Unravelling the complexity of microRNA-mediated gene regulation in black pepper (Piper nigrum L.) using high-throughput small RNA profiling

Plant Cell Reports

Volumn 35, Issue 1, 2016, Pages 53-63

  Asha, Srinivasan ^a   Sreekumar, Sweda ^a   Soniya, E V ^a  

^a RAJIV GANDHI CENTRE FOR BIOTECHNOLOGY   (India)

Author keywords

Black pepper; High throughput sequencing; microRNAs; miRNA isoforms; Spices; Targets

Indexed keywords

MESSENGER RNA; MICRORNA; PLANT RNA; RNA ISOFORM; TRANSCRIPTOME;

BIOLOGY; BLACK PEPPER; CONSERVED SEQUENCE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; NUCLEOTIDE SEQUENCE; PLANT LEAF; PLANT STEM; SEQUENCE ANALYSIS;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICRORNAS; PIPER NIGRUM; PLANT LEAVES; PLANT STEMS; RNA ISOFORMS; RNA, MESSENGER; RNA, PLANT; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84953367477     PISSN: 07217714     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00299-015-1866-x     Document Type: Article

References (36)

1. Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, Carrington JC (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet 36:1282–1290
2. Asha S, Nisha J, Soniya EV (2013) In silico characterisation and phylogenetic analysis of two evolutionarily conserved miRNAs (miR166 and miR171) from black pepper (Piper nigrum L.). Plant Mol Biol Rep 31:707–771
3. Chang TH, Horng JT, Huang HD (2008) RNALogo: a new approach to display structural RNA alignment. Nucleic Acids Res 36:W91–W96
4. Chao YT, Su CL, Jean WH, Chen WC, Chang YCA, Shih MC (2013) Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite. Plant Mol Biol 84:529–548
5. Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:9–155
6. de Felippes FF, Schneeberger K, Dezulian T, Huson DH, Weigel D (2008) Evolution of Arabidopsis thaliana microRNAs from random sequences. RNA 14:2455–2459
7. Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, Laubinger S, Smith LM, Dasenko M, Givan SA, Weigel D, Carrington JC (2010) MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell 22:1074–1089
8. Galli V, Guzman F, de Oliveira LFV, Loss-Morais G, Korbes AP, Silva SDA, Margis-Pinheiro MAN, Margis R (2014) Identifying MicroRNAs and transcript targets in Jatropha seeds. PLoS One 9:e83727
9. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53
10. Joy N, Soniya EV (2012) Identification of a miRNA candidate reflects the possible significance of transcribed microsatellites in the hairpin precursors of black pepper. Funct Integr Genomics 12:387–395
11. Joy N, Asha S, Mallika V, Soniya EV (2013) De novo transcriptome sequencing reveals a considerable bias in the incidence of simple sequence repeats towards the downstream of ‘Pre-miRNAs’ of black pepper. PLoS One 8:e56694
12. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39:D152–D157
13. Li R, Yu C, Li Y, Lam TM, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966–1967
14. Llave C, Kasschau KD, Rector MA, Carrington JC (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell 14:1605–1619
15. Lu C, Meyers BC, Green PJ (2007) Green construction of small RNA cDNA libraries for deep sequencing. Methods 43:110–117
16. Mandhan V, Kaur J, Singh K (2012) smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni. BMC Plant Biol 12:197
17. Meghwal M, Goswami TK (2012) Nutritional constituent of black pepper as medicinal molecules: a review. Sci Rep 1:129
18. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK (2008) Criteria for annotation of plant microRNAs. Plant Cell 20:3186–3790
19. Neilsen CT, Goodall GT, Bracken CP (2012) IsomiRs: the overlooked repertoire in the dynamic microRNAome. Trends Genet 28:544–549
20. Park W, Li J, Song R, Messing J, Chen X (2002) CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol 12:1484–1495
21. Park MY, Wu G, Gonzalez-Sulser A, Vaucheret H, Poethig PS (2005) Nuclear processing and export of microRNAs in Arabidopsis. Proc Natl Acad Sci USA 102:3691–3696
22. Piriyapongsa J, Jordan IK (2008) Dual coding of siRNAs and miRNAs by plant transposable elements. RNA 14:814–821
23. Shen J, Xie K, Xiong L (2010) Global expression profiling of rice microRNAs by one-tube stem-loop reverse transcription quantitative PCR revealed important roles of microRNAs in abiotic stress responses. Mol Genet Genomics 284:477–488
24. Shivaprasad PV, Chen HM, Patel K, Bond DM, Santos BA, Baulcombe DC (2012) A microRNA superfamily regulates nucleotide binding site—leucine-rich repeats and other mRNAs. Plant Cell 24:859–874
25. Sunkar R, Li YF, Jagadeeswaran G (2012) Functions of microRNAs in plant stress responses. Trends Plant Sci 17:196–203
26. 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 Method 3:12
27. Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687
28. Wan LC, Zhang H, Lu S, Zhang L, Qiu Z, Zhao Y, Zeng QY, Lin J (2012) Transcriptome-wide identification and characterization of miRNAs from Pinus densata. BMC Genomics 13:132
29. Wang L, Liu H, Li D, Chen H (2011) Identification and characterization of maize microRNAs involved in the very early stage of seed germination. BMC Genomics 12:154
30. Wu B, Wang M, Ma Y, Yuan L, Lu S (2012) High-throughput sequencing and characterization of the small RNA transcriptome reveal features of novel and conserved microRNAs in Panax ginseng. PLoS One 7:e44385
31. Xin M, Wang Y, Yao Y, Xie C, Peng H, Ni Z, Sun Q (2010) Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.). BMC Plant Biol 10:123–134
32. Xu W, Cui Q, Li F, Liu A (2013) Transcriptome-wide identification and characterization of microRNAs from Castor Bean (Ricinus communis L.). PLoS One 8:e69995
33. 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
34. Zhang R, Marshall D, Bryan GJ, Hornyik C (2013) Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing. PLoS One 8:e57233
35. Zhao JP, Jiang XL, Zhang BY, Su XH (2012) Involvement of microRNA-mediated gene expression regulation in the pathological development of stem canker disease in Populus trichocarpa. PLoS One 7(9):e44968
36. Zuker M, Mathews DH, Turner DH (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide in RNA biochemistry and biotechnology. In: Barciszewski J, Clark BFC (eds) NATO ASI series. Kluwer Academic Publishers, Dordrecht, The Netherlands, p 370