Scientia Agricultura Sinica ›› 2014, Vol. 47 ›› Issue (10): 1894-1903.doi: 10.3864/j.issn.0578-1752.2014.10.003

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

The Genome-Wide Analysis of MicroRNAs and Their Target Genes in Nicotiana tomentosiformis and Nicotiana sylvestris

 LI  Ling-1, 2 , ZHANG  Lei-3, CHAO  Jiang-Tao-1, GONG  Da-Ping-1, LI  Feng-Xia-1, WANG  Qian-1, DING  An-Ming-1, 2 , CHEN  Ya-Qiong-1, 2 , SUN  Ting-Ting-1, 2 , SUN  Yu-He-1   

  1. 1、Tobacco Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Qingdao 266101, Shandong;
    2、Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081;
    3、College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070
  • Received:2013-11-24 Online:2014-05-20 Published:2014-02-14

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Abstract: 【Objective】The objective of this study is to fill the gaps in miRNA-related fields of Nicotiana tomentosiformis and N. sylvestris research as quickly as possible, and to reveal the growth and development regulation mechanism in N. tobacum, 【Method】the microRNAs and their target genes of N. tomentosiformis and Nicotiana sylvestris were genome-wide predicted and analyzed. miRNAs were predicted by the method of homologous alignment and secondary structure characteristics of pre-miRNA: reference sequence in sequence alignment of N. tomentosiformis and N. sylvestris were allowed 1-2 mispairings; secondary structure of miRNA was classic stem loop structure, maximum value of MEF was -25, minimum value of MEFI was 0.85, the predicted miRNA and the same family miRNA located on the same arm of hairpin structure; E-values of encoding protein sequence less than or equal to 1e-6 were eliminated. 【Result】 A total 162 miRNAs belonging to 39 families were identified in N. tomentosiformis, including 14 pairs of sense and antisense strand miRNAs and 5 gene clusters. A total 169 miRNAs belonging to 40 families were identified in N. sylvestris, including 13 pairs of sense and antisense strand miRNAs and 3 gene clusters. In high degree of miRNA conservative families, members of the distribution and membership were near in 2 wild tobaccos. While in a relatively low degree of conservative families, members of 2 wild tobaccos differed obviously. Nine families like miR5021, miR5203 and so on, got members in N. tomentosiformis. Ten families like miR1446, miR1509 and so on, got members in N. sylvestris. Antisense miRNA and their sense partners from 2 wild tobaccos differed from 1 to 4 bases, these differences location presented preferences in different families, and the preferences were similar in 2 wild tobaccos: 9th, 12th, 13th base in miR164 family, 1st, 21st base in miR172 family, 2nd, 17th base in miR396 family, 15th, 20th base in miR399 family. Gene cluster of 2 wild tobaccos consisted of miR156 family and miR169 family, distance of pre-clusters was less than 350nt. miR6019/miR6020 gene clusters were found in N. tomentosiformis for the first time. Unigene of N. tabacum was used as target genes. In N. tomentosiformis, 749 target genes of 122 miRNAs were identified. With duplicate genes eliminated, 206 non-redundant target genes were identified, in which, 89 target genes (43%) got GO annotations. In N. sylvestris, 117 target genes of 650 miRNAs were identified. With duplicate genes eliminated, 169 non-redundant target genes were identified, in which, 78 target genes (46%) got GO annotations. In terms of molecular function, most of the target genes have binding activity. In the process of biology, target genes mainly involved in the development process, reproductive process, multicellular organ development process, stress response and so on. 【Conclusion】 In N. sylvestris, there are more target genes control development and multicellular development, while in N. tomentosiformis, there are more target genes control stimulus and press reply.

Key words: N. tomentosiformis , N. sylvestris , microRNA , bioinformatics , genome

[1]Gerstel D. Segregation in new allopolyploids of Nicotiana: I. Comparison of 6x (N. tabacum x tomentosiformis) and 6x (N. tabacum x otophora). Genetics, 1960, 45(12): 1723.

[2]Gerstel D. Tobacco: Nicotiana tabacum (Solanaceae). Evolution of Crop Plants, 1976: 273-277.

[3]张会娟, 胡志超, 谢焕雄, 王海欧, 陈有庆. 我国烟草的生产概况与发展对策. 安徽农业科学, 2008, 36(32): 14161-14162, 14213.

Zhang H J, Hu Z C, Xie H X, Wang H O, Chen Y Q. General situation and development strategy of tobacco production in china. Journal of Anhui Agricultural Sciences, 2008, 36(32): 14161-14162, 14213. (in Chinese)

[4]Lee R C, Feinbaum R L, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 1993, 75(5): 843-854.

[5]Jones-Rhoades M W, Bartel D P, Bartel B. MicroRNAs and their regulatory roles in plants. Annual Review of Plant Biology, 2006, 57(1): 19-53.

[6]Jung J H, Seo P, Park C M. MicroRNA biogenesis and function in higher plants. Plant Biotechnology Reports, 2009, 3(2): 111-126.

[7]Bartel D P. MicroRNAs: Target recognition and regulatory functions. Cell, 2009, 136(2): 215-233.

[8]Floyd S K, Bowman J L. Gene regulation: Ancient microRNA target sequences in plants. Nature, 2004, 428(6982): 485-486.

[9]Zhang B, Pan X, Cannon C H, Cobb G P, Anderson T A. Conservation and divergence of plant microRNA genes. The Plant Journal, 2006, 46(2): 243-259.

[10]Zhang B, Pan X, Stellwag E. Identification of soybean microRNAs and their targets. Planta, 2008, 229(1): 161-182.

[11]Zhang B, Pan X, Anderson T A. Identification of 188 conserved maize microRNAs and their targets. FEBS Letters, 2006, 580(15): 3753-3762.

[12]Yin Z, Li C, Han X, Shen F. Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene, 2008, 414(1/2): 60-66.

[13]Qiu C X, Xie F L, Zhu Y Y, Guo K, Huang S Q, Nie L, Yang Z M. Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags. Gene, 2007, 395(1/2): 49-61.

[14]Carra A, Mica E, Gambino G, Pindo M, Moser C, Pè M E, Schubert A. loning and characterization of small non-coding RNAs from grape. The Plant Journal, 2009, 59(5): 750-763.

[15] Sierro N, Battey J, N Ouadi S, Bovet L, Goepfert S, Bakaher N, Peitsch M C, Ivanov N V. Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. Genome Biology, 2013, 14(6): R60.

[16]Kozomara A, Griffiths-Jones S. miRBase: Integrating microRNA annotation and deep-sequencing data. Nucleic Acids Research, 2011, 39(suppl 1): 152-157.

[17]Langmead B, Trapnell C, Pop M, Salzberg S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 2009, 10(3): 1-10.

[18]Ye J, Fang Li, Zheng H K, Zhang Y, Chen J, Zhang Z J, Wang J, Li S T, Li R Q, Bolund L, Wang J. WEGO: A web tool for plotting GO annotations. Nucleic Acids Research, 2006, 34(suppl 2): 293-297.

[19]张磊, 晁江涛, 崔萌萌, 陈雅琼, 宗鹏, 孙玉合. 茄子microRNAs与其靶基因的生物信息学预测. 遗传, 2011, 33(7): 776-784.

Zhang L, Chao J T, Cui M M, Chen Y Q, Zong P, Sun Y H. Bioinformatic prediction of conserved microRNAs and their target genes in eggplant. Hereditas, 2011, 33(7): 776-784. (in Chinese)

[20]柳承璋, 李富花, 相建海. 淡水枝角水蚤miRNA的生物信息学发掘与分析. 海洋与湖沼, 2013, 44(4): 25-33.

Liu C Z, Li F H, Xiang J H. Bioinformatic analysis of miroRNA genes in daphnla pulex. Oceanologia Et Limnologia Sinica, 2013, 44(4): 25-33. (in Chinese)

[21]魏强, 梁永宏, 李广林. 植物miRNA的进化. 遗传, 2013, 35(3): 315-323.

Wei Q, Liang Y H, Li G L. Evolution of miRNA in plants. Hereditas, 2013, 35(3): 315-323. (in Chinese)

[22]Guo H, Kan Y, Liu W. Differential expression of miRNAs in response to topping in flue-cured tobacco roots. PLOS One, 2011, 6(12): 28565.

[23]Guo Y, Liu H, Yang Z, Chen J, Sun Y, Ren X. Identification and characterization of miRNAome in tobacco by deep sequencing combined with microarray. Gene, 2012, 501(1): 24-32.

[24]Kim H J, Baek K H, Lee B W, Choi D, Hur C G. In silico identification and characterization of microRNAs and their putative target genes in solanaceae plants. Genome, 2011, 54(2): 91-98.

[25]Tang S, Wang Y, Li Z, Gui Y, Xiao B, Xie J, Zhu Q H, Fan L. Identification of wounding and topping responsive small RNAs in tobacco. BMC Plant Biology, 2012, 12: 28.

[26]Frazier T, Xie F, Freistaedter A, Burklew C, Zhang B. Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta, 2010, 232(6): 1289-1308.

[27]Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T. New microRNAs from mouse and human. RNA, 2003, 9(2): 175-179.

[28]Lai E, Tomancak P, Williams R, Rubin G. Computational identification of Drosophila microRNA genes. Genome Biology, 2003, 4(7): 1-20.

[29]Ambros V. The functions of animal microRNAs. Nature, 2004, 431(7006): 350-355.

[30]Cullen B R. Transcription and processing of Human microRNA precursors. Molecular Cell, 2004, 16(6): 861-865.

[31]Wang S, Zhu Q H, Guo X, Gui Y, Bao J, Hellwell C, Fan L J. Molecular evolution and selection of a gene encoding two tandem microRNAs in rice. FEBS Letters, 2007, 581(24): 4789-4793.

[32]Chuck G, Cigan A M, Saeteurn K, Hake S. The heterochronic maize mutant corngrass1 results from overexpression of a tandem microRNA. Nature Genetics, 2007, 39(4): 544-549.

[33]Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto Y, Sieburth L, Voinnet O. Widespread translational inhibition by plant miRNAs and siRNAs. Science, 2008, 320(5880): 1185-1190.

[34]Stark A, Bushati N, Jan C, Kheradpour P, Hodges E, Brennecke J, Bartel D P, Cohen S M, Kellis M. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes and Development, 2008, 22(1): 8-13.
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