MicroRNAs (miRNAs) are important regulators of many cellular processes and exist in a wide range of eukaryotes. High-throughput sequencing is a mainstream method of miRNA identification through which it is possible to obtain the complete small RNA profile of an organism. Currently, most approaches to miRNA identification rely on a reference genome for the prediction of hairpin structures. However, many species of economic and phylogenetic importance are non-model organisms without complete genome sequences, and this limits miRNA discovery. Here, to overcome this limitation, we have developed a contig-based miRNA identification strategy. We applied this method to a triploid species of edible banana (GCTCV-119, Musa spp. AAA group) and identified 180 pre-miRNAs and 314 mature miRNAs, which is three times more than those were predicted by the available dataset-based methods (represented by EST+GSS). Based on the recently published miRNA data set of Musa acuminate, the recall rate and precision of our strategy are estimated to be 70.6% and 92.2%, respectively, significantly better than those of EST+GSS-based strategy (10.2% and 50.0%, respectively). Our novel, efficient and cost-effective strategy facilitates the study of the functional and evolutionary role of miRNAs, as well as miRNA-based molecular breeding, in non-model species of economic or evolutionary interest.
Carrington JC, Ambros V (2003) Role of microRNAs in plant and animal development. Science 301: 336–338. doi: 10.1126/science.1085242
[3]
Voinnet O (2009) Origin, Biogenesis, and Activity of Plant MicroRNAs. Cell 136: 669–687. doi: 10.1016/j.cell.2009.01.046
[4]
Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC (2007) miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 447: 1126–1129. doi: 10.1038/nature05903
[5]
Zhao T, Li G, Mi S, Li S, Hannon GJ, et al. (2007) A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev 21: 1190–1203. doi: 10.1101/gad.1543507
[6]
Bernstein E, Kim SY, Carmell MA, Murchison EP, Alcorn H, et al. (2003) Dicer is essential for mouse development. Nat Genet 35: 215–217. doi: 10.1038/ng1253
[7]
Lecellier CH, Dunoyer P, Arar K, Lehmann-Che J, Eyquem S, et al. (2005) A cellular microRNA mediates antiviral defense in human cells. Science 308: 557–560. doi: 10.1126/science.1108784
[8]
Ma Z, Coruh C, Axtell MJ (2010) Arabidopsis lyrata Small RNAs: Transient MIRNA and Small Interfering RNA Loci within the Arabidopsis Genus. Plant Cell 22: 1090–1103. doi: 10.1105/tpc.110.073882
[9]
Taganov KD, Boldin MP, Baltimore D (2007) MicroRNAs and immunity: tiny players in a big field. Immunity 26: 133–137. doi: 10.1016/j.immuni.2007.02.005
[10]
Wu G, Park MY, Conway SR, Wang JW, Weigel D, et al. (2009) The Sequential Action of miR156 and miR172 Regulates Developmental Timing in Arabidopsis. Cell 138: 750–759. doi: 10.1016/j.cell.2009.06.031
[11]
Xie K, Wu C, Xiong L (2006) Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiology 142: 280–293. doi: 10.1104/pp.106.084475
[12]
Yang WJ, Yang DD, Na S, Sandusky GE, Zhang Q, et al. (2005) Dicer is required for embryonic angiogenesis during mouse development. J Biol Chem 280: 9330–9335. doi: 10.1074/jbc.m413394200
[13]
Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, et al. (2008) A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Research 18: 1456–1465. doi: 10.1101/gr.075572.107
[14]
Willmann MR, Poethig RS (2007) Conservation and evolution of miRNA regulatory programs in plant development. Curr Opin Plant Biol 10: 503–511. doi: 10.1016/j.pbi.2007.07.004
[15]
Morozova O, Hirst M, Marra MA (2009) Applications of new sequencing technologies for transcriptome analysis. Annual Review of Genomics and Human Genetics 10: 135–151. doi: 10.1146/annurev-genom-082908-145957
[16]
Friedl？nder MR, Chen W, Adamidi C, Maaskola J, Einspanier R, et al. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nature Biotechnology 26: 407–415. doi: 10.1038/nbt1394
[17]
Guan DG, Liao JY, Qu ZH, Zhang Y, Qu LH (2011) mirExplorer: detecting microRNAs from genome and next generation sequencing data using the AdaBoost method with transition probability matrix and combined features. RNA Biol 8: 922–934. doi: 10.4161/rna.8.5.16026
[18]
Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA (2006) Conservation and divergence of plant microRNA genes. Plant J 46: 243–259. doi: 10.1111/j.1365-313x.2006.02697.x
[19]
Yao Y, Guo G, Ni Z, Sunkar R, Du J, et al. (2007) Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol 8: R96. doi: 10.1186/gb-2007-8-6-r96
[20]
Chi X, Yang Q, Chen X, Wang J, Pan L, et al. (2011) Identification and characterization of microRNAs from peanut (Arachis hypogaea L.) by high-throughput sequencing. PloS One 6: e27530. doi: 10.1371/journal.pone.0027530
[21]
Pelaez P, Trejo MS, Iniguez LP, Estrada-Navarrete G, Covarrubias AA, et al. (2012) Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing. BMC Genomics 13: 83. doi: 10.1186/1471-2164-13-83
[22]
Wang C, Han J, Liu C, Kibet KN, Kayesh E, et al. (2012) Identification of microRNAs from Amur grape (Vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics. BMC Genomics 13: 122. doi: 10.1186/1471-2164-13-122
[23]
Wang F, Li L, Liu L, Li H, Zhang Y, et al. (2012) High-throughput sequencing discovery of conserved and novel microRNAs in Chinese cabbage (Brassica rapa L. ssp pekinensis). Molecular Genetics and Genomics 287: 555–563. doi: 10.1007/s00438-012-0699-3
[24]
Catalano D, Pignone D, Sonnante G, Finetti-Sialer MM (2012) In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus. BMC Bioinformatics 13.
[25]
Gebelin V, Argout X, Engchuan W, Pitollat B, Duan CF, et al.. (2012) Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets. BMC Plant Biology 12.
[26]
Song C, Jia Q, Fang J, Li F, Wang C, et al. (2010) Computational identification of citrus microRNAs and target analysis in citrus expressed sequence tags. Plant Biology 12: 927–934. doi: 10.1111/j.1438-8677.2009.00300.x
[27]
Rudd S (2003) Expressed sequence tags: alternative or complement to whole genome sequences? Trends in Plant Science 8: 321–329. doi: 10.1016/s1360-1385(03)00131-6
[28]
Dong Q, Kroiss L, Oakley FD, Wang BB, Brendel V (2005) Comparative EST analyses in plant systems. Methods in Enzymology 395: 400–418. doi: 10.1016/s0076-6879(05)95022-2
[29]
Yu XM, Zhou Q, Li SC, Luo QB, Cai YM, et al.. (2008) The Silkworm (Bombyx mori) microRNAs and Their Expressions in Multiple Developmental Stages. PloS One 3.
[30]
D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, et al. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488: 213–217. doi: 10.1038/nature11241
[31]
Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, et al. (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37: 766–770. doi: 10.1038/ng1590
[32]
Xu MY, Dong Y, Zhang QX, Zhang L, Luo YZ, et al.. (2012) Identification of miRNAs and their targets from Brassica napus by high-throughput sequencing and degradome analysis. BMC Genomics 13.
[33]
Wang M, Wang Q, Wang B (2012) Identification and Characterization of MicroRNAs in Asiatic Cotton (Gossypium arboreum L.). PloS One 7.
[34]
Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Research 15: 336–360. doi: 10.1038/sj.cr.7290302
[35]
Ying SY, Lin SL (2004) Intron-derived microRNAs–fine tuning of gene functions. Gene 342: 25–28. doi: 10.1016/j.gene.2004.07.025
[36]
Ying SY, Lin SL (2005) Intronic microRNAs. Biochemical and Biophysical Research Communications 326: 515–520. doi: 10.1016/j.bbrc.2004.10.215
[37]
Bennetzen JL (2002) Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115: 29–36. doi: 10.1023/a:1016015913350
[38]
Nagaraj SH, Gasser RB, Ranganathan S (2007) A hitchhiker's guide to expressed sequence tag (EST) analysis. Briefings in Bioinformatics 8: 6–21. doi: 10.1093/bib/bbl015
[39]
Yang JH, Li JH, Shao P, Zhou H, Chen YQ, et al. (2011) starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res 39: D202–209. doi: 10.1093/nar/gkq1056
[40]
Zhang YC, Yu Y, Wang CY, Li ZY, Liu Q, et al. (2013) Overexpression of microRNA OsmiR397 improves rice yield by increasing grain size and promoting panicle branching. Nat Biotechnol 31: 848–852. doi: 10.1038/nbt.2646
Wen YZ, Zheng LL, Liao JY, Wang MH, Wei Y, et al. (2011) Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei. Proc Natl Acad Sci U S A 108: 8345–8350. doi: 10.1073/pnas.1103894108
[43]
Zheng LL, Wen YZ, Yang JH, Liao JY, Shao P, et al. (2013) Comparative transcriptome analysis of small noncoding RNAs in different stages of Trypanosoma brucei. RNA 19: 863–875. doi: 10.1261/rna.035683.112
[44]
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, et al. (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Research 33: D121–D124. doi: 10.1093/nar/gki081
[45]
Olson DL, Delen D (2008) Advanced data mining techniques [electronic resource]. Springer. 138.
