MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are short (19–25 nucleotides) non-coding RNA molecules that have large-scale regulatory effects on development and stress responses in plants. Verticillium wilt is a vascular disease in plants caused by the fungal pathogen Verticillium dahliae. The objective of this study is to investigate the transcriptional profile of miRNAs and other small non-coding RNAs in Verticillium–inoculated cotton roots. Four small RNA libraries were constructed from mocked and infected roots of two cotton cultured species which are with different Verticillium wilt tolerance (‘Hai-7124’, Gossypium barbadense L., a Verticillium-tolerant cultivar, and ‘Yi-11’, Gossypium hirsutum L. a Verticillium-sensitive cultivar). The length distribution of obtained small RNAs was significantly different between libraries. There were a total of 215 miRNA families identified in the two cotton species. Of them 14 were novel miRNAs. There were >65 families with different expression between libraries. We also identified two trans-acting siRNAs and thousands of endogenous siRNA candidates, and hundred of them exhibited altered expression after inoculation of Verticillium. Interesting, many siRNAs were found with a perfect match with retrotransposon sequences, suggested that retrotransposons maybe one of sources for the generation of plant endogenous siRNAs. The profiling of these miRNAs and other small non-coding RNAs lay the foundation for further understanding of small RNAs function in the regulation of Verticillium defence responses in cotton roots.
References
[1]
Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843–854.
[2]
Zhang B, Wang Q, Pan X (2007) MicroRNAs and their regulatory roles in animals and plants. Journal of Cellular Physiology 210: 279–289.
[3]
Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA (2006) Conservation and divergence of plant microRNA genes. Plant J 46: 243–259.
[4]
Vaucheret H (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20: 759–771.
[5]
Vazquez F (2006) Arabidopsis endogenous small RNAs: highways and byways. Trends Plant Sci 11: 460–468.
[6]
Chapman EJ, Carrington JC (2007) Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 8: 884–896.
[7]
Ding SW, Voinnet O (2007) Antiviral immunity directed by small RNAs. Cell 130: 413–426.
[8]
Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, et al. (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312: 436–439.
[9]
Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, et al. (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2: e219.
Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas A Jr, et al. (2006) A pathogen-inducible endogenous siRNA in plant immunity. Proc Natl Acad Sci U S A 103: 18002–18007.
[12]
Katiyar-Agarwal S, Gao S, Vivian-Smith A, Jin H (2007) A novel class of bacteria-induced small RNAs in Arabidopsis. Genes Dev 21: 3123–3134.
[13]
Li H, Deng Y, Wu T, Subramanian S, Yu O (2010) Misexpression of miR482, miR1512, and miR1515 increases soybean nodulation. Plant Physiol 153: 1759–1770.
[14]
Hewezi T, Howe P, Maier TR, Baum TJ (2008) Arabidopsis Small RNAs and Their Targets During Cyst Nematode Parasitism.1622–1634.
[15]
Bhat RG, Subbarao KV (1999) Host Range Specificity in Verticillium dahliae. Phytopathology 89: 1218–1225.
[16]
Ellendorff U, Fradin EF, de Jonge R, Thomma BPHJ (2009) RNA silencing is required for Arabidopsis defence against Verticillium wilt disease.591–602.
[17]
Cai Y, Xiaohong H, Mo J, Sun Q, Yang J, et al. (2009) Molecular research and genetic engineering of resistance to Verticillium wilt in cotton: A review. African Journal of Biotechnology 25: 7363–7372.
[18]
Yang C, Guo W, Li G, Gao F, Lin S, et al. (2008) QTLs mapping for Verticillium wilt resistance at seedling and maturity stages in Gossypium barbadense L. Plant Science 174: 290–298.
[19]
Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Res 15: 336–360.
[20]
Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, et al. (2008) Criteria for annotation of plant MicroRNAs. Plant Cell 20: 3186–3190.
[21]
Zhang BH, Pan XP, Cox SB, Cobb GP, Anderson TA (2006) Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci 63: 246–254.
[22]
Joshi T, Yan Z, Libault M, Jeong DH, Park S, et al. (2010) Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics 11: Suppl 1S14.
[23]
Shen D, Wang S, Chen H, Zhu Q-H, Helliwell C, et al. (2009) Molecular phylogeny of miR390-guided tran-acting siRNA genes (TAS3) in the grass family. Plant Systematics and Evolution 283: 125–132.
[24]
Zhou X, Sunkar R, Jin H, Zhu JK, Zhang W (2009) Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. Genome Res 19: 70–78.
[25]
Le Trionnaire G, Grant-Downton RT, Kourmpetli S, Dickinson HG, Twell D (2011) Small RNA activity and function in angiosperm gametophytes. J Exp Bot 62: 1601–1610.
[26]
Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF (2006) Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res 16: 1252–1261.
[27]
Hawkins JS, Proulx SR, Rapp RA, Wendel JF (2009) Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants.17811–17816.
[28]
Zaki EA (2005) Ty1-copia group retrotransposon families in cultivated cottons G. barbadense L. identified by reverse transcriptase domain analysis. DNA Seq 16: 288–294.
[29]
Tosak Seelanan CL, Brubaker CL, Green JM, Stewart LA, F. CaJ , et al. (1999) Molecular Systematics of Australian Gossypium Section Grandicalyx (Malvaceae). Systematic Botany 24: 183–208.
[30]
Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, et al. (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2: E104.
[31]
Jia Y, Lisch DR, Ohtsu K, Scanlon MJ, Nettleton D, et al. (2009) Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs. PLoS Genet 5: e1000737.
[32]
Chen X, Liu J, Cheng Y, Jia D (2002) HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower. Development 129: 1085–1094.
[33]
Li J, Yang Z, Yu B, Liu J, Chen X (2005) Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr Biol 15: 1501–1507.
[34]
Mallory AC, Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38: SupplS31–36.
[35]
Sunkar R, Chinnusamy V, Zhu J, Zhu JK (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 12: 301–309.
[36]
Zhang B, Pan X, Cobb GP, Anderson TA (2006) Plant microRNA: a small regulatory molecule with big impact. Dev Biol 289: 3–16.
[37]
Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, et al. (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res 18: 1602–1609.
[38]
Subramanian S, Fu Y, Sunkar R, Barbazuk WB, Zhu JK, et al. (2008) Novel and nodulation-regulated microRNAs in soybean roots. BMC Genomics 9: 160.
[39]
Sunkar R, Jagadeeswaran G (2008) In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol 8: 37.
[40]
Axtell MJ, Snyder JA, Bartel DP (2007) Common functions for diverse small RNAs of land plants. Plant Cell 19: 1750–1769.
[41]
Lu S, Sun YH, Shi R, Clark C, Li L, et al. (2005) Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17: 2186–2203.
[42]
Lu S, Sun YH, Chiang VL (2008) Stress-responsive microRNAs in Populus. Plant J 55: 131–151.
[43]
Jagadeeswaran G, Zheng Y, Li YF, Shukla LI, Matts J, et al. (2009) Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families. New Phytol 184: 85–98.
[44]
Allen E, Xie Z, Gustafson AM, Carrington JC (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121: 207–221.
[45]
Krasnikova MS, Milyutina IA, Bobrova VK, Ozerova LV, Troitsky AV, et al. (2009) Novel miR390-dependent transacting siRNA precursors in plants revealed by a PCR-based experimental approach and database analysis. J Biomed Biotechnol 2009: 952304.
[46]
Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, et al. (2006) Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr Biol 16: 939–944.
[47]
Yan Y, Zhang Y, Yang K, Sun Z, Fu Y, et al. (2011) Small RNAs from MITE-derived stem-loop precursors regulate abscisic acid signaling and abiotic stress responses in rice. Plant J 65: 820–828.
[48]
Kuang H, Padmanabhan C, Li F, Kamei A, Bhaskar PB, et al. (2009) Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs.42–56.
[49]
Zuo K, Wang J, Wu W, Chai Y, Sun X, et al. (2005) Identification and characterization of differentially expressed ESTs of Gossypium barbadense infected by Verticillium dahliae with suppression subtractive hybridization. Mol Biol (Mosk) 39: 214–223.
[50]
Carra A, Gambino G, Schubert A (2007) A cetyltrimethylammonium bromide-based method to extract low-molecular-weight RNA from polysaccharide-rich plant tissues. Anal Biochem 360: 318–320.
[51]
Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16: 2001–2019.
[52]
Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713–714.
[53]
Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7: 986–995.
[54]
Cotton EST database website. Available: http://www.ncbi.nlm.nih.gov/nucest/?term？=cotton. Accessed 2011 December 1.
[55]
Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, et al. (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8: 517–527.
[56]
Yin Z, Li C, Han X, Shen F (2008) Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene 414: 60–66.
[57]
Zhang B, Pan X, Wang Q, Cobb GP, Anderson TA (2006) Computational identification of microRNAs and their targets. Computational Biology and Chemistry 30: 395–407.
[58]
BLAST program website. Available: http://blast.ncbi.nlm.nih.gov/. Accessed 2012 Feb 17.
