Identification and characterization of novel and conserved microRNAs in radish (Raphanus sativus L.) using high-throughput sequencing

Plant Science

Volumn 201-202, Issue 1, 2013, Pages 108-114

  Xu, Liang ^a   Wang, Yan ^a   Xu, Yuanyuan ^a   Wang, Liangju ^a   Zhai, Lulu ^a   Zhu, Xianwen ^b   Gong, Yiqin ^a   Ye, Shan ^a   Liu, Liwang ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b NORTH DAKOTA STATE UNIVERSITY   (United States)

Author keywords

High throughput sequencing; MicroRNAs; QRT PCR; Radish (Raphanus sativus L); Target gene

Indexed keywords

MICRORNA; PLANT RNA; TRANSCRIPTOME;

ARTICLE; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; METHODOLOGY; NUCLEOTIDE SEQUENCE; PLANT GENE; PLANT ROOT; RAPHANUS; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SPECIES DIFFERENCE;

CONSERVED SEQUENCE; GENE LIBRARY; GENES, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICRORNAS; PLANT ROOTS; RAPHANUS; REAL-TIME POLYMERASE CHAIN REACTION; RNA, PLANT; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SPECIES SPECIFICITY; TRANSCRIPTOME;

ARABIDOPSIS; RAPHANUS SATIVUS;

EID: 84871980450     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2012.11.010     Document Type: Article

References (46)

1. Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009, 136:669-687.
2. Li Y.F., Zheng Y., Addo-Quaye C., Zhang L., Saini A., Jagadeeswaran G., Axtell M.J., Zhang W., Sunkar R. Transcriptome-wide identification of microRNA targets in rice. Plant J. 2010, 62:742-759.
3. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
4. Martínez G., Forment J., Llave C., Pallás V., Gómez G. High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs. PLoS ONE 2011, 6:e19523.
5. Xie F.L., Frazier T.P., Zhang B.H. Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta 2010, 232:417-434.
6. Chuck G., Candela H., Hake S. Big impacts by small RNAs in plant development. Curr. Opin. Plant Biol. 2009, 12:81-86.
7. Ruiz-Ferrer V., Voinnet O. Roles of plant small RNAs in biotic stress responses. Annu. Rev. Plant Biol. 2009, 60:485-510.
8. Li B.S., Qin Y.R., Duan H., Yin W.L., Xia X.L. Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. J. Exp. Bot. 2011, 62:3765-3779.
9. Wang C., Han J., Liu C.H., Nicholas K.K., Kayesh E., Shangguan L.F., Li X.Y., Fang J.G. Identification of microRNAs from Amur grape (vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics. BMC Genomics 2012, 13:122.
10. Zhang B.H., Pan X.P., Wang Q.L., Cobb G.P., Anderson T.A. Identification and characterization of new plant microRNAs using EST analysis. Cell Res. 2005, 15:336-360.
11. Mao W.H., Li Z.Y., Xia X.J., Li Y.D., Yu Q.J. A combined approach of high-throughput sequencing and degradome analysis reveals tissue specific expression of microRNAs and their targets in cucumber. PLoS ONE 2012, 7:e33040.
12. Fahlgren N., Howell M.D., Kasschau K.D., Chapman E.J., Sullivan C.M., Cumbie J.S., Givan S.A., Law T.F., Grant S.R., Dangl J.L., Carrington J.C. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS ONE 2007, 2:e219.
13. Sunkar R., Zhou X., Zheng Y., Zhang W., Zhu J.K. Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol. 2008, 8:25.
14. Wei L.Q., Yan L.F., Wang T. Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa. Genome Biol. 2011, 12:R53.
15. Chen L., Ren Y.Y., Zhang Y.Y., Xu J.C., Zhang Z.Y., Wang Y.W. Genome-wide profiling of novel and conserved Populus microRNAs involved in pathogen stress response by deep sequencing. Planta 2012, 235:873-883.
16. 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.
17. Song Q.X., Liu Y.F., Hu X.Y., Zhang W.K., Ma B., Chen S.Y., Zhang J.S. Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC Plant Biol. 2011, 11:5.
18. Zhang L., Chia J.M., Kumari S., Stein J.C., Liu Z., Narechania A., Maher C.A., Guill K., McMullen M.D., Ware D.A. A genome-wide characterization of microRNA genes in maize. PLoS Genet. 2009, 5:e1000716.
19. Ruan M.B., Zhao Y.T., Meng Z.H., Wang X.J., Yang W.C. Conserved miRNA analysis in Gossypium hirsutum through small RNA sequencing. Genomics 2009, 94:263-268.
20. Chi X.Y., Yang Q.L., Chen X.P., Wang J.Y., Pan L.J., Chen M.G., Yang Z., He Y.N., Liang X.Q., Yu S.L., Identification Characterization of microRNAs from peanut (Arachis hypogaea L.) by high-throughput sequencing. PLoS ONE 2011, 6:e27530.
21. Wei B., Cai T., Zhang R., Li A., Huo N., Li S., Gu Y.Q., Vogel J., Jia J., Qi Y., Mao L. Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Funct. Integr. Genomics 2009, 9:4991.
22. Wang Z.J., Huang J.Q., Huang Y.J., Li Z., Zheng B.S. Discovery and profiling of novel and conserved microRNAs during flower development in Carya cathayensis via deep sequencing. Planta 2012, 236:613-621.
23. Song C.N., Wang C., Zhang C.Q., Nicholas K.K., Yu H.P., Ma Z.Q., Fang J.G. Deep sequencing discovery of new and conserved microRNAs in trifoliate orange (Citrus trifoliate). BMC Genomics 2010, 11:431.
24. Ge A.J., Shangguan L.F., Zhang X., Dong Q.H., Han J., Liu H., Wang X.C., Fang J.G. Deep sequencing discovery of novel and conserved microRNAs in strawberry (Fragaria×ananassa). Physiol. Plant. 2012, 10.1111/j. 1399-3054.2012.01713.x.
25. Xu M.Y., Dong Y., Zhang Q.X., Zhang L., Luo Y.Z., Sun J., Fan Y.L., Wang L. Identification of miRNAs and their targets from Brassica napus by high-throughput sequencing and degradome analysis. BMC Genomics 2012, 13:421.
26. Wang F.D., Li L.B., Liu L.F., Li H.Y., Zhang Y.H., Yao Y.Y., Ni Z.F., Gao J.W. High-throughput sequencing discovery of conserved and novel microRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Mol. Genet. Genomics 2012, 287:555-563.
27. Moxon S., Jing R., Szittya G., Schwach F., Rusholme-Pilcher R.L., Moulton V., Dalmay T. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res. 2008, 18:1602-1609.
28. Molnár A., Schwach F., Studholme D.J., Thuenemann E., Baulcombe D. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 2007, 447:1126-1129.
29. Parchman T.L., Geist K.S., Grahnen J.A., Benkman C.W., Buerkle C.A. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 2010, 11:180.
30. Delsenya M., Hanb B., Hsing Y.I. High throughput DNA sequencing: the new sequencing revolution. Plant Sci. 2010, 179:407-422.
31. Morozova O., Marra M.A. Applications of next-generation sequencing technologies in functional genomics. Genomics 2008, 92:255-264.
32. Muvva C., Tewari L., Aruna K., Ranjit P., Zahoorullah S.M.D., Matheen K.A., Veeramachaneni M.D.H. In silico identification of miRNAs and their targets from the expressed sequence tags of Raphanus sativus. Bioinformation 2012, 8:98-103.
33. Hafner M., Landgraf P., Ludwig J., Rice A., Ojo T., Lin C., Holoch D., Lim C., Tuschl T. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 2008, 44:3-12.
34. Li R., Li Y., Kristiansen K., Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24:713-714.
35. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W. GenBank. Nucleic Acids Res. 2011, 39:D32-D37.
36. Gardner P.P., Daub J., Tate J.G., Nawrocki E.P., Kolbe D.L., Lindgreen S., Wilkinson A.C., Finn R.D., Griffiths-Jones S., Eddy S.R., Bateman A. Rfam: updates to the RNA families database. Nucleic Acids Res. 2009, 37:D136-D140.
37. Meyers B.C., Axtell M.J., Bartel B., Bartel D.P., Baulcombe D., Bowman J.L., Cao X., Carrington J.C., Chen X., Green P.J., Griffiths-Jones S., Jacobsen S.E., Mallory A.C., Martienssen R.A., Poethig R.S., Qi Y., Vaucheret H., Voinnet O., Watanabe Y., Weigel D., Zhu J.K. Criteria for annotation of plant microRNAs. Plant Cell 2008, 20:3186-3190.
38. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.
39. Ambros V., Bartel B., Bartel D.P., Burge C.B., Carrington J.C., Chen X., Dreyfuss G., Eddy S.R., Griffiths-Jones S., Marshall M., Matzke M., Ruvkun G., Tuschl T. A uniform system for microRNA annotation. RNA 2003, 9:277-279.
40. Allen E., Xie Z., Gustafson A.M., Carrington J.C. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005, 121:207-221.
41. Schwab R., Palatnik J.F., Riester M., Schommer C., Schmid M., Weigel D. Specific effects of microRNAs on the plant transcriptome. Dev. Cell 2005, 8:517-527.
42. Conesa A., Götz S., Garcia-Gömez J.M., Terol J., Talón M., Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21:3674-3676.
43. Wu G., Park M.Y., Conway S.R., Wang J.W., Weigel D., Poethig R.S. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 2009, 138:750-759.
44. Ludwig-Müller Auxin conjugates: their role for plant development and in the evolution of land plants. J. Exp. Bot. 2011, 62:1757-1773.
45. Wu M.F., Tian Q., Reed J.W. Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 2006, 133:4211-4218.
46. Zhao J.P., Diao S., Zhang B.Y., Niu B.Q., Wang Q.L., Wan X.C., Luo Y.Q. Phylogenetic analysis and molecular evolution patterns in the miR482-miR1448 polycistron of Populus L. PLoS ONE 2012, 7:e47811.