鹰嘴豆NF-Y基因家族的全基因组序列鉴定及生物信息学分析
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摘要
为了揭示鹰嘴豆NF-Y基因家族的功能,从鹰嘴豆全基因组中鉴定NF-Y基因,并利用生物信息学分析软件对其进行系统发育进化、染色体定位、基因结构、保守结构域以及microRNA的靶位点预测分析。结果表明,共鉴定出41个鹰嘴豆NF-Y基因家族成员,在进化上分为3个亚家族:CarNF-YA(8个)、CarNF-YB(22个)和CarNF-YC(11个);这些基因分布于7条(Ca1—Ca7)染色体上,另外还有3条序列未定位到染色体上。鹰嘴豆NF-Y家族基因序列大部分都含有1～5个内含子和1～6个外显子,少数序列如CarNF-YB9和CarNF-YC6等仅含有外显子结构;编码的蛋白质中共发现3个保守基序(Motif1、Motif2和Motif3),其中Motif1、Motif2在CarNF-YB和CarNF-YC亚家族中均有分布,而Motif3仅分布在CarNF-YA亚家族中。鹰嘴豆和拟南芥NF-Y蛋白家族成员系统进化树表明,Car/At NF-YA可以分成6类,分别由6、1、3、3、1、4种蛋白质组成; Car/At NF-YB可以分成4类,分别由21、8、2、4种蛋白质组成; Car/At NF-YC亚基可以分成3类,分别由17、4、4个蛋白质组成。对鹰嘴豆NF-Y基因家族成员的miRNA169靶位点预测发现,41个成员中仅有CarNF-YA亚家族中的6个成员受到miRNA169调控。
To reveal the function of the NF-Y gene family of Cicer arietinum,the NF-Y gene was identified from the whole genome of Cicer arietinum. The bioinformatics analysis was conducted to predict and analyze the phylogenetic evolution,chromosome localization,gene structure,conserved domain and microRNA target site. The results showed that 41 NF-Y family genes of Cicer arietinum were identified and divided into three subfamilies: CarNF-YA(8),CarNF-YB(22) and CarNF-YC(11). These genes were distributed on seven(Ca1—Ca7) chromosomes except three sequences which were not mapped to the chromosome.Most of the NF-Y family gene sequences of Cicer arietinum contained 1 to 5 introns and 1 to 6 exons,and a few sequences such as CarNF-YB9 and CarNF-YC6 contained only exon. Three conserved motifs(Motif1,Motif2 and Motif3) were found in the encoded protein,of which Motif1 and Motif2 were distributed in the CarNF-YB and CarNF-YC subfamilies,while Motif3 was only distributed in the CarNF-YA subfamily.The phylogenetic tree of NF-Y transcription factor of Cicer arietinum and Arabidopsis showed that Car/At-NF-YAs could be divided into six groups consisting of 6,1,3,3,1 and 4 proteins respectively. Car/At NFYBs could be divided into 4 different groups which were composed of 21,8,2 and 4 proteins respectively.Car/At NF-YCs subunits could be divided into 3 groups,which were composed of 17,4 and 4 proteins,respectively. The prediction of miRNA169 target sites of NF-Y family members of Cicer arietinum revealed that only 6 CarNF-YAs out of the 41 members of the NF-Y family were regulated by miRNA169.
To reveal the function of the NF-Y gene family of Cicer arietinum,the NF-Y gene was identified from the whole genome of Cicer arietinum. The bioinformatics analysis was conducted to predict and analyze the phylogenetic evolution,chromosome localization,gene structure,conserved domain and microRNA target site. The results showed that 41 NF-Y family genes of Cicer arietinum were identified and divided into three subfamilies: CarNF-YA(8),CarNF-YB(22) and CarNF-YC(11). These genes were distributed on seven(Ca1—Ca7) chromosomes except three sequences which were not mapped to the chromosome.Most of the NF-Y family gene sequences of Cicer arietinum contained 1 to 5 introns and 1 to 6 exons,and a few sequences such as CarNF-YB9 and CarNF-YC6 contained only exon. Three conserved motifs(Motif1,Motif2 and Motif3) were found in the encoded protein,of which Motif1 and Motif2 were distributed in the CarNF-YB and CarNF-YC subfamilies,while Motif3 was only distributed in the CarNF-YA subfamily.The phylogenetic tree of NF-Y transcription factor of Cicer arietinum and Arabidopsis showed that Car/At-NF-YAs could be divided into six groups consisting of 6,1,3,3,1 and 4 proteins respectively. Car/At NFYBs could be divided into 4 different groups which were composed of 21,8,2 and 4 proteins respectively.Car/At NF-YCs subunits could be divided into 3 groups,which were composed of 17,4 and 4 proteins,respectively. The prediction of miRNA169 target sites of NF-Y family members of Cicer arietinum revealed that only 6 CarNF-YAs out of the 41 members of the NF-Y family were regulated by miRNA169.
引文
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[14] Kumimoto R W,Zhang Y,Siefers N,et al. NF-YC3,NFYC4 and NF-YC9 are required for constans-mediated,photoperiod-dependent flowering in Arabidopsis thaliana[J]. Am J Transplant,2010,63(3):379-391.
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[17] Jain M,Misra G,Patel R K,et al. A draft genome sequence of the pulse crop chickpea(Cicer arietinum L.)[J]. Am J Transplant,2013,74(5):715-729.
[18]王小非,刘鑫,苏玲,等.番茄LBD基因家族的全基因组序列鉴定及其进化和表达分析[J].中国农业科学,2013,46(12):2501-2513.
[19] Shi H,Ye T,Zhong B,et al. At HAP5A modulates freezing stress resistance in Arabidopsis through binding to CCAAT motif of At XTH21[J]. New Phytologist,2014,9(7):554-567.
[20] Zhao B,Ge L,Liang R,et al. Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor[J]. BMC Mol Biol,2009,10:29.
[2] Petroni K,Kumimoto R W,Gnesutta N,et al. The promiscuous life of plant nuclear factor Y transcription factors[J]. Plant Cell Physiol,2012,24(12):4777-4792.
[3] Stephenson T J,Mcintyre C L,Collet C,et al. Genomewide identification and expression analysis of the NF-Y family of transcription factors in Triticum aestivum[J].Plant Mol Biol,2007,65(1/2):77-92.
[4] Mantovani R. The molecular biology of the CCAAT-binding factor NF-Y[J]. Gene,1999,239(1):15-27.
[5] Chong R,Zhan Z,Yi W,et al. Genome-wide identification and characterization of the NF-Y gene family in grape(Vitis vinifera L.)[J]. BMC Genomics,2016,17:605.
[6] Miyoshi K,Ito Y,Serizawa A,et al. Os HAP3 genes regulate chloroplast biogenesis in rice[J]. Am J Transplant,2010,36(4):532-540.
[7] Ni Z,Zheng H,Jiang Q,et al. Gm NFYA3,a target gene of miR169,is a positive regulator of plant tolerance to drought stress[J]. Plant Mol Biol,2013,82(1/2):113-129.
[8] Han X,Tang S,An Y,et al. Overexpression of the poplar NF-YB7 transcription factor confers drought tolerance and improves water-use efficiency in Arabidopsis[J]. J Exp Bot,2013,64(14):4589-4601.
[9] Li W X,Oono Y,Zhu J,et al. The Arabidopsis NFYA5transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance[J]. Plant Cell Physiol,2008,20(8):2238-2251.
[10] Siefers N,Dang K K,Kumimoto R W,et al. Tissue-specific expression patterns of Arabidopsis NF-Y transcription factors suggest potential for extensive combinatorial complexity[J]. Plant Physiol,2009,149(2):625-641.
[11] Kwong R W,Bui A Q,Lee H,et al. LEAFY cotyledon1-like defines a class of regulators essential for embryo development[J]. Plant Cell Physiol,2003,15(1):5-18.
[12] Junker A,M9nke G,Rutten T,et al. Elongation-related functions of LEAFY cotyledon1 during the development of Arabidopsis thaliana[J]. Am J Transplant,2012,71(3):427-442.
[13] Mu J,Tan H,Hong S,et al. Arabidopsis transcription factor genes NF-YA1,5,6,and 9 play redundant roles in male gametogenesis,embryogenesis,and seed development[J]. Plant Mol Biol,2013,6(1):188-201.
[14] Kumimoto R W,Zhang Y,Siefers N,et al. NF-YC3,NFYC4 and NF-YC9 are required for constans-mediated,photoperiod-dependent flowering in Arabidopsis thaliana[J]. Am J Transplant,2010,63(3):379-391.
[15] Laloum T,De M S,Gamas P,et al. CCAAT-box binding transcription factors in plants:Y so many[J]. Trends in Plant Sci,2013,18(3):157-166.
[16] Zhang J J,Xue H W. Os LEC1/Os HAP3E participates in the determination of meristem identity in both vegetative and reproductive developments of rice[J]. J Integr Plant Biol,2013,55(3):232-249.
[17] Jain M,Misra G,Patel R K,et al. A draft genome sequence of the pulse crop chickpea(Cicer arietinum L.)[J]. Am J Transplant,2013,74(5):715-729.
[18]王小非,刘鑫,苏玲,等.番茄LBD基因家族的全基因组序列鉴定及其进化和表达分析[J].中国农业科学,2013,46(12):2501-2513.
[19] Shi H,Ye T,Zhong B,et al. At HAP5A modulates freezing stress resistance in Arabidopsis through binding to CCAAT motif of At XTH21[J]. New Phytologist,2014,9(7):554-567.
[20] Zhao B,Ge L,Liang R,et al. Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor[J]. BMC Mol Biol,2009,10:29.