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

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