普通烟草SBP转录因子家族的全基因组鉴定及其进化和表达分析
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- 英文论文题名：Genome-Wide Identification, Phylogenetic Analysis and Expression Profiling of the SBP Transcription Factor Family in Nicotiana tabacum
- 论文作者：刘成 ; 李晓旭 ; 苏玉龙 ; 郭永峰
- 英文论文作者：LIU Cheng ; LI Xiaoxu ; SU Yulong ; GUO Yongfeng ; Tobacco Research Institute of Chinese Academy of Agricultural Sciences ; Graduate School of Chinese Academy of Agricultural Sciences
- 年：2016
- 作者机构：中国农业科学院烟草研究所;中国农业科学院研究生院;
- 论文关键词：生物信息学分析 ; SBP转录因子家族 ; 普通烟草
- 英文论文关键词：bioinformatics analysis ; SBP transcription factor family ; Nicotiana tabacum
- 会议召开时间：2016-12-01
- 会议录名称：中国烟草学会2016年度优秀论文汇编——烟草农业主题
- 语种：中文
- 分类号：S572
- 学会代码：ZGYG
- 学会名称：中国烟草学会
- 页数：11
- 文件大小：2075k
- 原文格式：D
摘要
SBP转录因子家族作为植物特异性的转录因子具有重要的生物学功能,广泛参与花和果实发育等诸多生命过程。利用普通烟草(Nicotiana tabacum)TN90基因组数据,通过隐马尔科夫模型检索,SMART和Pfam分析,鉴定了普通烟草SBP转录因子家族成员;通过多序列比对鉴定并分析了普通烟草SBP结构域的结构特征;通过邻接法、极大似然法进行了系统发育分析;分别利用GSDS和MEME对SBP转录因子家族成员的基因结构和蛋白保守结构域进行了分析;利用普通烟草TN90转录组数据分析了SBP转录因子家族成员在不同组织和时期的表达情况,并对鉴定出的SBP转录因子家族成员进行了GO注释分析。结果表明,普通烟草基因组编码32个SBP转录因子家族成员,氨基酸序列长度差异较大;系统发育分析表明,所有的SBP转录因子家族成员可分为8个亚家族。转录组数据显示,SBP基因家族成员在不同组织和时期中表达迥异,但在花器官中均有较高的表达量。GO注释结果表明,该家族成员作为转录因子,在植物的生长发育、逆境响应等过程中发挥作用。本研究为烟草及其他植物中SBP转录因子家族基因的鉴定和功能研究提供了基础。
The members of the SBP transcription factor family have been reported to play significant roles in regulating flower and fruit development as well as other biological processes. In this study, 32 SBP transcription factor family members were identified in Nicotiana tabacum with HMMER. Both Maximum-Likelihood phylogenetic tree and neighbor-joining tree were constructed and were found to possess similar topologies using the protein sequences of the SBP-domain. Results of phylogenetic analysis revealed that the SBP transcription factor family members could be classified into 8 subfamilies. The patterns of exon-intron structure and conserved domains in Arabidopsis and tobacco were consistent with the phylogenetic results. Transcriptome analysis showed that the expression patterns of Nt SPLs were different in different tissue types and the expression level of Nt SPLs in flower was found to be significantly higher than the other tissues. GO analysis suggested that as transcription factors, the SBP family members could be involved in a series of biological processes such as developmental regulation and defense response. The results of this study provide insight into the evolution of the SBP transcription factor family in Nicotiana tabacum and provide useful information for future research on these genes.
The members of the SBP transcription factor family have been reported to play significant roles in regulating flower and fruit development as well as other biological processes. In this study, 32 SBP transcription factor family members were identified in Nicotiana tabacum with HMMER. Both Maximum-Likelihood phylogenetic tree and neighbor-joining tree were constructed and were found to possess similar topologies using the protein sequences of the SBP-domain. Results of phylogenetic analysis revealed that the SBP transcription factor family members could be classified into 8 subfamilies. The patterns of exon-intron structure and conserved domains in Arabidopsis and tobacco were consistent with the phylogenetic results. Transcriptome analysis showed that the expression patterns of Nt SPLs were different in different tissue types and the expression level of Nt SPLs in flower was found to be significantly higher than the other tissues. GO analysis suggested that as transcription factors, the SBP family members could be involved in a series of biological processes such as developmental regulation and defense response. The results of this study provide insight into the evolution of the SBP transcription factor family in Nicotiana tabacum and provide useful information for future research on these genes.
引文
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[2]Guo A Y,Zhu Q H,Gu X,et al.Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family[J].Gene,2008,418(1-2):1-8.
[3]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.
[4]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.
[5]Unte U S.SPL8,an SBP-Box Gene That Affects Pollen Sac Development in Arabidopsis[J].The Plant Cell Online,2003,15(4):1009-1019.
[6]Stone J M,Liang X,Nekl E R,et al.Arabidopsis At SPL14,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.
[7]Yamasaki K,Kigawa T,Inoue M,et al.A novel zinc-binding motif revealed by solution structures of DNAbinding domains of Arabidopsis SBP-family transcription factors[J].Journal of Molecular Biology,2004,337(1):49-63.
[8]Rhoades M W,Reinhart B J,Lim L P,et al.Prediction of plant micro RNA targets[J].Cell,2002,110(4):513-520.
[9]Schwab R,Palatnik J F,Riester M,et al.Specific effects of micro RNAs on the plant transcriptome[J].Development Cell,2005,8(4):517-527.
[10]Xie K,Wu C,Xiong L.Genomic organization,differential expression,and interaction of SQUAMOSA promoter-binding-like transcription factors and micro RNA156 in rice[J].Plant Physiology,2006,142(1):280-293.
[11]陆莹,刘艳华,任民,等.烟草CONSTANS同源基因的克隆与分析[J].中国烟草科学,2013,34(3):60-64
[12]王倩,刘好宝.烟草重要基因篇:2.烟草钾吸收与转运相关基因[J].中国烟草科学,2014,35(2):139-142
[13]刘贯山.烟草重要基因篇:4.烟草钙依赖蛋白激酶基因[J].中国烟草科学,2014,35(4):109-111.
[14]Jin J,Zhang H,Kong L,et al.Plant TFDB 3.0:a portal for the functional and evolutionary study of plant transcription factors[J].Nucleic acids research,2014,42:D1182-D1187.
[15]Katoh K,Kuma K,Toh H,et al.MAFFT version 5:improvement in accuracy of multiple sequence alignment[J].Nucleic Acids Research,2005,33(2):511-518.
[16]Guindon S,Lethiec F,Duroux P,et al.PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference[J].Nucleic Acids Research,2005,33(suppl 2):W557-W559.
[17]Abascal F,Zardoya R,Posada D.Prot Test:selection of best-fit models of protein evolution[J].Bioinformatics,2005,21(9):2104-2105.
[18]Bailey T L,Boden M,Buske F A,et al.MEME SUITE:tools for motif discovery and searching[J].Nucleic acids research,2009,37:W202-W208.
[19]Conesa A,G?tz S,García-Gómez J M,et al.Blast2GO:a universal tool for annotation,visualization and analysis in functional genomics research[J].Bioinformatics,2005,21(18):3674-3676.
[20]Ye J,Fang L,Zheng H,et al.WEGO:a web tool for plotting GO annotations[J].Nucleic Acids Research,2006,34(suppl 2):W293-W297.
[21]Birkenbihl R P,Jach G,Saedler H,et al.Functional dissection of the plant-specific SBP-domain:overlap of the DNA-binding and nuclear localization domains[J].Journal of Molecular Biology,2005,352(3):585-596.
[22]Riese M,H?hmann S,Saedler H,et al.Comparative analysis of the SBP-box gene families in P.patens and seed plants[J].Gene,2007,401(1):28-37.
[23]朱红霞,胡利宗,邓小莉,等.大豆SBP基因家族的序列特征,表达及进化分析[J].东北农业大学学报,2012,43(7):26-33.