Identification of ta-siRNAs and Cis-nat-siRNAs in Cassava and Their Roles in Response to Cassava Bacterial Blight

Genomics, Proteomics and Bioinformatics

Volumn 11, Issue 3, 2013, Pages 172-181

  Quintero, Andrés ^a   Pérez Quintero, Alvaro L ^a   López, Camilo ^a  

^a UNIVERSIDAD NACIONAL DE COLOMBIA   (Colombia)

Author keywords

Cassava; Nat siRNA; Natural antisense transcript; Ta siRNA; Xanthomonas

Indexed keywords

COMPLEMENTARY RNA; SMALL INTERFERING RNA;

ARTICLE; BACTERIAL BLIGHT; CASSAVA; CONTROLLED STUDY; GENE LOCUS; GENE SEQUENCE; NONHUMAN; PLANT DISEASE; XANTHOMONAS; XANTHOMONAS AXONOPODIS; XANTHOMONAS MANIHOTIS;

BASE SEQUENCE; CONSERVED SEQUENCE; MANIHOT; MICRORNAS; MOLECULAR SEQUENCE DATA; RNA INTERFERENCE; RNA, PLANT; RNA, SMALL INTERFERING; XANTHOMONAS;

BACTERIA (MICROORGANISMS); MANIHOT ESCULENTA; XANTHOMONAS; XANTHOMONAS AXONOPODIS PV. MANIHOTIS;

EID: 84879780279     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/j.gpb.2013.03.001     Document Type: Article

References (44)

1. Axtell M.J., Westholm J.O., Lai E.C. Vive la difference: biogenesis and evolution of microRNAs in plants and animals. Genome Biol 2011, 12:221.
2. Li L., Liu Y. Diverse small non-coding RNAs in RNA interference pathways. Methods Mol Biol 2011, 764:169-182.
3. 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.
4. Zhang C., Ng D.W., Lu J., Chen Z.J. Roles of target site location and sequence complementarity in trans-acting siRNA formation in Arabidopsis. Plant J 2012, 69:217-226.
5. Montgomery T.A., Yoo S.J., Fahlgren N., Gilbert S.D., Howell M.D., Sullivan C.M., et al. AGO1-miR173 complex initiates phased siRNA formation in plants. Proc Natl Acad Sci U S A 2008, 105:20055-20062.
6. Axtell M.J., Jan C., Rajagopalan R., Bartel D.P. A two-hit trigger for siRNA biogenesis in plants. Cell 2006, 127:565-577.
7. Felippes F.F., Weigel D. Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173. EMBO Rep 2009, 10:264-270.
8. Montgomery T.A., Howell M.D., Cuperus J.T., Li D., Hansen J.E., Alexander A.L., et al. Specificity of argonaute7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 2008, 133:128-141.
9. Marin E., Jouannet V., Herz A., Lokerse A.S., Weijers D., Vaucheret H., et al. MiR390, Arabidopsis TAS3 tasiRNAs, and their auxin response factor targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell 2010, 22:1104-1117.
10. Yoon E.K., Yang J.H., Lim J., Kim S.H., Kim S.K., Lee W.S. Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development. Nucleic Acids Res 2010, 38:1382-1391.
11. Hsieh L.C., Lin S.I., Shih A.C., Chen J.W., Lin W.Y., Tseng C.Y., et al. Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol 2009, 151:2120-2132.
12. Luo Q.J., Mittal A., Jia F., Rock C.D. An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis. Plant Mol Biol 2012, 80:117-129.
13. Jin H., Vacic V., Girke T., Lonardi S., Zhu J.K. Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol Biol 2008, 9:6.
14. Zhou X., Sunkar R., Jin H., Zhu J.K., Zhang W. Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. Genome Res 2009, 19:70-78.
15. Zhang X., Xia J., Lii Y.E., Barrera-Figueroa B.E., Zhou X., Gao S., et al. Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function. Genome Biol 2012, 13:R20.
16. Grant-Downton R., Le Trionnaire G., Schmid R., Rodriguez-Enriquez J., Hafidh S., Mehdi S., et al. MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana. BMC Genomics 2009, 10:643.
17. Kume K., Tsutsumi K., Saitoh Y. TAS1 trans-acting siRNA targets are differentially regulated at low temperature, and TAS1 trans-acting siRNA mediates temperature-controlled At1g51670 expression. Biosci Biotechnol Biochem 2010, 74:1435-1440.
18. Moldovan D., Spriggs A., Yang J., Pogson B.J., Dennis E.S., Wilson I.W. Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis. J Exp Bot 2010, 61:165-177.
19. Ron M., Alandete Saez M., Eshed Williams L., Fletcher J.C., McCormick S. Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis. Genes Dev 2010, 24:1010-1021.
20. Navarro L., Dunoyer P., Jay F., Arnold B., Dharmasiri N., Estelle M., et al. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 2006, 312:436-439.
21. Zhang W., Gao S., Zhou X., Chellappan P., Chen Z., Zhang X., et al. Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks. Plant Mol Biol 2011, 75:93-105.
22. Li Y., Zhang Q., Zhang J., Wu L., Qi Y., Zhou J.M. Identification of microRNAs involved in pathogen-associated molecular pattern-triggered plant innate immunity. Plant Physiol 2010, 152:2222-2231.
23. Li F., Pignatta D., Bendix C., Brunkard J.O., Cohn M.M., Tung J., et al. MicroRNA regulation of plant innate immune receptors. Proc Natl Acad Sci U S A 2012, 109:1790-1795.
24. Zhai J., Jeong D.H., De Paoli E., Park S., Rosen B.D., Li Y., et al. MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev 2011, 25:2540-2553.
25. Katiyar-Agarwal S., Morgan R., Dahlbeck D., Borsani O., Villegas A., Zhu J.K., et al. A pathogen-inducible endogenous siRNA in plant immunity. Proc Natl Acad Sci U S A 2006, 103:18002-18007.
26. López C.E., Bernal A.J. Cassava bacterial blight: using genomics for the elucidation and management of an old problem. Trop Plant Biol 2012, 5:117-126.
27. Perez-Quintero A.L., Quintero A., Urrego O., Vanegas P., Lopez C. Bioinformatic identification of cassava miRNAs differentially expressed in response to infection by Xanthomonas axonopodis pv. manihotis. BMC Plant Biol 2012, 12:29.
28. Dai X., Zhao P.X. PsRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 2011, 39:W155-159.
29. Johnson C., Kasprzewska A., Tennessen K., Fernandes J., Nan G.L., Walbot V., et al. Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res 2009, 19:1429-1440.
30. Chisholm S.T., Coaker G., Day B., Staskawicz B.J. Host-microbe interactions: shaping the evolution of the plant immune response. Cell 2006, 124:803-814.
31. Chen H.M., Li Y.H., Wu S.H. Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis. Proc Natl Acad Sci U S A 2007, 104:3318-3323.
32. Fahlgren N., Montgomery T.A., Howell M.D., Allen E., Dvorak S.K., Alexander A.L., et al. Regulation of auxin response factor3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr Biol 2006, 16:939-944.
33. Yin Z., Li Y., Han X., Shen F. Genome-wide profiling of miRNAs and other small non-coding RNAs in the Verticillium dahliae-inoculated cotton roots. PLoS One 2012, 7:e35765.
34. Gonzalez-Ibeas D., Blanca J., Donaire L., Saladie M., Mascarell-Creus A., Cano-Delgado A., et al. Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing. BMC Genomics 2011, 12:393.
35. Talmor-Neiman M., Stav R., Klipcan L., Buxdorf K., Baulcombe D.C., Arazi T. Identification of trans-acting siRNAs in moss and an RNA-dependent RNA polymerase required for their biogenesis. Plant J 2006, 48:511-521.
36. Fu J., Liu H., Li Y., Yu H., Li X., Xiao J., et al. Manipulating broad-spectrum disease resistance by suppressing pathogen-induced auxin accumulation in rice. Plant Physiol 2011, 155:589-602.
37. Lamesch P., Berardini T.Z., Li D., Swarbreck D., Wilks C., Sasidharan R., et al. The Arabidopsis information resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 2012, 40:D1202-1210.
38. Griffiths-Jones S. miRBase: microRNA sequences and annotation. Curr Protoc Bioinformatics 2010; Chapter 12:Unit 12.9.1-10. http://dx.doi.org/10.1002/0471250953.bi1209s29.
39. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
40. Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9:357-359.
41. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
42. Carver T., Harris S.R., Otto T.D., Berriman M., Parkhill J., McQuillan J.A. BamView: visualizing and interpretation of next-generation sequencing read alignments. Brief Bioinform 2013, 14:203-212.
43. Rajeswaran R., Aregger M., Zvereva A.S., Borah B.K., Gubaeva E.G., Pooggin M.M. Sequencing of RDR6-dependent double-stranded RNAs reveals novel features of plant siRNA biogenesis. Nucleic Acids Res 2012, 40:6241-6254.
44. Rice P., Longden I., Bleasby A. EMBOSS: the european molecular biology open software suite. Trends Genet 2000, 16:276-277.