Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum): Characterization of flax miRNA genes

Planta

Volumn 237, Issue 4, 2013, Pages 1149-1161

  Barvkar, Vitthal T ^a   Pardeshi, Varsha C ^a   Kale, Sandip M ^a   Qiu, Shuqing ^b   Rollins, Meaghen ^b   Datla, Raju ^b   Gupta, Vidya S ^a   Kadoo, Narendra Y ^a  

^a NATIONAL CHEMICAL LABORATORY   (India)

^b NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

Digital expression analysis; Gene cluster; Linseed; MiRNA; MiRNA target transcript; Promoter analysis

Indexed keywords

LINUM USITATISSIMUM;

EID: 84875421915     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-012-1833-5     Document Type: Article

References (67)

1. Alexandrov NN, Troukhan ME, Brover VV, Tatarinova T, Flavell RB, Feldmann KA (2006) Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Mol Biol 60: 69-85.
2. Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H (2005) Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 33: 2697-2706.
3. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen XM, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T (2003) A uniform system for microRNA annotation. RNA 9: 277-279.
4. Arnaud D, Dejardin A, Leple JC, Lesage-Descauses MC, Boizot N, Villar M, Benedetti H, Pilate G (2012) Expression analysis of LIM gene family in poplar, toward an updated phylogenetic classification. BMC Res Notes 5: 102.
5. 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: 2730-2741.
6. Axtell MJ, Bartel DP (2005) Antiquity of microRNAs and their targets in land plants. Plant Cell 17: 1658-1673.
7. Barakat A, Wall PK, Diloreto S, Depamphilis CW, Carlson JE (2007) Conservation and divergence of microRNAs in Populus. BMC Genomics 8: 481.
8. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
9. Bentwich I (2005) Prediction and validation of microRNAs and their targets. FEBS Lett 579: 5904-5910.
10. 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.
11. Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of MicroRNA-target recognition. PLoS Biol 3: 404-418.
12. Calvino M, Bruggmann R, Messing J (2011) Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems. BMC Genomics 12: 356.
13. Cui X, Xu SM, Mu DS, Yang ZM (2009) Genomic analysis of rice microRNA promoters and clusters. Gene 431: 61-66.
14. Dai XB, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39: 155-159.
15. Deng W, Nickle DC, Learn GH, Maust B, Mullins JI (2007) ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets. Bioinformatics 23: 2334-2336.
16. Du Z, Zhou X, Ling Y, Zhang ZH, Su Z (2010) AgriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38: W64-W70.
17. Fenart S, Ndong YPA, Duarte J, Riviere N, Wilmer J, van Wuytswinkel O, Lucau A, Cariou E, Neutelings G, Gutierrez L, Chabbert B, Guillot X, Tavernier R, Hawkins S, Thomasset B (2010) Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray. BMC Genomics 11: 592.
18. Frazier TP, Xie FL, Freistaedter A, Burklew CE, Zhang BH (2010) Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta 232: 1289-1308.
19. Gou JY, Felippes FF, Liu CJ, Weigel D, Wang JW (2011) Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell 23: 1512-1522.
20. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-D158.
21. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database. Nucleic Acids Res 27: 297-300.
22. Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31: 3429-3431.
23. Huang Y, Niu BF, Gao Y, Fu LM, Li WZ (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26: 680-682.
24. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57: 19-53.
25. Jung JH, Seo PJ, Kang SK, Park CM (2011) miR172 signals are incorporated into the miR156 signaling pathway at the SPL3/4/5 genes in Arabidopsis developmental transitions. Plant Mol Biol 76: 35-45.
26. 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.
27. Lu C, Meyers BC, Green PJ (2007) Construction of small RNA cDNA libraries for deep sequencing. Methods 43: 110-117.
28. Masoudi-Nejad A, Tonomura K, Kawashima S, Moriya Y, Suzuki M, Itoh M, Kanehisa M, Endo T, Goto S (2006) EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res 34: W459-W462.
29. Mathews DH, Sabina J, Zuker M, Turner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288: 911-940.
30. McCarthy FM, Wang N, Magee GB, Nanduri B, Lawrence ML, Camon EB, Barrell DG, Hill DP, Dolan ME, Williams WP, Luthe DS, Bridges SM, Burgess SC (2006) AgBase: a functional genomics resource for agriculture. BMC Genomics 7: 229.
31. Megraw M, Baev V, Rusinov V, Jensen ST, Kalantidis K, Hatzigeorgiou AG (2006) MicroRNA promoter element discovery in Arabidopsis. RNA 12: 1612-1619.
32. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen XM, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi YJ, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhui JK (2008) Criteria for annotation of plant microRNAs. Plant Cell 20: 3186-3190.
33. Moss TY, Cullis CA (2012) Computational prediction of candidate microRNAs and their targets from the completed Linum usitatissimum genome and EST database. J Nucleic Acids Investig 3: e2.
34. Moxon S, Schwach F, Dalmay T, MacLean D, Studholme DJ, Moulton V (2008) A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics 24: 2252-2253.
35. Neutelings G, Fenart S, Lucau-Danila A, Hawkins S (2012) Identification and characterization of miRNAs and their potential targets in flax. J Plant Physiol 169: 1754-1766.
36. Prufer K, Stenzel U, Dannemann M, Green RE, Lachmann M, Kelso J (2008) PatMaN: rapid alignment of short sequences to large databases. Bioinformatics 24: 1530-1531.
37. 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.
38. Ruan MB, Zhao YT, Meng ZH, Wang XJ, Yang WC (2009) Conserved miRNA analysis in Gossypium hirsutum through small RNA sequencing. Genomics 94: 263-268.
39. Smale ST (2001) Core promoters: active contributors to combinatorial gene regulation. Genes Dev 15: 2503-2508.
40. Solovyev V, Salamov A (1997) The gene-finder computer tools for analysis of human and model organisms genome sequences. In: Rawling C, Clark D, Altman R, Hunter L, Lengauer T, Wodak S (eds) Fifth international conference on intelligent systems for molecular biology, proceedings. AAAI Press, Halkidiki, Greece, pp 294-302.
41. Song C, Jia Q, Fang J, Li F, Wang C, Zhang Z (2010) Computational identification of citrus microRNAs and target analysis in citrus expressed sequence tags. Plant Biology 12: 927-934.
42. Sun G (2012) MicroRNAs and their diverse functions in plants. Plant Mol Biol 80: 17-36.
43. Tang GL (2010) Plant microRNAs: an insight into their gene structures and evolution. Semin Cell Dev Biol 21: 782-789.
44. Thakur V, Wanchana S, Xu M, Bruskiewich R, Quick WP, Mosig A, Zhu XG (2011) Characterization of statistical features for plant microRNA prediction. BMC Genomics 12: 108.
45. Turner M, Yu O, Subramanian S (2012) Genome organization and characteristics of soybean microRNAs. BMC Genomics 13: 169.
46. Unver T, Budak H (2009) Conserved microRNAs and their targets in model grass species Brachypodium distachyon. Planta 230: 659-669.
47. Venglat P, Xiang D, Qiu S, Stone SL, Tibiche C, Cram D, Alting-Mees M, Nowak J, Cloutier S, Deyholos M, Bekkaoui F, Sharpe A, Wang E, Rowland G, Selvaraj G, Datla R (2011) Gene expression analysis of flax seed development. BMC Plant Biol 11: 74.
48. Wang YP, Li KB (2009) Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data. BMC Genomics 10: 218.
49. Wang JW, Czech B, Weigel D (2009) miR156-Regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell 138: 738-749.
50. Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe A, Wong GK, Wang J, Deyholos MK (2012) The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J 72: 461-473.
51. Weber MJ (2005) New human and mouse microRNA genes found by homology search. FEBS J 272: 59-73.
52. Wightman B, Ha I, Ruvkun G (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855-862.
53. Wu MF, Tian Q, Reed JW (2006) Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 133: 4211-4218.
54. Xie ZX, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC (2005) Expression of Arabidopsis MIRNA genes. Plant Physiol 138: 2145-2154.
55. Xie FL, Xiao P, Zhang BH (2011) Target-align: a tool for plant MicroRNA target identification. In Vitro Cell Dev Biol-Animal 47: S71-S72.
56. Yang TW, Xue LG, An LZ (2007) Functional diversity of miRNA in plants. Plant Sci 172: 423-432.
57. Zeng CY, Wang WQ, Zheng Y, Chen X, Bo WP, Song S, Zhang WX, Peng M (2010) Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants. Nucleic Acids Res 38: 981-995.
58. Zhang BH, Pan XP, Anderson TA (2006a) Identification of 188 conserved maize microRNAs and their targets. FEBS Lett 580: 3753-3762.
59. Zhang BH, Pan XP, Cannon CH, Cobb GP, Anderson TA (2006b) Conservation and divergence of plant microRNA genes. Plant J 46: 243-259.
60. Zhang BH, Pan XP, Cox SB, Cobb GP, Anderson TA (2006c) Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci 63: 246-254.
61. Zhang BH, Wang QL, Wang KB, Pan XP, Liu F, Guo TL, Cobb GP, Anderson TA (2007) Identification of cotton microRNAs and their targets. Gene 397: 26-37.
62. Zhang BH, Pan XP, Stellwag EJ (2008) Identification of soybean microRNAs and their targets. Planta 229: 161-182.
63. Zhang LF, Chia JM, Kumari S, Stein JC, Liu ZJ, Narechania A, Maher CA, Guill K, McMullen MD, Ware D (2009) A genome-wide characterization of microRNA genes in Maize. PLoS Genet 5: 11.
64. Zhao BT, Ge LF, Liang RQ, Li W, Ruan KC, Lin HX, Jin YX (2009) Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor. BMC Mol Biol 10: 29.
65. Zhong R, Ye ZH (2007) Regulation of HD-ZIP III Genes by MicroRNA 165. Plant Signal Behav 2: 351-353.
66. Zhou M, Sun J, Wang QH, Song LQ, Zhao GA, Wang HZ, Yang HX, Li X (2011) Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes. FEBS J 278: 929-940.
67. Zhu RS, Li X, Chen QS (2011) Discovering numerical laws of plant microRNA by evolution. Biochem Biophys Res Commun 415: 313-318.