MicroRNAs (miRNAs), a recently discovered class of small (~21nt), non-coding, endogenous, single-stranded RNAs in eukaryotes, regulate gene expression negatively at the post-transcriptional levels depending on the extent of com-plementation between miRNA and mRNA. To date, a large number of miRNAs have been reported in many species, but none for eggplant (Solanum melongena L.). In this paper, a computational homology search approach based on the conservation of miRNA sequences and the stem-loop hairpin secondary structures of miRNAs was adopted. The search was started with the known plant miRNAs compared to eggplant expressed sequence tags (EST) databases to find potential miRNAs. Following a range of filtering criteria, a total of 16 potential miRNAs belonging to 12 families were identified. Three pairs of sense and antisense strand eggplant miRNAs belonging to three different miRNA families were also found. Furthermore, miR390 and miR399 sense/antisense pairs are identified for the first time in plants. Using online software psRNATarget, we further predicted the target genes of these 16 miRNAs and got 71 potential targets genes on base of 15 eggplant miRNAs. Most of these target genes were predicted to encode proteins that play key role in eggplant growth, de-velopment, metabolism, and stress responses.
ZHANG Lei, CHAO Jiang-Chao, CUI Meng-Meng, CHEN Ya-Qiong, ZONG Feng, SUN Yu-Ge
. Bioinformatic prediction of conserved microRNAs and their target genes in eggplant (Solanum melongena L.)[J]. Hereditas(Beijing), 2011
, 33(7)
: 776
-784
.
DOI: 10.3724/SP.J.1005.2011.00776
[1] Bartel DP. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 2004, 116(2): 281-297.
[2] Zhang BH, Pan XP, Cobb GP, Anderson TA. Plant microRNA: A small regulatory molecule with big impact. Dev Biol, 2006, 289(1): 3-16.
[3] Chen XM. MicroRNA biogenesis and function in plants. FEBS Lett, 2005, 579(26): 5923-5931.
[4] Taylor PF, Zhang BH. Identification of plant microRNAs using expressed sequence tag analysis. Methods Mol Biol, 2011, 678: 13-25.
[5] Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 1993, 75(5): 843-854.
[6] Baker CC, Sieber P, Wellmer F, Meyerowitz EM. The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis. Curr Biol, 2005, 15(4): 303-315.
[7] Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol, 2006, 57(1): 19-53.
[8] 卫波, 张荣志, 李爱丽, 毛龙. 利用高通量测序技术发现植物小分子RNA研究进展. 中国农业科学, 2009, 42(11): 3755-3764.
[9] Zhang BH, Pan XP, Cannon CH, Cobb GP, Anderson TA. Conservation and divergence of plant microRNA genes. Plant J, 2006, 46(2): 243-259.
[10] Floyd SK, Bowman JL. Gene regulation: ancient mi-croRNA target sequences in plants. Nature, 2004, 428(6982): 485-486.
[11] Wang JF, Zhou H, Chen YQ, Luo QJ, Qu LH. Identification of 20 microRNAs from Oryza sativa. Nucleic Acids Res, 2004, 32(5): 1688-1695.
[12] Jones-Rhoades MW, Bartel DP. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell, 2004, 14(6): 787-799.
[13] Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA. Identification and characterization of new plant microR-NAs using EST analysis. Cell Res, 2005, 15(5): 336-360.
[14] Yin ZJ, Li CH, Han XL, Shen FF. Identification of con-served microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene, 2008, 414(1-2): 60-66.
[15] Zhang BH, Wang QL, Wang KB, Pan XP, Liu F, Gou TL, Cobb GP, Anderson TA. Identification of cotton microR-NAs and their targets. Gene, 2007, 397(1-2): 26-37.
[16] Zhang BH, Pan XP, Anderson TA. Identification of 188 conserved maize microRNAs and their targets. FEBS Lett, 2006, 580(15): 3753-3762.
[17] Lang QL, Jin CZ, Lai LY, Feng JL, Chen SN, Chen JH. Tobacco microRNAs prediction and their expression infected with Cucumber mosaic virus and Potato virus X. Mol Biol Rep, 2010, 38(3): 1523-1531.
[18] Frazier TP, Xie FL, Freistaedter A, Burklew CE, Zhang BH. Identification and characterization of microRNAs and their target genes in bobacco (Nicotiana tabacum). Planta, 2010, 232(6): 1289-1308.
[19] Daunay MC, Lester RN. The usefulness of taxonomy for Solanaceae breeders, with special reference to the genus Solanum and to Solanum melongena L. (eggplant). Capsicum Newslett, 1988, (7): 70-79.
[20] Griffiths-Jones S, Saini HK, Dongen SV, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res, 2008, 36(S1): D154-D158.
[21] Song CN, Fang JG, Wang C, Guo L, Nicholas KK, Ma ZQ. MiR-RACE, a new efficient approach to determine the precise sequences of computationally identied trifoliate orange (Poncirus trifoliata) microRNAs. PLoS ONE, 2010, 5(6): e10861.
[22] Dsouza M, Larsen N, Overbeek R. Searching for patterns in genomic data. Trends Genet, 1997, 13(12): 497-498.
[23] Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P. Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie, 1994, 125(2): 167-188.
[24] Dai XB, Zhuang ZH, Zhao PX. Computational analysis of miRNA targets in plants: current status and challenges. Brief
