Bioinformatic identification and expression analysis of banana MicroRNAs and their targets

PLoS ONE

Volumn 10, Issue 4, 2015, Pages

  Chai, Juan ^a   Feng, Renjun ^a   Shi, Hourui ^a,b   Ren, Mengyun ^a,b   Zhang, Yindong ^b   Wang, Jingyi ^a  

^a INSTITUTE OF TROPICAL BIOSCIENCE AND BIOTECHNOLOGY   (China)

^b HAINAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 156; MICRORNA 156A 3P; MICRORNA 156A 5P; MICRORNA 156D; MICRORNA 156G; MICRORNA 156H; MICRORNA 157; MICRORNA 157B; MICRORNA 159; MICRORNA 160; MICRORNA 162; MICRORNA 164; MICRORNA 164E; MICRORNA 166; MICRORNA 166B; MICRORNA 167; MICRORNA 167D; MICRORNA 169; MICRORNA 169H; MICRORNA 172; MICRORNA 172B; MICRORNA 319; MICRORNA 319C; MICRORNA 397; MICRORNA 399; MICRORNA 399A; MICRORNA 4995; MICRORNA 5538; UNCLASSIFIED DRUG; PRIMER DNA;

ARTICLE; BANANA; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; FLOWER; FRUIT; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC CONSERVATION; GENOMIC SURVEY SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT DEVELOPMENT; PLANT GROWTH; PLANT LEAF; PLANT METABOLISM; PLANT ROOT; PLANT STRESS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SEQUENCE HOMOLOGY; TRANSCRIPTION REGULATION; TRANSLATION REGULATION; BIOLOGY; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; METABOLISM; MUSA; PLANT GENE;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA PRIMERS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; MICRORNAS; MUSA; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 84928901958     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0123083     Document Type: Article

References (65)

1. Bartel DP. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116:281-297. doi:http://dx.doi.org/10.1016/S0092-8674(04)00045-5 PMID: 14744438
2. Park MY, Wu G, Gonzalez-Sulser A, Vaucheret H, Poethig RS. (2005) Nuclear processing and export of microRNAs in Arabidopsis. Proc Natl Acad Sci USA; 102:3691-3696. doi: 10.1073/pnas.0405570102 PMID: 15738428
3. Papp I, Mette MF, Aufsatz W, Daxinger L, Schauer SE, Ray A, et al. (2003) Evidence for nuclear processing plant microRNA and short interfering precursors. Plant Physiol. 132:1382-1390. doi: http://dx.doi.org/10.1104/pp.103. PMID: 12857820
4. Khvorova A, Reynolds A, Jayasena SD. (2007) Functional siRNAs and miRNAs exhibit strand bias. Cell, 131: 41-49. doi: 10.1016/S0092-8674(03)00801-8
5. Hake S. (2003) MicroRNAs: A role in plant development. Curr Biol, 13: R851-R852. doi: 10.1016/j.cub.2003.10.021 PMID: 14588265
6. Valencia-Sanchez M A, Liu J D, Hannon G J, Parker R. (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Gene Dev, 20: 515-524. doi: 10.1101/gad.1399806 PMID: 16510870
7. Dong QH, Han J, Yu HP, Wang C, Zhao MZ, Liu H, et al. (2012) Computational identification of micro-RNAs in strawberry expressed sequence tags and validation of their precise sequences by miR-RACE. J. Heredity, 103(2):268-277. doi: 10.1093/jhered/esr127
8. Llave C, Kasschau KD, Rector MA, Carrington JC. (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell, 14: 1605-1619. doi: http://dx.doi.org/10.1105/tpc.003210 PMID: 12119378
9. Floyd SK, Bowman JL. (2004) Gene regulation: ancient microRNA target sequences in plants. Nature, 428:485-486. doi: 10.1038/428485a PMID: 15057819
10. Jones-Rhoades MW, Bartel DP. (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell, 14:787-799. doi: 10.1016/j.molcel.2004.05.027 PMID: 15200956
11. Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA. (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Res, 15: 336-360. doi: 10.1038/sj.cr.7290302 PMID: 15916721
12. Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, et al. (2005) Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res, 15:78-91. doi: 10.1101/gr.2908205 PMID: 15632092
13. Archak S, Nagaraju J (2007) Computational prediction of rice (Oryza sativa) miRNA targets. Genomics Proteomics Bioinformatics, 5:196-206. doi: 10.1016/S1672-0229(08)60007-8 PMID: 18267301
14. Jin WB, Li NN, Zhang B, Wu FL, Li WJ, Guo A, et al. (2008) Identification and verification of microRNA in wheat (Triticum aestivum). J Plant Res., 121:351-355. doi: 10.1007/s10265-007-0139-3 PMID: 18357413
15. Zhang BH, Pan XP, Anderson TA. (2006) Identification of 188 conserved maize microRNAs and their targets. FEBS Lett., 580:3753-3762. doi: 10.1016/j.febslet.2006.05.063 PMID: 16780841
16. Colaiacovo M, Subacchi A, Bagnaresi P, Lamontanara A, Cattivelli L, Faccioli P. (2010) A computational-based update on microRNAs and their targets in barley (Hordeum vulgare L.). BMC Genomics, 11:595-609. doi: 10.1186/1471-2164-11-595 PMID: 20969764
17. Du JF, Wu YJ, Fang XF, Cao JX, Zhao L, Tao SH. (2010) Prediction of sorghum miRNAs and their targets with computational methods. Chin Sci Bull., 55:1263-1270. doi: 10.1007/s11434-010-0035-4
18. Zhang BH, Wang QL, Wang KB, Pan XP, Liu F, Guo T, et al. (2007) Identification of cotton microRNAs and their targets. Gene, 397:26-37. doi: 10.1016/j.gene.2007.03.020 PMID: 17574351
19. Zhang B, Pan X, Stellwag EJ. (2008) Identification of soybean microRNAs and their targets. Planta, 229:161-182. doi: 10.1007/s00425-008-0818-x PMID: 18815805
20. Zhang WW, Luo YP, Gong X, Zeng WH, Li SG. (2009) Computational identification of 48 potato microRNAs and their targets. Comput Biol Chem, 33: 84-93. doi: 10.1016/j.compbiolchem.2008.07.006 PMID: 18723398
21. Yin Z, Li C, Han X, Shen F. (2008) Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene, 414:60-66. doi: 10.1016/j.gene.2008.02.007 PMID: 18387754
22. Song CN, Jia QD, Fang JG, Li F, Wang C, Zhang Z. (2010) Computational identification of citrus micro-RNAs and target analysis in citrus expressed sequence tags. Plant Biol (Stuttg), 12:927-934. doi: 10.1111/j.1438-8677.2009.00300.x PMID: 21040308
23. Ye KY, Chen Y, Hu XW, Guo JC. (2013) Computational identification of microRNAs and their targets in apple. Genes Genom., 35:377-385. doi: 10.1007/s13258-013-0070-z
24. Zhou ZS, Huang SQ, Yang ZM. (2008) Bioinformatic identification and expression analysis of new microRNAs from Medicago truncatula. Biochem Biophys Res Commun, 374:538-42. doi: 10.1016/j.bbrc.2008.07.083 PMID: 18662674
25. Xie FL, Huang SQ, Guo K, Xiang AL, Zhu YY, Nie L, et al. (2007) Computational identification of novel microRNAs and targets in Brassica napus. FEBS Lett, 581:1464-1474. doi: 10.1016/j.febslet.2007.02.074 PMID: 17367786
26. Pani A, Mahapatra RK. (2013) Computational identification of microRNAs and their targets in Catharanthus roseus expressed sequence tags. Genomics Data, 1: 2-6. doi: 10.1016/j.gdata.2013.06.001 PMID: 23311594
27. D'Hont A, Denoeud F, Aury J-M, Baurens F-C, Carreel F, Garsmeur O, et al. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488: 213-217. doi: 10.1038/nature11241 PMID: 22801500
28. Baurens FC, Bocs S, Rouard M, Matsumoto T, Miller RN, Rodier-Goud M, et al. (2010) Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana). BMC Plant Biol., 10:149. doi: 10.1186/1471-2229-10-149 PMID: 20637079
29. Simmonds N. W. (1962) The Evolution of the Bananas. Longman press. 101p-131p.
30. FAOSTAT, banana production. http://faostat3.fao.org/faostat-gateway/go/to/browse/Q/∗/E
31. Kozomara A, Griffiths-Jones S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucl. Acids Res. 42:D68-D73. doi: 10.1093/nar/gkt1181 PMID: 24275495
32. Davey MW, Gudimella R, Harikrishna JA, Sin LW, Khalid N, Keulemans J. (2013) A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids. BMC Genomics, 14:683. doi: 10.1186/1471-2164-14-683 PMID: 24094114
33. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. (2013) GenBank. Nucleic Acids Res., 41: D36-D42. doi: 10.1093/nar/gks119523193287 PMID: 23193287
34. Zuker M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucl. Acids Res., 31 (13):3406-3415. doi: 10.1093/nar/gkg595 PMID: 12824337
35. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, et al. (2003) A uniform system for microRNA annotation. RNA, 9: 277-279. doi: 10.1261/rna.2183803 PMID: 12592000
36. Zhang BH, Pan XP, Cannon CH, Cobb GP, Anderson TA. (2006) Conservation and divergence of plant microRNA genes. Plant J., 46, 243-259. doi: 10.1111/j.1365-313X.2006.02697.x PMID: 16623887
37. Dai XB, Zhao PX. (2011) psRNATarget: A Plant Small RNA Target Analysis Server. Nucl. Acids Res., 39: w155-w159. doi: 10.1093/nar/GKR319 PMID: 21622958
38. Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep., 11:113-116. doi: 10.1007/BF02670468
39. 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. doi: 10.1006/meth.2001.1262 PMID: 11846609
40. Gorodkin J, Havgaard JH, Enstero M, Sawera M, Jensen P, Ohman M, et al. (2006). MicroRNA sequence motifs reveal asymmetry between the stem arms. Comput. Biol. Chem., 30: 249-254. doi: 10.1016/j.compbiolchem.2006.04.006 PMID: 16798093
41. Frazier TP, Xie FL, LFreistaedter A, Burklew CE, Zhang BH. (2010) Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta, 232(6):1289-1308. doi: 10.1007/s00425-010-1255-1 PMID: 20803216
42. Zhang BH, Pan XP, Cox SB, Cobb GP, Anderson TA. (2006). Evidence that miRNAs are different from other RNAs. Cell. Mol. Life Sci. 63, 246-254. doi: 10.1007/s00018-005-5467-7 PMID: 16395542
43. Dryanova A, Zakharov A, Gulicka PJ. (2008) Data mining for miRNAs and their targets in the Triticeae. Genome, 51(6): 433-443. doi: 10.1139/G08-025 PMID: 18521122
44. Frazier TP, Sun G, Burklew CE, Zhang BH. (2011) Salt and drought stresses induce the aberrant expression of microRNA genes in tobacco. Mol. Biotechnol., 49 (2):159-165. doi: 10.1007/s12033-011-9387-5 PMID: 21359858
45. Wei LQ, Yan LF, 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 Biol., 12(6): R53-R68. doi: 10.1186/gb-2011-12-6-r53 PMID: 21679406
46. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. (2002) Prediction of plant microRNA targets. Cell 110:513-520. doi: 10.1016/S0092-8674(02)00863-2 PMID: 12202040
47. Bonnet E, Wuyts J, Rouze P, Peer VY. (2004) Detection of 91 potential in plant conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci USA, 101:11511-11516. doi: 10.1073/pnas.0404025101 PMID: 15272084
48. Zeng CY, Wang WQ, Zheng Y, Chen X, Bo WP, Song S, et al. (2009) Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants. Nucl. Acids Res., 38(3),981-995. doi: 10.1093/nar/gkp1035 PMID: 19942686
49. Liang G, Li Y, He H, Wang F, Yu DQ. (2013) Identification of miRNAs and miRNA-mediated regulatory pathways in Carica papaya. Planta, 238:739-752. doi: 10.1007/s00425-013-1929-6 PMID: 23851604
50. Sunkar R, Zhu J K. (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 16(8):2001-2019. doi: http://dx.doi.org/10.1105/tpc.104 PMID: 15258262
51. Thiebaut F, Rojas CA, Almeida KL, Grativol C, Domiciano GC, Lamb CR, et al. (2012) Regulation of miR319 during cold stress in sugarcane. Plant Cell Environ., 35 (3):502-512. doi: 10.1111/j.1365-3040.2011.02430.x PMID: 22017483
52. Unver T, Parmaksiz I, Dündar E. (2010) Identification of conserved micro-RNAs and their target transcripts in opium poppy (Papaver somniferum L.). Plant Cell Rep., 29 (7):757-769. doi: 10.1007/s00299-010-0862-4 PMID: 20443006
53. Manning K, Tör M, Poole M, Hong Y, Thompson AJ, King GJ, et al. (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat. Genet. 38:948-952. doi: 10.1038/ng1841 PMID: 16832354
54. Silva GFFe, Silva EM, da Silva Azevedo M, Guivin MAC, Ramiro DA, et al. (2014) microRNA156-targeted SPL/SBP box transcription factors regulate tomato ovary and fruit development. Plant J., 78:604-618. doi: 10.1111/tpj.12493
55. Wang SK, Wu K, Yuan QB, Liu XY, Liu ZB, Lin X, et al. (2012) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet., 44(8):950-954. doi: 10.1038/ng.2327 PMID: 22729225
56. Chen XB, Zhang ZL, Liu DM, Zhang K, Li AL, Mao L. (2010) SQUAMOSA promoter-binding protein-like transcription factors: star players for plant growth and development. J Integr Plant Biol., 52(11): 946-951. doi: 10.1111/j.1744-7909.2010.00987.x PMID: 20977652
57. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D. (2005) Specific effects of microRNAs on the plant transcriptome. Dev. Cell 8, 517-527. doi: 10.1016/j.devcel.2005.01.018 PMID: 15809034
58. Murray F, Kalla R, Jacobsen J, Gubler F. (2003) A role for HvGAMYB in anther development. Plant J., 33: 481-491. doi: 10.1046/j.1365-313X.2003.01641.x PMID: 12581306
59. Liu Z, Bao W, Liang W, Yin J, Zhang D. (2010) Identification of gamyb-4 and analysis of the regulatory role of GAMYB in rice anther development. J Integr Plant Biol., 52:670-678. doi: 10.1111/j.1744-7909.2010.00959.x PMID: 20590996
60. 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. doi: http://dx.doi.org/10.1105/tpc.104.027920 PMID: 15722475
61. Aya K, Ueguchi-Tanaka M, Kondo M, Hamada K, Yano K, Nishimura M, et al. (2009) Gibberellin modulates anther development in rice via the transcriptional regulation of GAMYB. Plant Cell 21, 1453-1472. doi: http://dx.doi.org/10.1105/tpc.108. doi: 10.1105/tpc.108.062935 PMID: 19454733
62. Winkel-Shirley B (2001) It takes a garden. How work on diverse plant species has contributed to an understanding of flavonoid metabolism. Plant Physiol., 127:1399-1404. doi: http://dx.doi.org/10.1104/pp.010675 PMID: 11743081
63. Martens S, Knott J, Seitz CA, Janvari L, Yub SN, Forkmanna G. (2003) Impact of biochemical pre-studies on specific metabolic engineering strategies of flavonoid biosynthesis in plant tissues. Biochem Eng J, 14: 227-235. doi: 10.1016/S1369-703X(02)00224-3
64. Peer WA, Murphy AS (2007) Flavonoids and auxin transport: modulators orregulators? Trends in plant science, 12: 556-563. doi: 10.1016/j.tplants.2007.10.003 PMID: 18198522
65. Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M, et al. (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science, 312:436-439. doi: 10.1126/science.1126088 PMID: 16627744