Genome-Wide Identification and Comparative Analysis of Conserved and Novel MicroRNAs in Grafted Watermelon by High-Throughput Sequencing

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Liu, Na ^a,b   Yang, Jinghua ^a,b   Guo, Shaogui ^c   Xu, Yong ^c   Zhang, Mingfang ^a,b  

^a ZHEJIANG UNIVERSITY   (China)

^b BEIJING HOSPITAL   (China)

^c BEIJING VEGETABLE RESEARCH CENTER   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PRIMER DNA;

ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; GENE EXPRESSION; HIGH THROUGHPUT SEQUENCING; LAGENARIA SICERARIA; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT DEVELOPMENT; PLANT GRAFTING; PLANT GROWTH; PREDICTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RHIZOME; SQUASH; WATERMELON; CITRULLUS; COMPARATIVE STUDY; GENETICS; HIGH THROUGHPUT SCREENING; PLANT GENOME; REAL TIME POLYMERASE CHAIN REACTION;

BASE SEQUENCE; CITRULLUS; DNA PRIMERS; GENOME, PLANT; HIGH-THROUGHPUT SCREENING ASSAYS; MICRORNAS; REAL-TIME POLYMERASE CHAIN REACTION;

EID: 84874497646     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0057359     Document Type: Article

References (63)

1. Davis AR, Perkins-Veazie P, Sakata Y, Lopez-Galarza S, Maroto JV, et al. (2008) Cucurbit grafting. Critical Reviews in Plant Sciences 27: 50-74.
2. Colla G, Rouphael Y, Leonardi C, Bie ZL, (2010) Role of grafting in vegetable crops grown under saline conditions. Scientia Horticulturae 127: 147-155.
3. Lee JM, (1994) Cultivation of Grafted Vegetables.1. Current Status, Grafting Methods, and Benefits. Hortscience 29: 235-239.
4. Venema JH, Dijk BE, Bax JM, van Hasselt PR, Elzenga JTM, (2008) Grafting tomato (Solanum lycopersicum) onto the rootstock of a high-altitude accession of Solanum habrochaites improves suboptimal-temperature tolerance. Environmental and Experimental Botany 63: 359-367.
5. Colla G, Suarez CMC, Cardarelli M, Rouphael Y, (2010) Improving Nitrogen Use Efficiency in Melon by Grafting. Hortscience 45: 559-565.
6. Rouphael Y, Cardarelli M, Colla G, Rea E, (2008) Yield, mineral composition, water relations, and water use efficiency of grafted mini-watermelon plants under deficit irrigation. Hortscience 43: 730-736.
7. Savvas D, Papastavrou D, Ntatsi G, Ropokis A, Olympios C, et al. (2009) Interactive Effects of Grafting and Manganese Supply on Growth, Yield, and Nutrient Uptake by Tomato. Hortscience 44: 1978-1982.
8. Aloni B, Cohen R, Karni L, Aktas H, Edelstein M, (2010) Hormonal signaling in rootstock-scion interactions. Scientia Horticulturae 127: 119-126.
9. Rouphael Y, Schwarz D, Krumbein A, Colla G, (2010) Impact of grafting on product quality of fruit vegetables. Scientia Horticulturae 127: 172-179.
10. Zamore PD, Haley B, (2005) Ribo-gnome: The big world of small RNAs. Science 309: 1519-1524.
11. Zhang BH, Pan XP, Cobb GP, Anderson TA, (2006) Plant microRNA: A small regulatory molecule with big impact. Developmental Biology 289: 3-16.
12. Jones-Rhoades MW, Bartel DP, Bartel B, (2006) MicroRNAs and their regulatory roles in plants. Annual Review of Plant Biology 57: 19-53.
13. Chen XM, (2005) microRNA biogenesis and function in plants. Febs Letters 579: 5923-5931.
14. Baumberger N, Baulcombe DC, (2005) Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits rnicroRNAs and short interfering RNAs. Proceedings of the National Academy of Sciences of the United States of America 102: 11928-11933.
15. Lanet E, Delannoy E, Sormani R, Floris M, Brodersen P, et al. (2009) Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs. Plant Cell 21: 1762-1768.
16. Khraiwesh B, Arif MA, Seumel GI, Ossowski S, Weigel D, et al. (2010) Transcriptional Control of Gene Expression by MicroRNAs. Cell 140: 111-122.
17. Khraiwesh B, Zhu JK, Zhu J, (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta 1819: 137-148.
18. Wu G, Poethig RS, (2006) Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 133: 3539-3547.
19. Wang JW, Schwab R, Czech B, Mica E, Weigel D, (2008) Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell 20: 1231-1243.
20. Chen X, (2009) Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 25: 21-44.
21. Mallory AC, Reinhart BJ, Jones-Rhoades MW, Tang G, Zamore PD, et al. (2004) MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region. EMBO J 23: 3356-3364.
22. Dalmay T, (2006) Short RNAs in environmental adaptation. Proc Biol Sci 273: 1579-1585.
23. Sunkar R, Zhu JK, (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16: 2001-2019.
24. Sunkar R, Kapoor A, Zhu JK, (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell 18: 2051-2065.
25. Allen E, Xie ZX, Gustafson AM, Sung GH, Spatafora JW, et al. (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nature Genetics 36: 1282-1290.
26. Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, et al. (2009) Computational and analytical framework for small RNA profiling by high-throughput sequencing. Rna-a Publication of the Rna Society 15: 992-1002.
27. Creighton CJ, Reid JG, Gunaratne PH, (2009) Expression profiling of microRNAs by deep sequencing. Brief Bioinform 10: 490-497.
28. Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, et al. (2010) Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 16: 991-1006.
29. Martinez G, Forment J, Llave C, Pallas V, Gomez G, (2011) High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs. PLoS One 6: e19523.
30. Lough TJ, Lucas WJ, (2006) Integrative plant biology: Role of phloem long-distance macromolecular trafficking. Annual Review of Plant Biology 57: 203-232.
31. Buhtz A, Pieritz J, Springer F, Kehr J, (2010) Phloem small RNAs, nutrient stress responses, and systemic mobility. BMC Plant Biol 10: 64.
32. Lin SI, Chiang SF, Lin WY, Chen JW, Tseng CY, et al. (2008) Regulatory network of microRNA399 and PHO2 by systemic signaling. Plant Physiol 147: 732-746.
33. Harada T, (2010) Grafting and RNA transport via phloem tissue in horticultural plants. Scientia Horticulturae 125: 545-550.
34. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP, (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20: 3407-3425.
35. Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, et al. (2008) A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res 18: 1456-1465.
36. Song C, Wang C, Zhang C, Korir NK, Yu H, et al. (2010) Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics 11: 431.
37. Chen XM, (2009) Small RNAs and Their Roles in Plant Development. Annual Review of Cell and Developmental Biology 25: 21-44.
38. Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, et al. (2003) Control of leaf morphogenesis by microRNAs. Nature 425: 257-263.
39. 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.
40. Sunkar R, Jagadeeswaran G, (2008) In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol 8: 37.
41. Axtell MJ, Snyder JA, Bartel DP, (2007) Common functions for diverse small RNAs of land plants. Plant Cell 19: 1750-1769.
42. Axtell MJ, Bowman JL, (2008) Evolution of plant microRNAs and their targets. Trends in Plant Science 13: 343-349.
43. Bonnet E, Wuyts J, Rouze P, Van de Peer Y, (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20: 2911-2917.
44. Liu HH, Tian X, Li YJ, Wu CA, Zheng CC, (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. Rna-a Publication of the Rna Society 14: 836-843.
45. Zhou LG, Liu YH, Liu ZC, Kong DY, Duan M, et al. (2010) Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. Journal of Experimental Botany 61: 4157-4168.
46. Zhu C, Ding Y, Liu H, (2011) MiR398 and plant stress responses. Physiol Plant 143: 1-9.
47. Allen RS, Li J, Stahle MI, Dubroue A, Gubler F, et al. (2007) Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family. Proc Natl Acad Sci U S A 104: 16371-16376.
48. Chen XM, (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022-2025.
49. Jung JH, Seo YH, Seo PJ, Reyes JL, Yun J, et al. (2007) The GIGANTEA-regulated MicroRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. Plant Cell 19: 2736-2748.
50. Wang JW, Schwab R, Czech B, Mica E, Weigel D, (2008) Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell 20: 1231-1243.
51. Jaeger KE, Wigge PA, (2007) FT protein acts as a long-range signal in Arabidopsis. Current Biology 17: 1050-1054.
52. Palauqui JC, Elmayan T, Pollien JM, Vaucheret H, (1998) Systemic acquired silencing: transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions (vol 16, pg 4738, 1997). Embo Journal 17: 2137-2137.
53. Ruiz-Medrano R, Xoconostle-Cazares B, Lucas WJ, (2001) The phloem as a conduit for inter-organ communication. Current Opinion in Plant Biology 4: 202-209.
54. Yoo BC, Kragler F, Varkonyi-Gasic E, Haywood V, Archer-Evans S, et al. (2004) A systemic small RNA signaling system in plants. Plant Cell 16: 1979-2000.
55. Buhtz A, Springer F, Chappell L, Baulcombe DC, Kehr J, (2008) Identification and characterization of small RNAs from the phloem of Brassica napus. Plant Journal 53: 739-749.
56. Rodriguez-Medina C, Atkins CA, Mann AJ, Jordan ME, Smith PMC (2011) Macromolecular composition of phloem exudate from white lupin (Lupinus albus L.). Bmc Plant Biology 11.
57. Marin-Gonzalez E, Suarez-Lopez P, (2012) "And yet it moves": Cell-to-cell and long-distance signaling by plant microRNAs. Plant Science 196: 18-30.
58. Pant BD, Buhtz A, Kehr J, Scheible WR, (2008) MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. Plant Journal 53: 731-738.
59. Buhtz A, Pieritz J, Springer F, Kehr J (2010) Phloem small RNAs, nutrient stress responses, and systemic mobility. Bmc Plant Biology 10.
60. Martin A, Adam H, Diaz-Mendoza M, Zurczak M, Gonzalez-Schain ND, et al. (2009) Graft-transmissible induction of potato tuberization by the microRNA miR172. Development 136: 2873-2881.
61. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, et al. (2008) Criteria for Annotation of Plant MicroRNAs. Plant Cell 20: 3186-3190.
62. Chen CF, Ridzon DA, Broomer AJ, Zhou ZH, Lee DH,et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research 33.
63. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408.