Integrative Analysis of miRNA and mRNA Profiles in Response to Ethylene in Rose Petals during Flower Opening

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Pei, Haixia ^a   Ma, Nan ^a   Chen, Jiwei ^a   Zheng, Yi ^a,b   Tian, Ji ^a   Li, Jing ^a   Zhang, Shuai ^a   Fei, Zhangjun ^b,c   Gao, Junping ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b Boyce Thompson Institute for Plant Research   (United States)

^c ROBERT W HOLLEY CENTER FOR AGRICULTURE AND HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ETHYLENE; MESSENGER RNA; MICRORNA; MICRORNA 139; MICRORNA 156; MICRORNA 164; MICRORNA 166; PLANT RNA; RHY MIRC1; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DEVELOPMENTAL STAGE; FLOWER DEVELOPMENT; FLOWER OPENING; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE TARGETING; GENETIC CORRELATION; HIGH THROUGHPUT SEQUENCING; NONHUMAN; PETAL; RNA ANALYSIS; RNA SEQUENCE; ROSE;

ETHYLENES; FLOWERS; GENE EXPRESSION REGULATION, PLANT; MICRORNAS; RNA, MESSENGER; ROSA;

EID: 84877806210     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0064290     Document Type: Article

References (68)

1. Chen X, (2009) Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 25: 21-44.
2. Voinnet O, (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136: 669-687.
3. Jones-Rhoades MW, (2011) Conservation and divergence in plant microRNAs. Plant Mol Biol 80: 3-16.
4. Axtell MJ, Bowman JL, (2008) Evolution of plant microRNAs and their targets. Trends Plant Sci 13: 343-349.
5. Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, et al. (2009) High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera. BMC Genomics 10: 558.
6. Schreiber AW, Shi BJ, Huang CY, Langridge P, Baumann U, (2011) Discovery of barley miRNAs through deep sequencing of short reads. BMC Genomics 12: 129.
7. 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.
8. Donaire L, Pedrola L, Rosa R, Llave C, (2011) High-throughput sequencing of RNA silencing-associated small RNAs in olive (Olea europaea L.). PLoS One 6: e27916.
9. Zuo J, Zhu B, Fu D, Zhu Y, Ma Y, et al. (2012) Sculpting the maturation, softening and ethylene pathway: The influences of microRNAs on tomato fruits. BMC Genomics 13: 7.
10. Xia R, Zhu H, An Y, Beers E, Liu Z, (2012) Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biol 13: R47.
11. Zhu H, Xia R, Zhao B, An Y, Dardick C, et al. (2012) Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs. BMC Plant Biol 12: 149.
12. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ, (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-D158.
13. Ruiz-Ferrer V, Voinnet O, (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60: 485-510.
14. Jay F, Renou J-P, Voinnet O, Navarro L, (2010) Biotic stress-associated microRNAs: identification, detection, regulation, and functional analysis. Methods Mol Biol 592: 183-202.
15. 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.
16. Zhang Y, Yu M, Yu H, Han J, Song C, et al. (2011) Computational identification of microRNAs in peach expressed sequence tags and validation of their precise sequences by miR-RACE. Mol Biol Rep 39: 1975-1987.
17. Gao Z, Luo X, Shi T, Cai B, Zhang Z, et al. (2012) Identification and validation of potential conserved microRNAs and their targets in peach (Prunus persica). Mol Cells 34: 239-249.
18. Heinrichs F, (2008) International statistics flowers and plants. AIPH/Union Fleurs 56: 16-90.
19. Debener Th, Linde M, (2009) Exploring complex ornamental genomes: The rose as a model plant. Critical Rev Plant Sci 28: 267-280.
20. Abeles FB, Morgan PW, Saltveit ME (1992) Ethylene in Plant Biology, Ed 2. Academic Press, San Diego.
21. Wang K, Li H, Ecker J, (2002) Ethylene biosynthesis and signaling networks. Plant Cell 14: S131-S151.
22. Reid MS, Dodge LL, Mor Y, Evans RY, (1989) Effects of ethylene on rose opening. Acta Horti 261: 215-220.
23. Muller R, Lind-Iversen S, Stummann BM, Serek M, (2000) Expression of genes for ethylene biosynthetic enzymes and an ethylene receptor in senescing flowers of miniature potted roses. J Hort Sci Biotech 75: 12-18.
24. Muller R, Stummann BM, (2003) Genetic regulation of ethylene perception and signal transduction related to flower senescence. J. Food Agr Environ 1: 87-94.
25. Ma N, Cai W, Lu W, Tan H, Gao J, (2005) Exogenous ethylene influences flower opening of cut roses (Rosa hybrida) by regulating the gene encoding ethylene biosynthesis enzymes. Sci China C Life Sci 48: 434-444.
26. Tan H, Liu X, Ma N, Xue J, Lu W, et al. (2006) Ethylene influenced flower opening and expression of genes encoding Etrs, Ctrs, and Ein3s in two cut rose cultivars. Postharvest Biol Tech 40: 97-105.
27. Xue JQ, Li YH, Tan H, Yang F, Ma N, et al. (2008) Expression of ethylene biosynthetic and receptor genes in rose floral tissues during ethylene-enhanced flower opening. J Exp Bot 59: 2161-2169.
28. Kim J, Park JH, Lim CJ, Lim JY, Ryu JY, et al. (2012) Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars. BMC Genomics 13: 657.
29. Wang D, Fan J, Ranu RS, (2004) Cloning and expression of 1-aminocyclopropane-1-carboxylate synthase cDNA from rosa (Rosa x hybrida). Plant Cell Rep 22: 422-429.
30. Ma N, Xue J, Li Y, Liu X, Dai F, et al. (2008) Rh-PIP2;1, a rose aquaporin gene, is involved in ethylene-regulated petal expansion. Plant Physiol 148: 894-907.
31. Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, et al. (2007) Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol 5: e57.
32. Jeong DH, Park S, Zhai J, Gurazada SG, De Paoli E, et al. (2012) Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell 23: 4185-4207.
33. Mi S, Cai T, Hu Y, Chen Y, Hodges E, et al. (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133: 116-127.
34. Czech B, Hannon GJ, (2011) Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet 12: 19-31.
35. Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, et al. (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43: 109-116.
36. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, et al. (2008) Criteria for Annotation of Plant MicroRNAs. Plant Cell 20: 3186-3190.
37. Zhao YT, Wang M, Fu SX, Yang WC, Qi CK, et al. (2012) Small RNA profiling in two Brassica napus cultivars identifies microRNAs with oil production and developmental correlated expressions and new small RNA classes. Plant Physiol 158: 813-823.
38. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, et al. (2002) Prediction of plant microRNA targets. Cell 110: 513-520.
39. Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, et al. (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320: 1185-1190.
40. Bennett BC Economic Botany: Twenty-five economically important plant families. Encyclopedia of Life Support Systems (EOLSS) e-book.
41. Yasumura Y, Pierik R, Fricker MD, Voesenek LACJ, Harberd NP, (2012) Studies of Physcomitrella patens reveal that ethylene mediated submergence responses arose relatively early in land-plant evolution. Plant J 72: 947-959.
42. Zhang T-C, Qiao Q, Zhong Y, (2012) Detecting adaptive evolution and functional divergence in aminocyclopropane-1-carboxylate synthase (ACS) gene family. Comput Biol Chem 38: 10-16.
43. Chen L, Wang T, Zhao M, Zhang W, (2011) Ethylene-responsive miRNAs in roots of Medicago truncatula identified by high-throughput sequencing at whole genome level. Plant Sci 184: 14-19.
44. Tang Z, Zhang L, Xu C, Yuan S, Zhang F, et al. (2012) Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male-sterile line by deep sequencing. Plant Physiol 159: 721-738.
45. Channeliere S, Riviere S, Scalliet G, Jullien F, Szecsi J, et al. (2002) Analysis of gene expression in rose petals using expressed sequence tags. FEBS Lett 515: 35-38.
46. Guterman I, Shalit M, Menda M, Piestun D, Dafny-Yelin M, et al. (2002) Rose scent: genomics approach to discovering novel floral fragrance-related genes. Plant Cell 14: 2325-2338.
47. Bendahmane M, Dubois A, Raymond O, Le Bris M, (2013) Genetics and genomics of flower initiation and development in roses. J Exp Bot 64: 847-857.
48. Dubois A, Remay A, Raymond O, Balzergue S, Chauvet A, et al. (2011) Genomic approach to study floral development genes in Rosa sp. PLoS One 6: e28455.
49. Dubois A, Carrere S, Raymond O, Pouvreau B, Cottret L, et al. (2012) Transcriptome database resource and gene expression atlas for the rose. BMC Genomics 13: 638.
50. Laufs P, Peaucelle A, Morin H, Traas J, (2004) MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development 131: 4311-4322.
51. Peaucelle A, Morin H, Traas J, Laufs P, (2007) Plants expressing a miR164-resistant CUC2 gene reveal the importance of post-meristematic maintenance of phyllotaxy in Arabidopsis. Development 134: 1045-1050.
52. Raman S, Greb T, Peaucelle A, Blein T, Laufs P, et al. (2008) Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana. Plant J 55: 65-76.
53. He XJ, Mu RL, Cao WH, Zhang ZG, Zhang JS, et al. (2005) AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant J 44: 903-916.
54. Kim JH, Woo HR, Kim J, Lim PO, Lee IC, et al. (2009) Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis. Science 323: 1053-1057.
55. 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.
56. El-Kereamy A, Chervin C, Roustan JP, Cheynier V, Souquet J-M, et al. (2003) Exogenous ethylene stimulates the long-term expression of genes related to anthocyanin biosynthesis in grape berries. Physiologia Plantarum 119: 175-182.
57. Gantulga D, Ahn YO, Zhou C, Battogtokh D, Bevan DR, et al. (2009) Comparative characterization of the Arabidopsis subfamily a1 β-galactosidases. Phytochemistry 70: 1999-2009.
58. Cosgrove DJ, (2005) Growth of the plant cell wall. Nat Rev Mol Cell Biol 6: 850-861.
59. Zhong GV, Burns JK, (2003) Profiling ethylene-regulated gene expression in Arabidopsis thaliana by microarray analysis. Plant Mol Biol 53: 117-131.
60. De Paepe A, Vuylsteke M, Van Hummelen P, Zabeau M, Van Der Straeten D, (2004) Transcriptional profiling by cDNA-AFLP and microarray analysis reveals novel insights into the early response to ethylene in Arabidopsis. Plant J 39: 537-559.
61. Alba R, Payton P, Fei ZJ, McQuinn R, Debbie P, et al. (2005) Transcriptome and selected metabolite analyses reveal multiple points of ethylene control during tomato fruit development. Plant Cell 17: 2954-2965.
62. Ma N, Tan H, Liu XH, Xue JQ, Li YH, et al. (2006) Transcriptional regulation of ethylene receptor and CTR genes involved in ethylene-induced flower opening in cut rose (Rosa hybrida) cv. Samantha. J Exp Bot 57: 2763-2773.
63. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
64. Hofacker IL, (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31: 3429-3431.
65. 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.
66. Jones-Rhoades MW, Bartel DP, (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14: 787-799.
67. Varkonyi-Gasic E, Wu R, Wood M, Walton EF, Hellens RP, (2007) Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods 3: 12.
68. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods 25: 402-408.