Bioinformatic identification and experimental validation of miRNAs from foxtail millet (Setaria italica)

Gene

Volumn 546, Issue 2, 2014, Pages 367-377

  Han, Jun ^a   Xie, Hao ^a   Sun, Qingpeng ^a   Wang, Jun ^b   Lu, Min ^a   Wang, Weixiang ^a   Guo, Erhu ^b   Pan, Jinbao ^a  

^a BEIJING UNIVERSITY OF AGRICULTURE   (China)

^b Shanxi Academy of Agricultural Sciences   (China)

Author keywords

Bioinformat ic identification; Foxtail millet; MicroRNA; QRT PCR; Targets

Indexed keywords

MESSENGER RNA; MICRORNA; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DISEASE RESISTANCE; ENVIRONMENTAL STRESS; EXPRESSED SEQUENCE TAG; FOXTAIL MILLET; GENE FUNCTION; GENE SEQUENCE; GENETIC CONSERVATION; HIGH THROUGHPUT SEQUENCING; NONHUMAN; PLANT DEVELOPMENT; PLANT METABOLISM; PRIORITY JOURNAL; RNA EXTRACTION; RNA FOLDING; SIGNAL TRANSDUCTION; TIME; GENE ONTOLOGY; METABOLISM; PROTEIN EXPRESSION; VALIDATION STUDY;

SETARIA ITALICA;

BIOINFORMATIC IDENTIFICATION; FOXTAIL MILLET; MICRORNA; QRT-PCR; TARGETS;

COMPUTATIONAL BIOLOGY; DISEASE RESISTANCE; GENE EXPRESSION REGULATION, PLANT; MICRORNAS; RNA, PLANT; SETARIA PLANT; SIGNAL TRANSDUCTION;

EID: 84903536645     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.05.050     Document Type: Article

References (57)

1. Adai A., et al. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res. 2005, 15:78-91.
2. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
3. Bennetzen J.L., et al. Reference genome sequence of the model plant Setaria. Nat. Biotechnol. 2012, 30:555-561.
4. Boualem A., et al. MicroRNA166 controls root and nodule development in Medicago truncatula. Plant J. 2008, 54:876-887.
5. Calviño M., Messing J. Discovery of microRNA169 gene copies in genomes of flowering plants through positional information. Genome Biol. Evol. 2013, 5:402-417.
6. Chen L., Wang T., Zhao M., Tian Q., Zhang W.H. Identification of aluminum-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. Planta 2012, 235:375-386.
7. Chi X., et al. Identification and characterization of microRNAs from peanut (Arachis hypogaea L.) by high-throughput sequencing. PLoS One 2011, 6:e27530.
8. Chuck G., Candela H., Hake S. Big impacts by small RNAs in plant development. Curr. Opin. Plant Biol. 2009, 12:81-86.
9. Dai X., Zhao P.X. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 2011, 39:W155-W159.
10. Ding D., et al. MicroRNA transcriptomic analysis of heterosis during maize seed germination. PLoS One 2012, 15:e39578.
11. Dryanova A., Zakharov A., Gulick P.J. Data mining for miRNAs and their targets in the Triticeae. Genome 2008, 51:433-443.
12. Du Z., Zhou X., Ling Y., Zhang Z., Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010, 38:W64-W70.
13. Frazier T.P., Xie F., Freistaedter A., Burklew C.E., Zhang B. Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta 2010, 232:1289-1308.
14. Guddeti S., et al. Molecular evolution of the rice miR395 gene family. Cell Res. 2005, 15:631-638.
15. Hasson A., et al. Evolution and diverse roles of the CUP-SHAPED COTYLEDON genes in Arabidopsis leaf development. Plant Cell 2011, 23:54-68.
16. Jiao Y., Song W., Zhang M., Lai J. Identification of novel maize miRNAs by measuring the precision of precursor processing. BMC Plant Biol. 2011, 15:141.
17. Johnson C., et al. Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res. 2009, 19:1429-1440.
18. Jones-Rhoades M.W., Bartel D.P., Bartel B. MicroRNAS and their regulatory roles in plants. Annu. Rev. Plant Biol. 2006, 57:19-53.
19. Katiyar A., Smita S., Chinnusamy V., Pandey D.M., Bansal K. Identification of miRNAs in sorghum by using bioinformatics approach. Plant Signal. Behav. 2012, 7:246-259.
20. Khraiwesh B., Zhu J.K., Zhu J. Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim. Biophys. Acta 2012, 1819:137-148.
21. Lata C., Gupta S., Prasad M. Foxtail millet: a model crop for genetic and genomic studies in bioenergy grasses. Crit. Rev. Biotechnol. 2013, 33:328-343.
22. Li P., Brutnell T.P. Setaria viridis and Setaria italica, model genetic systems for Panicoid grasses. J. Exp. Bot. 2011, 62:3031-3037.
23. Li A., Mao L. Evolution of plant microRNA gene families. Cell Res. 2007, 17:212-218.
24. Li Y.F., et al. Transcriptome-wide identification of microRNA targets in rice. Plant J. 2010, 62:742-759.
25. Li B., Qin Y., Duan H., Yin W., Xia X. Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. J. Exp. Bot. 2011, 62:3765-3779.
26. Li F., et al. MicroRNA regulation of plant innate immune receptors. Proc. Natl. Acad. Sci. U. S. A. 2011, 109:1790-1795.
27. Ling L.Z., Zhang S.D. Exploring the evolutionary differences of SBP-box genes targeted by miR156 and miR529 in plants. Genetica 2012, 140:317-324.
28. Liu N., Yang J., Guo S., Xu Y., Zhang M. Genome-wide identification and comparative analysis of conserved and novel microRNAs in grafted watermelon by high-throughput sequencing. PLoS One 2013, 8:e57359.
29. Lu C., et al. Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc. Natl. Acad. Sci. U. S. A. 2008, 105:4951-4956.
30. Merchan F., Boualem A., Crespi M., Frugier F. Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins. Genome Biol. 2009, 10:R136.
31. Monavar Feshani A., et al. Identification and validation of Asteraceae miRNAs by the expressed sequence tag analysis. Gene 2012, 493:253-259.
32. Neutelings G., Fénart S., Lucau-Danila A., Hawkins S. Identification and characterization of miRNAs and their potential targets in flax. J. Plant Physiol. 2012, 169:1754-1766.
33. Patanun O., Lertpanyasampatha M., Sojikul P., Viboonjun U., Narangajavana J. Computational identification of microRNAs and their targets in cassava (Manihot esculenta Crantz.). Mol. Biotechnol. 2013, 53:257-269.
34. Shamimuzzaman M., Vodkin L. Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing. BMC Genomics 2012, 13:310.
35. Song X., et al. Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. Plant J. 2012, 69:462-474.
36. Stark A., et al. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 2008, 22:8-13.
37. Sunkar R., Li Y.F., Jagadeeswaran G. Functions of microRNAs in plant stress responses. Trends Plant Sci. 2012, 17:196-203.
38. Unver T., Budak H. Conserved microRNAs and their targets in model grass species Brachypodium distachyon. Planta 2009, 230:659-669.
39. Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009, 136:669-687.
40. Wang J., Yang X., Xu H., Chi X., Zhang M., Hou X. Identification and characterization of microRNAs and their target genes in Brassica oleracea. Gene 2012, 505:300-308.
41. Wang K., Li M., Gao F., Li S., Zhu Y., Yang P. Identification of conserved and novel microRNAs from Liriodendron chinense floral tissues. PLoS One 2012, 7:e44696.
42. Wollmann H., Mica E., Todesco M., Long J.A., Weigel D. On reconciling the interactions between APETALA2, miR172 and AGAMOUS with the ABC model of flower development. Development 2011, 137:3633-3642.
43. Xie K., Wu C., Xiong L. Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiol. 2006, 142:280-293.
44. Xie F., Frazier T.P., Zhang B. Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta 2010, 232:417-434.
45. Xie F., Frazier T.P., Zhang B. Identification, characterization and expression analysis of microRNAs and their targets in the potato (Solanum tuberosum). Gene 2011, 473:8-22.
46. Yao Y., et al. Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol. 2007, 8:R96.
47. Yi F., Xie S., Liu Y., Qi X., Yu J. Genome-wide characterization of microRNA in foxtail millet (Setaria italica). BMC Plant Biol. 2013, 13:212.
48. Yin Z.J., Shen F.F. Identification and characterization of conserved microRNAs and their target genes in wheat (Triticum aestivum). Genet. Mol. Res. 2010, 9:1186-1196.
49. Zhang B., Pan X., Cannon C.H., Cobb G.P., Anderson T.A. Conservation and divergence of plant microRNA genes. Plant J. 2006, 46:243-259.
50. Zhang B.H., Pan X.P., Cox S.B., Cobb G.P., Anderson T.A. Evidence that miRNAs are different from other RNAs. Cell. Mol. Life Sci. 2006, 63:246-254.
51. Zhang B., Pan X., Stellwag E.J. Identification of soybean micro-RNAs and their targets. Planta 2008, 229:161-182.
52. Zhang B., Stellwag E.J., Pan X. Large-scale genome analysis reveals unique features of microRNAs. Gene 2009, 443:100-109.
53. Zhao Y., et al. Combined small RNA and degradome sequencing reveals novel miRNAs and their targets in response to low nitrate availability in maize. Ann. Bot. 2013, 15:633-642.
54. Zhou M., et al. Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L., ssp. Indica). Front. Biol. 2010, 5:67-90.
55. Zhou Z.S., Zeng H.Q., Liu Z.P., Yang Z.M. Genome-wide identification of Medicago truncatula microRNAs and their targets reveals their differential regulation by heavy metal. Plant Cell Environ. 2012, 35:86-99.
56. Zhu Q.H., Helliwell C.A. Regulation of flowering time and floral patterning by miR172. J. Exp. Bot. 2011, 62:487-495.
57. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.