Identification and comparative profiling of micrornas in wild-type xanthoceras sorbifolia and its double flower mutant

Genes and Genomics

Volumn 34, Issue 5, 2012, Pages 561-568

  Ao, Yan ^a,b   Wang, Yanwei ^a   Chen, Lei ^a   Wang, Tao ^c   Yu, Haiyan ^c   Zhang, Zhixiang ^a  

^a BEIJING FORESTRY UNIVERSITY   (China)

^b National Energy R D Center for Biomass (NECB)   (China)

^c RESEARCH INSTITUTE OF FORESTRY   (China)

Author keywords

Double flower; MicroRNA; QRT PCR; Simple flower; Xanthoceras sorbifolia

Indexed keywords

CELECOXIB; MICRORNA; MICRORNA 162; MICRORNA 164A; MICRORNA 164B; MICRORNA 166G; MICRORNA 319; MICRORNA 395A; MICRORNA 395B; MICRORNA 396; MICRORNA 397; MICRORNA 479; MICRORNA 482; MICRORNA 530; MICRORNA 535; MICRORNA 827; RIBOSOME RNA; RNA; RNA DIRECTED DNA POLYMERASE; RNA LIGASE; SMALL NUCLEAR RNA; SMALL NUCLEOLAR RNA; TRANSFER RNA; UNCLASSIFIED DRUG;

ARTICLE; BIOFUEL PRODUCTION; BUD; CONTROLLED STUDY; DNA LIBRARY; ENERGY CROP; FLOWER; FLOWER DEVELOPMENT; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE TARGETING; GENETIC IDENTIFICATION; NONHUMAN; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RNA ISOLATION; SEQUENCE ANALYSIS; WILD TYPE; XANTHOCERAS SORBIFOLIA;

EID: 84867236672     PISSN: 19769571     EISSN: 20929293     Source Type: Journal    
DOI: 10.1007/s13258-012-0065-1     Document Type: Article

References (47)

1. Aida M, Ishida T, Fukaki H, Fujisawa H, and Tasaka M (1997) Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell 9: 841-857.
2. Allen RS, Li J, Stahle MI, Dubroue A, Gubler F, and Millar AA (2007) Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family. Proc. Natl. Acad. Sci. USA 104: 16371-16376.
3. APGIII (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot. J. Linn. Soc. 161: 105-121.
4. Aukerman MJ and Sakai H (2003) Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15: 2730-2741.
5. Cartolano M, Castillo R, Efremova N, Kuckenberg M, Zethof J, Gerats T, Schwarz-Sommer Z, and Vandenbussche M (2007) A conserved microRNA module exerts homeotic control over Petunia hybrida and Antirrhinum majus floral organ identity. Nat. Genet. 39: 901-905.
6. Chen X (2005) MicroRNA biogenesis and function in plants. FEBS Lett. 579: 5923-5931.
7. Dai X and Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucl. Acids Res. 39: W155-159.
8. Dolgosheina EV, Morin RD, Aksay G, Sahinalp SC, Magrini V, Mardis ER, Mattsson J, and Unrau PJ (2008) Conifers have a unique small RNA silencing signature. RNA 14: 1508-1515.
9. Gandikota M, Birkenbihl RP, Hohmann S, Cardon GH, Saedler H, and Huijser P (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. Plant J. 49: 683-693.
10. Gao SM, Ma K, Du XH, and Li FL (2002) Advances in research on Xanthoceras sorbifolia. Chin. Bull. Bot.(English edn) 19: 296-301.
11. Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, Lin C, Holoch D, Lim C, and Tuschl T (2008) Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 44: 3-12.
12. Hsieh LC, Lin SI, Shih AC, Chen JW, Lin WY, Tseng CY, Li WH, and Chiou TJ (2009) Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol. 151: 2120-2132.
13. Jones-Rhoades MW and Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14: 787-799.
14. Juarez MT, Kui JS, Thomas J, Heller BA, and Timmermans MC (2004) microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature 428: 84-88.
15. Jung JH and Park CM (2007) MIR166/165 genes exhibit dynamic expression patterns in regulating shoot apical meristem and floral development in Arabidopsis. Planta 225: 1327-1338.
16. Kozomara A and Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucl. Acids Res. 39: D152-157.
17. Kwak PB, Wang QQ, Chen XS, Qiu CX, and Yang ZM (2009) Enrichment of a set of microRNAs during the cotton fiber development. BMC Genomics 10: 457.
18. Laufs P, Peaucelle A, Morin H, and Traas J (2004) MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development 131: 4311-4322.
19. Lauter N, Kampani A, Carlson S, Goebel M, and Moose SP (2005) microRNA172 down-regulates glossy15 to promote vegetative phase change in maize. Proc. Natl. Acad. Sci. USA 102: 9412-9417.
20. Li R, Li Y, Kristiansen K, and Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-714.
21. Liang G, Yang F, and Yu D (2010) MicroRNA395 mediates regulation of sulfate accumulation and allocation in Arabidopsis thaliana. Plant J. 62: 1046-1057.
22. Liu HH, Tian X, Li YJ, Wu CA, and Zheng CC (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14: 836-843.
23. Mallory AC, Reinhart BJ, Jones-Rhoades MW, Tang G, Zamore PD, Barton MK, and Bartel DP (2004) MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region. EMBO J. 23: 3356-3364.
24. Mathews DH, Sabina J, Zuker M, and Turner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940.
25. McHale NA and Koning RE (2004) MicroRNA-directed cleavage of Nicotiana sylvestris PHAVOLUTA mRNA regulates the vascular cambium and structure of apical meristems. Plant Cell 16: 1730-1740.
26. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, et al. (2008) Criteria for annotation of plant MicroRNAs. Plant Cell 20: 3186-3190.
27. Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, Mardis ER, Sahinalp SC, and Unrau PJ (2008) Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res. 18: 571-584.
28. Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, Moulton V, and Dalmay T (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res. 18: 1602-1609.
29. Nag A and Jack T (2010) Sculpting the flower; the role of microRNAs in flower development. Curr. Top. Dev. Biol. 91: 349-378.
30. Nag A, King S, and Jack T (2009) miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis. Proc. Natl. Acad. Sci. USA 106: 22534-22539.
31. Nagpal P, Ellis CM, Weber H, Ploense SE, Barkawi LS, Guilfoyle TJ, Hagen G, Alonso JM, Cohen JD, Farmer EE, et al. (2005) Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development 132: 4107-4118.
32. Peng WX, Li FL, and Wang BZ (1999) A Discovery of Homeotic Mutant of Xanthoceras sorbifolia Bunge. J. Beijing For. Uni. (English edn) 21: 92-94.
33. Rajagopalan R, Vaucheret H, Trejo J, and Bartel DP (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev. 20: 3407-3425.
34. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, and Bartel DP (2002) Prediction of plant microRNA targets. Cell 110: 513-520.
35. Ruan MB, Zhao YT, Meng ZH, Wang XJ, and Yang WC (2009) Conserved miRNA analysis in Gossypium hirsutum through small RNA sequencing. Genomics 94: 263-268.
36. Rubio-Somoza I and Weigel D (2011) MicroRNA networks and developmental plasticity in plants. Trends Plant Sci. 16: 258-264.
37. Schwarz S, Grande AV, Bujdoso N, Saedler H, and Huijser P (2008) The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis. Plant Mol. Biol. 67: 183-195.
38. Shao HB and Chu LY (2008) Resource evaluation of typical energy plants and possible functional zone planning in China. Biomass and Bioenergy 32: 283-288.
39. Shi R and Chiang VL (2005) Facile means for quantifying microRNA expression by real-time PCR. Biotechniques 39: 519-525.
40. Szittya G, Moxon S, Santos DM, Jing R, Fevereiro MP, Moulton V, and Dalmay T (2008) High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics 9: 593.
41. Wang JW, Czech B, and Weigel D (2009) miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell 138: 738-749.
42. Wang QL and Li ZH (2007) The functions of microRNAs in plants. Front Biosci. 12: 3975-3982.
43. Wu G, Park MY, Conway SR, Wang JW, Weigel D, and Poethig RS (2009) The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 138: 750-759.
44. Yu HY and Zhou SJ (2009) Preparation of biodiesel from Xanthoceras sorblfolia Bunge. seed oil. China Oils and Fats (English edn) 1: 43-45.
45. Zhang B, Pan X, Cobb GP, and Anderson TA (2006) Plant microRNA: a small regulatory molecule with big impact. Dev. Biol. 289: 3-16.
46. Zhang L, Zheng Y, Jagadeeswaran G, Li Y, Gowdu K, and Sunkar R (2011) Identification and temporal expression analysis of conserved and novel microRNAs in Sorghum. Genomics 98: 460-468.
47. Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP, Li AQ, Li MJ, Li CS, Zhang BH, and Wang XJ (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol. 10: 3.