Identification of Conserved and Novel microRNAs from Liriodendron chinense Floral Tissues

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Wang, Kun ^a,b   Li, Ming ^a   Gao, Feng ^b   Li, Shaoqing ^b   Zhu, Yingguo ^b   Yang, Pingfang ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b WUHAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; FLOWER; GENE EXPRESSION; GENE EXPRESSION PROFILING; GYMNOSPERM; LIRIODENDRON; LIRIODENDRON CHINENSE; NONHUMAN; PLANT REPRODUCTION; REGULATORY MECHANISM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

COMPUTATIONAL BIOLOGY; FLOWERS; GENE EXPRESSION REGULATION, PLANT; LIRIODENDRON; MICRORNAS; REAL-TIME POLYMERASE CHAIN REACTION; RNA, PLANT;

GYMNOSPERMAE; LIRIODENDRON CHINENSE; MAGNOLIOPHYTA;

EID: 84866511727     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0044696     Document Type: Article

References (59)

1. Mosher RA, Lewsey MG, Shivaprasad PV, (2010) RNA silencing in plants: Flash report! Silence. 1: 13.
2. Zhang B, Pan X, Cobb G, Anderson T, (2006) Plant microRNA: A small regulatory molecule with big impact. Developmental Biology 289: 3-16.
3. Wu L, Zhou H, Zhang Q, Zhang J, Ni F, et al. (2010) DNA Methylation Mediated by a MicroRNA Pathway. Molecular Cell 38: 465-475.
4. Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
5. Voinnet O, (2009) Origin, Biogenesis, and Activity of Plant MicroRNAs. Cell 136: 669-687.
6. Mallory AC, Vaucheret H, (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38: S31-S36.
7. Millar AA, Gubler F, (2005) The Arabidopsis GAMYB-Like Genes, MYB33 and MYB65, Are MicroRNA-Regulated Genes That Redundantly Facilitate Anther Development. Plant Cell 17: 705-721.
8. Olmedo-Monfil V, Durán-Figueroa N, Arteaga-Vázquez M, Demesa-Arévalo E, Autran D, et al. (2010) Control of female gamete formation by a small RNA pathway in Arabidopsis. Nature 464: 628-632.
9. Kozomara A, Griffiths-Jones S, (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Research 39: D152-D157.
10. Zhao T, Li G, Mi S, Li S, Hannon GJ, et al. (2007) A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes & Development 21: 1190-1203.
11. Liang C, Zhang X, Zou J, Xu D, Su F, et al. (2010) Identification of miRNA from Porphyra yezoensis by High-Throughput Sequencing and Bioinformatics Analysis. PLoS ONE 5: e10698.
12. Arazi T, Talmor-Neiman M, Stav R, Riese M, Huijser P, et al. (2005) Cloning and characterization of micro-RNAs from moss. The Plant Journal 43: 837-848.
13. Lu S, Sun Y-H, Amerson H, Chiang VL, (2007) MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development. The Plant Journal 51: 1077-1098.
14. Yakovlev IA, Fossdal CG, Johnsen Ø, (2010) MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce. New Phytologist 187: 1154-1169.
15. Zhang J, Xu Y, Huan Q, Chong K, (2009) Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genomics 10: 449.
16. Yao Y, Guo G, Ni Z, Sunkar R, Du J, et al. (2007) Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol 8: R96.
17. Zhang B, Pan X, Anderson TA, (2006) Identification of 188 conserved maize microRNAs and their targets. FEBS Lett 580: 3753-3762.
18. Barakat A, Wall K, Leebens-Mack J, Wang YJ, Carlson JE, et al. (2007) Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. The Plant Journal 51: 991-1003.
19. Puzey JR, Kramer EM, (2009) Identification of conserved Aquilegia coerulea microRNAs and their targets. Gene 448: 46-56.
20. Zhao C-Z, Xia H, Frazier T, Yao Y-Y, Bi Y-P, et al. (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biology 10: 3.
21. Li B, Yin W, Xia X, (2009) Identification of microRNAs and their targets from Populus euphratica. Biochemical and Biophysical Research Communications 388: 272-277.
22. Szittya G, Moxon S, Santos DM, Jing R, Fevereiro MP, et al. (2008) High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics 9: 593.
23. 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.
24. Zeng C, Wang W, Zheng Y, Chen X, Bo W, et al. (2009) Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants. Nucleic Acids Research 38: 981-995.
25. Axtell MJ, Snyder JA, Bartel DP, (2007) Common Functions for Diverse Small RNAs of Land Plants. Plant Cell 19: 1750-1769.
26. Kim S, Koh J, Yoo M-J, Kong H, Hu Y, et al. (2005) Expression of floral MADS-box genes in basal angiosperms: implications for the evolution of floral regulators. The Plant Journal 43: 724-744.
27. Cartolano M, Castillo R, Efremova N, Kuckenberg M, Zethof J, et al. (2007) A conserved microRNA module exerts homeotic control over Petunia hybrida and Antirrhinum majus floral organ identity. Nature Genetics 39: 901-905.
28. Axtell MJ, Bartel DP, (2005) Antiquity of microRNAs and their targets in land plants. Plant Cell 17: 1658-1673.
29. Cuperus JT, Fahlgren N, Carrington JC, (2011) Evolution and Functional Diversification of MIRNA Genes. Plant Cell 23: 431-442.
30. Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, et al. (2008) Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Research 18: 571-584.
31. Lu C, (2005) Elucidation of the Small RNA Component of the Transcriptome. Science 309: 1567-1569.
32. Schulte JH, Marschall T, Martin M, Rosenstiel P, Mestdagh P, et al. (2010) Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma. Nucleic Acids Research 38: 5919-5928.
33. Anselmo A, Flori L, Jaffrezic F, Rutigliano T, Cecere M, et al. (2011) Co-Expression of Host and Viral MicroRNAs in Porcine Dendritic Cells Infected by the Pseudorabies Virus. PLoS ONE 6: e17374.
34. Zhang L, Chia J-M, Kumari S, Stein JC, Liu Z, et al. (2009) A Genome-Wide Characterization of MicroRNA Genes in Maize. PLoS Genet 5: e1000716.
35. Gandikota M, Birkenbihl RP, Höhmann S, Cardon GH, Saedler H, et al. (2007) The miRNA156/157 recognition element in the 3′ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. The Plant Journal 49: 683-693.
36. Aukerman MJ, (2003) Regulation of Flowering Time and Floral Organ Identity by a MicroRNA and Its APETALA2-Like Target Genes. Plant Cell 15: 2730-2741.
37. Baker CC, Sieber P, Wellmer F, Meyerowitz EM, (2005) The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis. Curr Biol 15: 303-315.
38. Chen XM, (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022-2025.
39. Wei L, Yan L, Wang T, (2011) Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa. Genome Biology 12: R53.
40. Jung J-H, Park C-M, (2006) MIR166/165 genes exhibit dynamic expression patterns in regulating shoot apical meristem and floral development in Arabidopsis. Planta 225: 1327-1338.
41. Jones-Rhoades MW, Bartel DP, Bartel B, (2006) MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 57: 19-53.
42. Johnson C, Kasprzewska A, Tennessen K, Fernandes J, Nan GL, et al. (2009) Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Research 19: 1429-1440.
43. Song X, Li P, Zhai J, Zhou M, Ma L, et al. (2012) Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. The Plant Journal 69: 462-474.
44. Huang SQ, Guo YH, (2002) Variation of pollination and resource limitation in a low seed-set tree, Liriodendron chinense (Magnoliaceae). Botanical Journal of the Linnean Society 140: 31-38.
45. Kollöffel C, Verkerk BC, (1982) Carbamoyl Phosphate Synthetase Activity from the Cotyledons of Developing and Germinating Pea Seeds. Plant Physiology 69: 143-145.
46. Brady BS, Hyman BC, Lovatt CJ, (2010) Regulation of CPSase, ACTase, and OCTase genes in Medicago truncatula: Implications for carbamoylphosphate synthesis and allocation to pyrimidine and arginine de novo Biosynthesis. Gene 462: 18-25.
47. Kamboj RK, Jackson JF, (1987) Purine Nucleoside Transport in Petunia Pollen Is an Active, Carrier-Mediated System Not Sensitive to Nitrobenzylthioinosine and Not Renewed during Pollen Tube Growth. Plant Physiol 84: 688-691.
48. Chen Z, (2001) A Superfamily of Proteins with Novel Cysteine-Rich Repeats. Plant Physiology 126: 473-476.
49. Ohtake Y, Takahashi T, Komeda Y, (2000) Salicylic Acid Induces the Expression of a Number of Receptor-Like Kinase Genes in Arabidopsis thaliana. Plant and Cell Physiology 41: 1038-1044.
50. Ivanov R, Gaude T, (2009) Endocytosis and Endosomal Regulation of the S-Receptor Kinase during the Self-Incompatibility Response in Brassica oleracea. Plant Cell 21: 2107-2117.
51. Liang H, Carlson J, Leebens-Mack J, Wall P, Mueller L, et al. (2008) An EST database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron. Tree Genetics & Genomes 4: 419-433.
52. Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research.
53. Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, et al. (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Research 36: 3420-3435.
54. Valoczi A, (2004) Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Research 32: e175-e175.
55. Kim SW, Li Z, Moore PS, Monaghan AP, Chang Y, et al. (2010) A sensitive non-radioactive northern blot method to detect small RNAs. Nucleic Acids Research 38: e98-e98.
56. Chen C, (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research 33: e179-e179.
57. Pfaffl MW, (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Research 29: e45.
58. Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, et al. (2011) Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97-100.
59. Zhou L, Liu Y, Liu Z, Kong D, Duan M, et al. (2010) Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. Journal of Experimental Botany 61: 4157-4168.