毛竹GRF转录因子的生物信息学及表达分析
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摘要
通过生物信息学手段,对毛竹GRF(Growth-regulating factors, GRFs)转录因子基因家族成员展开研究,主要包括对毛竹转录因子家族成员的鉴定、基本信息的分析、进化分析、基因结构分析、保守基序分析、保守结构域分析、以及在不同组织中的表达分析。一共鉴定了18条毛竹GRF转录因子。根据拟南芥、水稻的系统进化树分析,将毛竹GRF转录因子划分为6个家族。利用Gene structure、NCBI和MEME在线分析软件,发现毛竹GRF转录因子的基因结构和氨基酸序列较为保守。表达量分析发现GRF转录因子普遍在花中表达丰度最高,其次在竹笋侧芽中表达丰度较高,而在叶片中表达量较低,表明GRF转录因子在毛竹花发育以及笋尖生长发育过程过程中发挥着重要的作用。
引文
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[2] Vercruyssen L, Tognetti VB, Gonzalez N, et al. Growth regulating factor5 stimulates Arabidopsis chloroplast division, photosynthesis, and leaf longevity[J]. Plant Physiology, 2015, 167: 817-832.
[3] Hoe K J, Tsukaya H. Regulation of plant growth and development by the growth-regulating factor and grf-interacting factor duo[J]. Journal of Experimental Botany, 2015, 66(20): 6093.
[4] Treich I, Cairns B R, De I S T, et al. SNFll,A new component of the yeast SNF-SWI complex that interacts with a conserved region of SNF2[J]. Molecular and Cellular Biology, 1995, 15(8): 4240-4248.
[5] Kim J H, Kende H. A transcriptional coactivator, AtGIFl, is involved in regulating leaf growth and morphology in Arabidopsis[J]. PNAS, 2004, 101(36): 13374-13379.
[6] Kim J H, Choi D, Kende H. The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis[J]. Plant Journal, 2003, 36 (1): 94-104.
[7] Omidbakhshfard M A, Proost S, Fujikura U,et al.Growth-regulating factors (GRFs): a small transcription factor family with important functions in plant biology[J]. Molecular Plant, 2015, 8(7): 998-1010.
[8] He Y, Wu J,Lv B,et al. Involvement of 14-3-3 protein GRF9 in root growth and response under polyethylene glycol-induced water stress[J]. Journal of Experimental Botany, 2015, 66(8): 2271.
[9] Lee S J, Lee B H, Jung J K, et al. The growth regulating and growth interacting factor duo is essential for specification of carpel margin meristems[J]. Plant Physiology, 2017.
[10] Debernardi J M, Mecchia M A, Vercruyssen L, et al. Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity[J]. Plant Journal, 2014, 79(3): 413-426.
[11] Knaap E V D,Kende H. A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth[J]. Plant Physiol, 2000,122(3): 695-704.
[12] Kuijt S J, Greco R, Agalou A, et al. Interaction between the growth-regulating factor and knotted1-like homeobox families of transcription factors[J]. Plant Physiology, 2014, 164(4): 1952-1966.
[13] Kim J H, Lee B H. GROWTH-REGULATING FACTOR4, of Arabidopsis thaliana, is required for development of leaves, cotyledons, and shoot apical meristem[J]. Journal of Plant Biology, 2006, 49(6): 463-468.
[14] 周厚君.杨树GRF基因家族分析及PtGRF1/2d功能研究[D].北京:中国林业科学研究院,2016.
[15] Thompson J D, Gibson T J, Plewniak F, et al. The CLUSTAL_X windows interface: flexible strategies for mul-tiple sequence alignment aided by quality analysis tools[J]. Nucleic Acids Res, 1997, 25(24): 4876-4882.
[16] Tamura K, Stecher G, Peterson D, et al.MEGA6: molecular evolutionary genetics analysis version 6.0[J]. Mol Biol Evol, 2013, 30(12): 2725-2729.
[17] Bailey T L, Elkan C. The value of prior knowledge in discovering motifs with MEME [J] . Proc Third Int ConfIntel Syst Mol Biol, California: AAAI Press, 1995,3: 21-29.
[18] Wang T, Wang H, Cai D, et al. Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis)[J]. Plant Journal, 2017,91(4):684-699.
[19] Gao J, Zhang Y, Zhang C L, et al. Characterization of the floral transcriptome of moso bamboo (Phyllostachys edulis) at different flowering developmental stages by transcriptome sequencing and RNA-Seq analysis[J]. 2013, 9(6).
[20] Saldanha A J. Java treeview-extensible visualization of microarray data[J]. Bioinformatics, 2004, 20(17): 3246-3248.
[2] Vercruyssen L, Tognetti VB, Gonzalez N, et al. Growth regulating factor5 stimulates Arabidopsis chloroplast division, photosynthesis, and leaf longevity[J]. Plant Physiology, 2015, 167: 817-832.
[3] Hoe K J, Tsukaya H. Regulation of plant growth and development by the growth-regulating factor and grf-interacting factor duo[J]. Journal of Experimental Botany, 2015, 66(20): 6093.
[4] Treich I, Cairns B R, De I S T, et al. SNFll,A new component of the yeast SNF-SWI complex that interacts with a conserved region of SNF2[J]. Molecular and Cellular Biology, 1995, 15(8): 4240-4248.
[5] Kim J H, Kende H. A transcriptional coactivator, AtGIFl, is involved in regulating leaf growth and morphology in Arabidopsis[J]. PNAS, 2004, 101(36): 13374-13379.
[6] Kim J H, Choi D, Kende H. The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis[J]. Plant Journal, 2003, 36 (1): 94-104.
[7] Omidbakhshfard M A, Proost S, Fujikura U,et al.Growth-regulating factors (GRFs): a small transcription factor family with important functions in plant biology[J]. Molecular Plant, 2015, 8(7): 998-1010.
[8] He Y, Wu J,Lv B,et al. Involvement of 14-3-3 protein GRF9 in root growth and response under polyethylene glycol-induced water stress[J]. Journal of Experimental Botany, 2015, 66(8): 2271.
[9] Lee S J, Lee B H, Jung J K, et al. The growth regulating and growth interacting factor duo is essential for specification of carpel margin meristems[J]. Plant Physiology, 2017.
[10] Debernardi J M, Mecchia M A, Vercruyssen L, et al. Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity[J]. Plant Journal, 2014, 79(3): 413-426.
[11] Knaap E V D,Kende H. A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth[J]. Plant Physiol, 2000,122(3): 695-704.
[12] Kuijt S J, Greco R, Agalou A, et al. Interaction between the growth-regulating factor and knotted1-like homeobox families of transcription factors[J]. Plant Physiology, 2014, 164(4): 1952-1966.
[13] Kim J H, Lee B H. GROWTH-REGULATING FACTOR4, of Arabidopsis thaliana, is required for development of leaves, cotyledons, and shoot apical meristem[J]. Journal of Plant Biology, 2006, 49(6): 463-468.
[14] 周厚君.杨树GRF基因家族分析及PtGRF1/2d功能研究[D].北京:中国林业科学研究院,2016.
[15] Thompson J D, Gibson T J, Plewniak F, et al. The CLUSTAL_X windows interface: flexible strategies for mul-tiple sequence alignment aided by quality analysis tools[J]. Nucleic Acids Res, 1997, 25(24): 4876-4882.
[16] Tamura K, Stecher G, Peterson D, et al.MEGA6: molecular evolutionary genetics analysis version 6.0[J]. Mol Biol Evol, 2013, 30(12): 2725-2729.
[17] Bailey T L, Elkan C. The value of prior knowledge in discovering motifs with MEME [J] . Proc Third Int ConfIntel Syst Mol Biol, California: AAAI Press, 1995,3: 21-29.
[18] Wang T, Wang H, Cai D, et al. Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis)[J]. Plant Journal, 2017,91(4):684-699.
[19] Gao J, Zhang Y, Zhang C L, et al. Characterization of the floral transcriptome of moso bamboo (Phyllostachys edulis) at different flowering developmental stages by transcriptome sequencing and RNA-Seq analysis[J]. 2013, 9(6).
[20] Saldanha A J. Java treeview-extensible visualization of microarray data[J]. Bioinformatics, 2004, 20(17): 3246-3248.