References

References:

1. Kim,V.N., Han,J. and Siomi,M.C. (2009) Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell. Biol., 10, 126-139.
2. Voinnet,O. (2009) Origin, biogenesis, and activity of plant microRNAs. Cell, 136, 669-687.
3. Jones-Rhoades,M.W., Bartel,D.P. and Bartel,B. (2006) MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol., 57, 19-53.
4. Morozova,O. and Marra,M.A. (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics, 92, 255-264.
5. Simon,S.A., Zhai,J., Nandety,R.S., McCormick,K.P., Zeng,J., Mejia,D. and Meyers,B.C. (2009) Short-read sequencing technologies for transcriptional analyses. Annu. Rev. Plant Biol., 60, 305-333.
6. Griffiths-Jones,S., Saini,H.K., van Dongen,S. and Enright,A.J. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res., 36, D154-158.
7. Zhang,Z., Yu,J., Li,D., Zhang,Z., Liu,F., Zhou,X., Wang,T., Ling,Y. and Su,Z. (2010) PMRD: plant microRNA database. Nucleic Acids Res., 38, D806-813.
8. Huala,E., Dickerman,A.W., Garcia-Hernandez,M., Weems,D., Reiser,L., LaFond,F., Hanley,D., Kiphart,D., Zhuang,M., Huang,W. et al. (2001) The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res., 29, 102-105.
9. Yuan,Q., Ouyang,S., Liu,J., Suh,B., Cheung,F., Sultana,R., Lee,D., Quackenbush,J. and Buell,C.R. (2003) The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res., 31, 229-233.
10. Clark,R.M., Schweikert,G., Toomajian,C., Ossowski,S., Zeller,G., Shinn,P., Warthmann,N., Hu,T.T., Fu,G., Hinds,D.A. et al. (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science, 317, 338-342.
11. Feltus,F.A., Wan,J., Schulze,S.R., Estill,J.C., Jiang,N. and Paterson,A.H. (2004) An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome. Res., 14, 1812-1819.
12. McNally,K.L., Childs,K.L., Bohnert,R., Davidson,R.M., Zhao,K., Ulat,V.J., Zeller,G., Clark,R.M., Hoen,D.R., Bureau,T.E. et al. (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc. Natl. Acad. Sci. USA., 106, 12273-12278.
13. McNally,K.L., Bruskiewich,R., Mackill,D., Buell,C.R., Leach,J.E. and Leung,H. (2006) Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes. Plant Physiol., 141, 26-31.
14. Nakano,M., Nobuta,K., Vemaraju,K., Tej,S.S., Skogen,J.W. and Meyers,B.C. (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res., 34, D731-735.
15. German,M.A., Pillay,M., Jeong,D.H., Hetawal,A., Luo,S., Janardhanan,P., Kannan,V., Rymarquis,L.A., Nobuta,K., German,R. et al. (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat. Biotechnol., 26, 941-946.
16. Zhou,M., Gu,L., Li,P., Song,X., Wei,L., Chen,Z. and Cao,X. (2010) Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica). Front. Biol., 5, 67-90.
17. Li,Y.F., Zheng,Y., Addo-Quaye,C., Zhang,L., Saini,A., Jagadeeswaran,G., Axtell,M.J., Zhang,W. and Sunkar, R. (2010) Transcriptome-wide identification of microRNA targets in rice. Plant J., 10.1111/j.1365-313X.2010.04187.x
18. Addo-Quaye,C., Eshoo,T.W., Bartel,D.P. and Axtell,M.J. (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr. Biol., 18, 758-762.
19. Zhang,G., Guo,G., Hu,X., Zhang,Y., Li,Q., Li,R., Zhuang,R., Lu,Z., He,Z., Fang,X. et al. (March 19, 2010) Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome. Res., 10.1101/gr.100677.109
20. Zhang,Y. (2005) miRU: an automated plant miRNA target prediction server. Nucleic Acids Res., 33, W701-704.
21. Hofacker,I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431.
22. Brenner,S., Johnson,M., Bridgham,J., Golda,G., Lloyd,D.H., Johnson,D., Luo,S., McCurdy,S., Foy,M., Ewan,M. et al. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol., 18, 630-634.
23. Lee,Y., Kim,M., Han,J., Yeom,K.H., Lee,S., Baek,S.H. and Kim,V.N. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J., 23, 4051-4060.
24. Meng,Y., Gou,L., Chen,D., Wu,P. and Chen,M. (July 19, 2010) High-throughput degradome sequencing can be used to gain insights into microRNA precursor metabolism. J. Exp. Bot., 10.1093/jxb/erq209

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