Catalog of Erycina pusilla miRNA and categorization of reproductive phase-related miRNAs and their target gene families

详细信息    查看全文

• 作者：Choun-Sea Lin (1)
  Jeremy J. W. Chen (2)
  Yao-Ting Huang (3)
  Chen-Tran Hsu (1)
  Hsiang-Chia Lu (4)
  Ming-Lun Chou (5)
  Li-Chi Chen (2)
  Chia-I Ou (3)
  Der-Chih Liao (1)
  Ysuan-Yu Yeh (6)
  Song-Bing Chang (6)
  Su-Chen Shen (7)
  Fu-Huei Wu (1)
  Ming-Che Shih (1)
  Ming-Tsair Chan (1) (4)
  
• 关键词：Orchid ; Micro RNA ; Transcriptome ; Phase transition ; sRNA library ; AP2 family ; SPL family
• 刊名：Plant Molecular Biology
• 出版年：2013
• 出版时间：2 - May 2013
• 年：2013
• 卷：82
• 期：1
• 页码：193-204
• 全文大小：775KB
• 参考文献：1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-10
  2. An FM, Hsiao SR, Chan MT (2011) Sequencing-based approaches reveal low ambient temperature-responsive and tissue-specific microRNAs in phalaenopsis orchid. PLoS ONE 6:e18937 CrossRef
  3. Aukerman MJ, Sakai H (2003) Regulation of flowering time and floral organ identity by a MicroRNA and its / APETALA2-like target genes. Plant Cell 15:2730-741 CrossRef
  4. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:W202–W208 CrossRef
  5. Birkenbihl RP, Jach G, Saedler H, Huijser P (2005) Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains. J Mol Biol 352:585-96 CrossRef
  6. Calderon-Villalobos LIA, Kuhnle C, Dohmann EMN, Li H, Bevan M, Schwechheimer C (2005) The evolutionarily conserved TOUGH protein is required for proper development of / Arabidopsis thaliana. Plant Cell 17:2473-485 CrossRef
  7. Chang WC, Lee TY, Huang HD, Huang HY, Pan RL (2008) PlantPAN: plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. BMC Genomics 9:561 CrossRef
  8. Chase MW, Hanson L, Albert VA, Whitten WM, Williams NH (2005) Life history evolution and genome size in subtribe Oncidiinae (Orchidaceae). Ann Bot 95:191-99 CrossRef
  9. Chen X (2004) A MicroRNA as a translational repressor of / APETALA2 in / Arabidopsis flower development. Science 303:2022-025 CrossRef
  10. Chen X (2009) Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 25:21-4 CrossRef
  11. Chi X, Yang Q, Chen X, Wang J, Pan L, Chen M, Yang Z, He Y, Liang X, Yu S (2011) Identification and characterization of microRNAs from peanut ( / Arachis hypogaea L.) by high-throughput sequencing. PLoS ONE 6:e27530 CrossRef
  12. Chiu YT, Lin CS, Chang C (2011) / In vitro fruting and seed production in / Erycina Pusilla (L.) N. H. Willams and M. W. Chase. Propag Ornam Plants 11:131-36
  13. Chou ML, Shih MC, Chan MT, Liao SY, Hsu CT, Haung YT, Chen JJ, Liao DC, Wu FH, Lin CS (2013) Global transcriptome analysis and identification of a CONSTANS-like gene family in the orchid / Erycina pusilla. Planta. doi:10.1007/s00425-013-1850-z
  14. Chuck G, Cigan AM, Saeteurn K, Hake S (2007) The heterochronic maize mutant / Corngrass1 results from overexpression of a tandem microRNA. Nat Genet 39:544-49 CrossRef
  15. Cuperus JT, Fahlgren N, Carrington JC (2011) Evolution and functional diversification of MIRNA genes. Plant Cell 23:431-42 CrossRef
  16. Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:W155–W159 CrossRef
  17. Felix LP, Guerra M (1999) Chromosome analysis in / Psygmorchis pusilla (L.) Dodson and Dressler: the smallest chromosome number known in Orchidaceae. Caryologia 52:165-68 CrossRef
  18. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158 CrossRef
  19. Hsu CT, Liao DC, Wu FH, Liu NT, Shen SC, Chou SJ, Tung SY, Yang CH, Chan MT, Lin CS (2011) Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of / Oncidium Gower Ramsey. BMC Plant Biol 11:60 CrossRef
  20. Hunter C, Poethig RS (2003) miSSING LINKS: miRNAs and plant development. Curr Opin Genet Dev 13:372-78 CrossRef
  21. Jamalkandi SA, Masoudi-Nejad A (2009) Reconstruction of / Arabidopsis thaliana fully integrated small RNA pathway. Funct Integr Genomics 9:419-32 CrossRef
  22. Karimi M, Inze D, Depicker A (2002) GATEWAY vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci 7:193-95 CrossRef
  23. Kim S, Soltis PS, Wall K, Soltis DE (2006) Phylogeny and domain evolution in the / APETALA2- / like gene family. Mol Biol Evol 23:107-20 CrossRef
  24. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-20 CrossRef
  25. Klein J, Saedler H, Huijser P (1996) A new family of DNA binding proteins includes putative transcriptional regulators of the / Antirrhinum majus floral meristem identity gene / SQUAMOSA. Mol Gen Genet 250:7-6
  26. Lee DY, Lee J, Moon S, Park SY, An G (2007) The rice heterochronic gene / SUPERNUMERARY BRACT regulates the transition from spikelet meristem to floral meristem. Plant J 49:64-8 CrossRef
  27. Ling LZ, Zhang SD (2012) Unraveling the distribution and evolution of miR156-targeted / SPLs in plants by phylogenetic analysis. Plant Div Res 34:33-6
  28. Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of / Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297:2053-056 CrossRef
  29. Mathieu J, Yant LJ, Murdter F, Kuttner F, Schmid M (2009) Repression of flowering by the miR172 target / SMZ. PLoS Biol 7:e1000148 CrossRef
  30. Miura K, Ikeda M, Matsubara A, Song XJ, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M (2010) / OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet 42:545-49 CrossRef
  31. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH (2005) InterPro, progress and status in 2005. Nucleic Acids Res 33:D201–D205 CrossRef
  32. Nakano T, Suzuki K, Fujimura T, Shinshi H (2006) Genome-wide analysis of the / ERF gene family in Arabidopsis and rice. Plant Physiol 140:411-32 CrossRef
  33. Pan IC, Liao DC, Wu FH, Daniell H, Singh ND, Chang C, Shih MC, Chan MT, Lin CS (2012) Complete chloroplast genome sequence of an orchid model plant candidate: / Erycina pusilla apply in tropical / Oncidium breeding. PLoS ONE 7:e34738 CrossRef
  34. Pelaez P, Trejo MS, Iniguez LP, Estrada-Navarrete G, Covarrubias AA, Reyes JL, Sanchez F (2012) Identification and characterization of microRNAs in / Phaseolus vulgaris by high-throughput sequencing. BMC Genomics 13:83 CrossRef
  35. Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu G (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105-110 CrossRef
  36. Shigyo M, Ito M (2004) Analysis of gymnosperm two-AP2-domain-containing genes. Dev Genes Evol 214:105-14 CrossRef
  37. Shigyo M, Hasebe M, Ito M (2006) Molecular evolution of the / AP2 subfamily. Gene 366:256-65 CrossRef
  38. Su CL, Chao YT, Yen SH, Chen CY, Chen WC, Chang YC, Shih MC (2013) Orchidstra: an integrated orchid functional genomics database. Plant Cell Physiol 54:e11 CrossRef
  39. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-599 CrossRef
  40. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-680 CrossRef
  41. Unte US, Sorensen AM, Pesaresi P, Gandikota M, Leister D, Saedler H, Huijser P (2003) / SPL8, an SBP-box gene that affects pollen sac development in Arabidopsis. Plant Cell 15:1009-019 CrossRef
  42. Varkonyi-Gasic E, Lough RH, Moss SM, Wu R, Hellens RP (2012) Kiwifruit floral gene / APETALA2 is alternatively spliced and accumulates in aberrant indeterminate flowers in the absence of miR172. Plant Mol Biol 78:417-29 CrossRef
  43. Wu G, Poethig RS (2006) Temporal regulation of shoot development in / Arabidopsis thaliana by miR156 and its target / SPL3. Development 133:3539-547 CrossRef
  44. Wu G, Park MY, Conway SR, Wang JW, Weigel D, Poethig RS (2009) The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 138:750-59 CrossRef
  45. Xie K, Wu C, Xiong L (2006) Genomic organization, differential expression, and interaction of / SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiol 142:280-93 CrossRef
  46. Zhang B, Pan X, Cobb GP, Anderson TA (2006) Plant microRNA, a small regulatory molecule with big impact. Dev Biol 289:3-6 CrossRef
  
• 作者单位：Choun-Sea Lin (1)
  Jeremy J. W. Chen (2)
  Yao-Ting Huang (3)
  Chen-Tran Hsu (1)
  Hsiang-Chia Lu (4)
  Ming-Lun Chou (5)
  Li-Chi Chen (2)
  Chia-I Ou (3)
  Der-Chih Liao (1)
  Ysuan-Yu Yeh (6)
  Song-Bing Chang (6)
  Su-Chen Shen (7)
  Fu-Huei Wu (1)
  Ming-Che Shih (1)
  Ming-Tsair Chan (1) (4)
  
  1. Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
  2. Institute of Biomedical Sciences, National Chung-Hsing University, Taichung, Taiwan
  3. Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-i, Taiwan
  4. Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
  5. Department of Life Sciences, Tzu Chi University, Hualien, Taiwan
  6. Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
  7. Scientific Instrument Center, Academia Sinica, Taipei, 115, Taiwan
  
• ISSN：1573-5028

文摘

The orchid Erycina pusilla has a short life cycle and relatively low chromosome number, making it a potential model plant for orchid functional genomics. To that end, small RNAs (sRNAs) from different developmental stages of different organs were sequenced. In this miRNA mix, 33 annotated miRNA families and 110 putative miRNA-targeted transcripts were identified in E. pusilla. Fifteen E. pusilla miRNA target genes were found to be similar to those in other species. There were putative novel miRNAs identified by 3 different strategies. The genomic sequences of the four miRNAs that were identified using rice genome as the reference can form the stem loop structure. The t0000354 miRNA, identified using rice genome sequences and a Phalaenopsis study, had a high read count. The target gene of this miRNA is MADS (unigene30603), which belongs to the AP3-PI subfamily. The most abundant miRNA was E. pusilla miR156 (epu-miR156), orthologs of which work to maintain the vegetative phase by repressing the expression of the SQUAMOSA promoter-binding-like (SPL) transcription factors. Fifteen genes in the E. pusilla SPL (EpSPL) family were identified, nine of which contained the putative epu-miR156 target site. Target genes of epu-miR172, also a key regulator of developmental changes in the APETALA2 (EpAP2) family, were identified. Experiments using 5′RLM-RACE demonstrated that the genes EpSPL1, 2, 3, 4, 7, 9, 10, 14 and EpAP2-9, -10, -11 were regulated by epu-miR156 and epu-miR172, respectively.