D.,Huazhong Agricultural University,Supervisor:Guo W W pp.83-84.)
罗光宇,叶玲飞,陈信波.2013.拟南芥B3转录因子基因超家族[J].生命的化学,33(3):287-293.(Luo G Y,Ye L F,Chen X B.2013.Arabidopsis thaliana B3 transcription factor gene superfamily[J].Chemistry of Life,33(3):287-293.)
苏慧慧,李涛,黎振兴,等.2015,番茄GRX基因家族的鉴定及表达分析[J].核农学报,29(4):663-673.(Su H H,Li T,Li Z X,et al.2013.Identification and gene expression analysis of GRX gene family in tomato[J].Journal of Nuclear Agricultural Sciences,29(4):663-673)
孙亭亭,王大伟,龚达平,等.2015.番茄B3超家族成员鉴定及生物信息学分析[J].植物遗传资源学报,16(4):806-814.(Sun T T,Wang D W,Gong D P,et al.2015.Genome-wide identification and bioinformatic analysis of B3 superfamily in tomato[J].Journal of Plant Genetic Resources,16(04):806-814.)
谭河林,王莉欢,李云,等.2014.油菜LEAFY COTYLEDON2(BnLEC2)基因的克隆及表达分析[J].核农学报,28(12):2175-2183.(Tan H L,Wang L H,Li Y,et al.2014.Cloning and expression analysis LEAFY COTYLEDON 2(BnLEC2)in Brassica napus[J].Journal of Nuclear Agricultural Sciences,28(12):2175-2183.)
陶贵耘,傅鹰,周明兵.2018.竹类植物快速生长的机理研究进展[J].农业生物技术学报,26(5):871-887.(Tao G Y,Fu Y,Zhou M B.Advances in studies on molecular mechanisms of rapid growth of bamboo specie[J].Journal of Agricultural Biotechnology,26(5):871-887.)
王思雨,傅鹰,周明兵.2018.毛竹NF-Y家族基因的鉴定与表达分析[J].核农学报,32(8):1513-1527.(Wang S YFu Y,Zhou M B.2018.Genome-wide identification and expression analysis of the nf-y family genes in Phyllostachys edulis[J].Journal of Nuclear Agricultural Sciences,32(8):1513-1527.)
王志鹏,郭媛媛,梁美景.2014.动物转录因子相关数据库研究进展[J].畜牧与饲料科学,(12):28-30.(Wang Z PGuo Y Y,Liang M J.2014.Advances in animal transcription factor related databases[J].Animal Husbandry and Feed Science,35(12):28-30.)
瓮巧云,赵彦敏,张贺,等.2016.玉米ZmREM基因的克隆与逆境胁迫后表达分析[J].浙江农业学报,28(11)1822-1827.(Weng Q Y,Zhao Y M,Zhang H,et al.2016Cloning of ZmREM and its expression analysis in maize under stress[J].Acta Agriculturae Zhejiangensis,28(11)1822-1827.)
张韬.2009.拟南芥DNaseI超敏感位点及野生大麦适应性进化研究[D].博士学位论文,电子科技大学,导师:杨足君,pp.1-4(Zhang T.2009.Study on adaptability of DNaseI hypersensitive site and wild barley in Arabidopsis thaliana[D].Thesis for Ph.D.,University of Electronic Science and Technology of China,Supervisor:Yang ZJ.PP.1-4)
庄静,周熙荣,孙超才,等.2008.油菜沪油15中AP2/ERF-B3亚族转录因子的克隆和生物信息学分析[J].分子细胞生物学报,41(3):192-206.(Zhuang J,Zhou X R,Sun C C,et al.2008.Cloning and bioinformatics analyzing oftranscription factor AP2/ERF-B3 subfamily genes from Brassica napus L.Huyou 15[J].Journal of Molecular Cell Biology,41(3):192-206.)
Bailey T L,Elkan C.1995.The value of prior knowledge in discovering motifs with MEMEC[C].Proc.Third Internat.Conf.on Intelligent Systems for Molecular Biology California:AAAI Press,1995:21-29.
Edgar R C.2004.MUSCLE:A multiple sequence alignmen method with reduced time and space complexity.[J]Bmc Bioinformatics,5(5):113.
Fan C,Ma J,Guo Q,et al.2013.Selection of reference genes for quantitative real-time PCR in bamboo(Phyllostachys edulis)[J].PloS One,8(2):e56573.
Guilfoyle T J,Hagen G.2007.Auxin response factors[J].Current Opinion in Plant Biology,10(5):453-460.
Gao Z M,Li X P,Li L B,et al.2006.An effective method for total RNA isolation from bamboo[J].Chinese Forestry Science and Technology,5(3):52-54.
Hu Y X,Wang Y H,Liu X F,et al.2004.Arabidopsis RAV1 is down-regulated by brassinosteroid and may a ct as anegative regulator during plant development[J].Cell Research,14(1):8-15.
King G J,Chanson A H,McCallum E J,et al.2013.The Arabidopsis B3 domain protein VERNALIZATION1(VRN1)is involved in porocesses essential for development,with structural and mutational studies revealing its DNA-binding surface[J].Journal of Biological Chemistry,288(5):3198-3207.
Mylne J S,Mas C,Hill J M.2012.NMR assignment and secondary structure of the C-terminal DNA binding domain of Arabidopsis thaliana VERNALIZATION1[J].Biomolecular NMR Assignments,6(1):5-8.
Mantegazza O,Gregis V,Mendes M A,et al.2014.Analysis of the arabidopsis REM gene family predicts functions during flower development[J].Annals of Botany,114(7):1507-1515.
Peng F Y,Weselake R J.2013.Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants[J].Theoretical&Applied Genetics,126(5):1305-1319.
Peng Z,Lu Y,Li L,et al.2013.The draft genome of the fastgrowing non-timber forest species moso bamboo(Phyllostachys heterocycla)[J].Nature Genetics,45(4):456-461.
Suzuki M,Wang H H,Mccarty D R.2007.Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACIDINSENSITIVE 3-LIKE B3 genes[J].Plant Physiology,143(2):902-911.
Swaminathan K,Peterson K,Jack T.2008.The plant B3 superfamily[J].Trends in Plant Science,13(12):647-655.
Tsukagoshi H,Morikami A,Nakamura K.2007.Two B3 domain transcriptional repressors prevent sugar-inducible expression of seed maturation genes in Arabidopsis seedlings[J].Proceedingsof the National Academy of Sciences of the USA,104(7):2543-2547.
程占超,侯丹,马艳军,等.2017.毛竹生长素反应因子基因的生物信息学分析及差异表达[J].浙江农林大学学报,34(4):574-580.(Cheng Z C,Hou D,Ma Y J,et al2017.Bioinformatic analysis and differential expression of auxin response factor(ARF)gene in Phyllostachys edulis[J].Journal of Zhejiang A&F University,34(4)574-580.)
李冬梅,张可欣,李文滨.2017.大豆Gm MP基因的功能预测及表达分析[J].大豆科学,36(1):28-32.(Li D MZhang K X,Li W B.2017.Functional prediction and expression analysis of GmMP in soybean[J].Soybean Science,36(1):28-32.)
梁超琼,孟嫣,罗来鑫,等.2015.基于复制酶基因序列的黄瓜绿斑驳花叶病毒系统进化及生物信息学分析[J].病毒学报,31(6):620-628.(Liang C Q,Meng M,Luo L X,et al.2015.Phylogenetic analysis and bioinformatics analysis of Cucumber green marker mosaic virus based on replicase gene sequences[J].Chinese Journal of Virology,31(6):620-628.)
刘颖慧,董志平.2017.植物B3转录因子的结构和功能[J].分子植物育种,(05):1868-1873.(Liu Y H,Dong Z P.2017.Structure and function of plant B3 transcription factor[J].Molecular Plant Breeding,(05):1868-1873.)
刘政.2015.柑橘珠心胚起始转录组分析及体细胞胚发生相关基因CsFUS3功能鉴定[D].博士学位论文,华中农业大学,导师:郭文武.pp.83-84.(Liu Z.2015.Analysis of CsFUS3 function of citrus bead embryo initiation transcriptome and somatic embryogenesis related gene[D].Thesis for Ph.D.,Huazhong Agricultural University,Supervisor:Guo W W pp.83-84.)
罗光宇,叶玲飞,陈信波.2013.拟南芥B3转录因子基因超家族[J].生命的化学,33(3):287-293.(Luo G Y,Ye L F,Chen X B.2013.Arabidopsis thaliana B3 transcription factor gene superfamily[J].Chemistry of Life,33(3):287-293.)
苏慧慧,李涛,黎振兴,等.2015,番茄GRX基因家族的鉴定及表达分析[J].核农学报,29(4):663-673.(Su H H,Li T,Li Z X,et al.2013.Identification and gene expression analysis of GRX gene family in tomato[J].Journal of Nuclear Agricultural Sciences,29(4):663-673)
孙亭亭,王大伟,龚达平,等.2015.番茄B3超家族成员鉴定及生物信息学分析[J].植物遗传资源学报,16(4):806-814.(Sun T T,Wang D W,Gong D P,et al.2015.Genome-wide identification and bioinformatic analysis of B3 superfamily in tomato[J].Journal of Plant Genetic Resources,16(04):806-814.)
谭河林,王莉欢,李云,等.2014.油菜LEAFY COTYLEDON2(BnLEC2)基因的克隆及表达分析[J].核农学报,28(12):2175-2183.(Tan H L,Wang L H,Li Y,et al.2014.Cloning and expression analysis LEAFY COTYLEDON 2(BnLEC2)in Brassica napus[J].Journal of Nuclear Agricultural Sciences,28(12):2175-2183.)
陶贵耘,傅鹰,周明兵.2018.竹类植物快速生长的机理研究进展[J].农业生物技术学报,26(5):871-887.(Tao G Y,Fu Y,Zhou M B.Advances in studies on molecular mechanisms of rapid growth of bamboo specie[J].Journal of Agricultural Biotechnology,26(5):871-887.)
王思雨,傅鹰,周明兵.2018.毛竹NF-Y家族基因的鉴定与表达分析[J].核农学报,32(8):1513-1527.(Wang S YFu Y,Zhou M B.2018.Genome-wide identification and expression analysis of the nf-y family genes in Phyllostachys edulis[J].Journal of Nuclear Agricultural Sciences,32(8):1513-1527.)
王志鹏,郭媛媛,梁美景.2014.动物转录因子相关数据库研究进展[J].畜牧与饲料科学,(12):28-30.(Wang Z PGuo Y Y,Liang M J.2014.Advances in animal transcription factor related databases[J].Animal Husbandry and Feed Science,35(12):28-30.)
瓮巧云,赵彦敏,张贺,等.2016.玉米ZmREM基因的克隆与逆境胁迫后表达分析[J].浙江农业学报,28(11)1822-1827.(Weng Q Y,Zhao Y M,Zhang H,et al.2016Cloning of ZmREM and its expression analysis in maize under stress[J].Acta Agriculturae Zhejiangensis,28(11)1822-1827.)
张韬.2009.拟南芥DNaseI超敏感位点及野生大麦适应性进化研究[D].博士学位论文,电子科技大学,导师:杨足君,pp.1-4(Zhang T.2009.Study on adaptability of DNaseI hypersensitive site and wild barley in Arabidopsis thaliana[D].Thesis for Ph.D.,University of Electronic Science and Technology of China,Supervisor:Yang ZJ.PP.1-4)
庄静,周熙荣,孙超才,等.2008.油菜沪油15中AP2/ERF-B3亚族转录因子的克隆和生物信息学分析[J].分子细胞生物学报,41(3):192-206.(Zhuang J,Zhou X R,Sun C C,et al.2008.Cloning and bioinformatics analyzing oftranscription factor AP2/ERF-B3 subfamily genes from Brassica napus L.Huyou 15[J].Journal of Molecular Cell Biology,41(3):192-206.)
Bailey T L,Elkan C.1995.The value of prior knowledge in discovering motifs with MEMEC[C].Proc.Third Internat.Conf.on Intelligent Systems for Molecular Biology California:AAAI Press,1995:21-29.
Edgar R C.2004.MUSCLE:A multiple sequence alignmen method with reduced time and space complexity.[J]Bmc Bioinformatics,5(5):113.
Fan C,Ma J,Guo Q,et al.2013.Selection of reference genes for quantitative real-time PCR in bamboo(Phyllostachys edulis)[J].PloS One,8(2):e56573.
Guilfoyle T J,Hagen G.2007.Auxin response factors[J].Current Opinion in Plant Biology,10(5):453-460.
Gao Z M,Li X P,Li L B,et al.2006.An effective method for total RNA isolation from bamboo[J].Chinese Forestry Science and Technology,5(3):52-54.
Hu Y X,Wang Y H,Liu X F,et al.2004.Arabidopsis RAV1 is down-regulated by brassinosteroid and may a ct as anegative regulator during plant development[J].Cell Research,14(1):8-15.
King G J,Chanson A H,McCallum E J,et al.2013.The Arabidopsis B3 domain protein VERNALIZATION1(VRN1)is involved in porocesses essential for development,with structural and mutational studies revealing its DNA-binding surface[J].Journal of Biological Chemistry,288(5):3198-3207.
Mylne J S,Mas C,Hill J M.2012.NMR assignment and secondary structure of the C-terminal DNA binding domain of Arabidopsis thaliana VERNALIZATION1[J].Biomolecular NMR Assignments,6(1):5-8.
Mantegazza O,Gregis V,Mendes M A,et al.2014.Analysis of the arabidopsis REM gene family predicts functions during flower development[J].Annals of Botany,114(7):1507-1515.
Peng F Y,Weselake R J.2013.Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants[J].Theoretical&Applied Genetics,126(5):1305-1319.
Peng Z,Lu Y,Li L,et al.2013.The draft genome of the fastgrowing non-timber forest species moso bamboo(Phyllostachys heterocycla)[J].Nature Genetics,45(4):456-461.
Suzuki M,Wang H H,Mccarty D R.2007.Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACIDINSENSITIVE 3-LIKE B3 genes[J].Plant Physiology,143(2):902-911.
Swaminathan K,Peterson K,Jack T.2008.The plant B3 superfamily[J].Trends in Plant Science,13(12):647-655.
Tsukagoshi H,Morikami A,Nakamura K.2007.Two B3 domain transcriptional repressors prevent sugar-inducible expression of seed maturation genes in Arabidopsis seedlings[J].Proceedingsof the National Academy of Sciences of the USA,104(7):2543-2547.