Novel microRNAs regulating ripening-associated processes in banana fruit

  • Deepika Lakhwani
  • Sanchita
  • Ashutosh Pandey
  • Deepika Sharma
  • Mehar H. AsifEmail author
  • Prabodh K. TrivediEmail author
Original paper


MicroRNAs (miRNAs) modulate gene expression and regulate various physiological and developmental processes in plants. During fruit ripening phase, several physiological and biochemical variations take place resulting changes in colour and texture, softening and production of aroma volatiles. A number of pathways leading to cell wall hydrolysis, ethylene signaling, biosynthesis of fatty acids, esters and a number of secondary plant products play important role during fruit ripening. However, detailed analysis of various processes regulated by miRNAs has not been studied in detailed in a number of fruits. In this study, we sequenced small RNA libraries from ripe and un-ripe fruit of Banana (Musa acuminata), an important and staple food crop, to identify miRNAs regulating fruit ripening. Our analysis identified a number of novel miRNAs which are differentially expressed during fruit ripening. These novel miRNAs were analyzed for their precursors, chromosome localization and targets. Some of these miRNAs were identified to target genes involved in miRNA biogenesis, fruit softening and aroma biosynthesis. This study advances our knowledges in the area of fruit ripening process regulated by miRNAs.


Musa acuminata Ethylene Fruit ripening miRNA Small RNA sequencing 



This work was supported by the Department of Biotechnology, New Delhi under NER-Banana Programme and Council of Scientific and Industrial Research, New Delhi (Network Project-BSC 107).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10725_2020_572_MOESM1_ESM.docx (16 kb)
Supplementary file1 (DOCX 16 kb)
10725_2020_572_MOESM2_ESM.tif (122 kb)
Supplementary file2 (TIF 122 kb)
10725_2020_572_MOESM3_ESM.docx (18 kb)
Supplementary file3 (DOCX 17 kb)
10725_2020_572_MOESM4_ESM.xlsx (72 kb)
Supplementary file4 (XLSX 72 kb)
10725_2020_572_MOESM5_ESM.xlsx (72 kb)
Supplementary file5 (XLSX 71 kb)
10725_2020_572_MOESM6_ESM.xlsx (20 kb)
Supplementary file6 (XLSX 19 kb)
10725_2020_572_MOESM7_ESM.xlsx (326 kb)
Supplementary file7 (XLSX 325 kb)


  1. Alscher RG, Erturk N, Heath LS (2002) Role of superoxide dismutases (SODs) in controlling oxidative stress in plants. J Exp Bot 53:1331–1341PubMedCrossRefGoogle Scholar
  2. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106PubMedPubMedCentralCrossRefGoogle Scholar
  3. Anjali N, Nadiya F, Thomas J, Sabu KK (2019) Identification and characterization of drought responsive microRNAs and their target genes in cardamom (Elettaria cardamomum Maton). Plant Growth Regul 87:201–216CrossRefGoogle Scholar
  4. Asif M, Trivedi P, Solomos T, Tucker M (2006) Isolation of high-quality RNA from apple (Malus domestica) fruit. J Agric Food Chem 54:5227–5229PubMedCrossRefGoogle Scholar
  5. Asif MH, Pathak N, Solomos T, Trivedi PK (2009) Effect of low oxygen, temperature and 1-methylcyclopropene on the expression of genes regulating ethylene biosynthesis and perception during ripening in apple. S Afr J Bot 75:137–144CrossRefGoogle Scholar
  6. Asif MH, Lakhwani D, Pathak S, Gupta P, Bag SK, Nath P, Trivedi PK (2014) Transcriptome analysis of ripe and unripe fruit tissue of banana identifies major metabolic networks involved in fruit ripening process. BMC Plant Biol 14:316PubMedPubMedCentralCrossRefGoogle Scholar
  7. Bapat VA, Trivedi PK, Ghosh A, Sane VA, Ganapathi TR, Nath P (2010) Ripening of fleshy fruit: molecular insight and the role of ethylene. Biotechnol Adv 28:94–107PubMedCrossRefGoogle Scholar
  8. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297CrossRefGoogle Scholar
  9. Bhatia C, Pandey A, Gaddam SR, Hoecker U, Trivedi PK (2018) Low temperature-enhanced flavonol synthesis requires light-associated regulatory components in Arabidopsis thaliana. Plant Cell Physiol 59:2099–2112PubMedCrossRefGoogle Scholar
  10. Bi F, Meng X, Ma C, Yi G (2015) Identification of miRNAs involved in fruit ripening in Cavendish bananas by deep sequencing. BMC Genomics 16:776PubMedPubMedCentralCrossRefGoogle Scholar
  11. Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320:1185–1190PubMedCrossRefGoogle Scholar
  12. Chung MY, Vrebalov J, Alba R, Lee J, McQuinn R, Chung JD, Klein P, Giovannoni J (2010) A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening. Plant J 64:936–947PubMedCrossRefGoogle Scholar
  13. Csukasi F, Donaire L, Casanal A, Martinez-Priego L, Botella MA, Medina-Escobar N, Llave C, Valpuesta V (2012) Two strawberry miR159 family members display developmental-specific expression patterns in the fruit receptacle and cooperatively regulate Fa-GAMYB. New Phytol 195:47–57PubMedCrossRefGoogle Scholar
  14. Dai XB, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:W155–W159PubMedPubMedCentralCrossRefGoogle Scholar
  15. Debernardi JM, Rodriguez RE, Mecchia MA, Palatnik JF (2012) Functional specialization of the plant miR396 regulatory network through distinct microRNA-target interactions. PLoS Genet 8:e1002419PubMedPubMedCentralCrossRefGoogle Scholar
  16. Dhar YV, Lakhwani D, Pandey A, Singh S, Trivedi PK, Asif MH (2019) Genome-wide identification and interactome analysis of members of two-component system in Banana. BMC Genomics 20:674PubMedPubMedCentralCrossRefGoogle Scholar
  17. D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengelle J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, McKain MR, Leebens-Mack J, Burgess D, Freeling M, Mbeguie AMD, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quetier F, Yahiaoui N, Wincker P (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488:213–217PubMedCrossRefGoogle Scholar
  18. Droc G, Lariviere D, Guignon V, Yahiaoui N, This D, Garsmeur O, Dereeper A, Hamelin C, Argout X, Dufayard JF, Lengelle J, Baurens FC, Cenci A, Pitollat B, D'Hont A, Ruiz M, Rouard M, Bocs S (2013) The banana genome hub. Database. CrossRefPubMedPubMedCentralGoogle Scholar
  19. Elitzur T, Yakir E, Quansah L, Fei ZJ, Vrebalov J, Khayat E, Giovannoni JJ, Friedman H (2016) Banana MaMADS transcription factors are necessary for fruit ripening and molecular tools to promote shelf-life and food security. Plant Physiol 171:380–391PubMedPubMedCentralCrossRefGoogle Scholar
  20. Eriksson EM, Bovy A, Manning K, Harrison L, Andrews J, De Silva J, Tucker GA, Seymour GB (2004) Effect of the colorless non-ripening mutation on cell wall biochemistry and gene expression during tomato fruit development and ripening. Plant Physiol 136:4184–4197PubMedPubMedCentralCrossRefGoogle Scholar
  21. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of miRNA genes. PLoS ONE 2:e219PubMedPubMedCentralCrossRefGoogle Scholar
  22. Friedlander MR, Mackowiak SD, Li N, Chen W, Rajewsky N (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 40:37–52CrossRefGoogle Scholar
  23. Fujisawa M, Shima Y, Higuchi N, Nakano T, Koyama Y, Kasumi T, Ito Y (2012) Direct targets of the tomato-ripening regulator RIN identified by transcriptome and chromatin immunoprecipitation analyses. Planta 235:1107–1122PubMedCrossRefGoogle Scholar
  24. Gao C, Ju Z, Cao D, Zhai B, Qin G, Zhu H, Fu D, Luo Y, Zhu B (2015) MicroRNA profiling analysis throughout tomato fruit development and ripening reveals potential regulatory role of RIN on microRNAs accumulation. Plant Biotechnol J 13:370–382PubMedCrossRefGoogle Scholar
  25. Hou YM, Zhai LL, Li XY, Xue Y, Wang JJ, Yang PJ, Cao CM, Li HX, Cui YH, Bian SM (2017) Comparative analysis of fruit ripening-related miRNAs and their targets in Blueberry using small RNA and degradome sequencing. Int J Mol Sci 18:2767PubMedCentralCrossRefPubMedGoogle Scholar
  26. Howe EA, Sinha R, Schlauch D, Quackenbush J (2011) RNA-Seq analysis in MeV. Bioinformatics 27:3209–3210PubMedPubMedCentralCrossRefGoogle Scholar
  27. Jain M, Chevala VV, Garg R (2014) Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing. J Exp Bot 65:5945–5958PubMedPubMedCentralCrossRefGoogle Scholar
  28. Kamthan A, Chaudhuri A, Kamthan M, Datta A (2015) Small RNAs in plants: recent development and application for crop improvement. Front Plant Sci 6:208PubMedPubMedCentralCrossRefGoogle Scholar
  29. Karlova R, van Haarst JC, Maliepaard C, van de Geest H, Bovy AG, Lammers M, Angenent GC, de Maagd RA (2013) Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis. J Exp Bot 64:1863–1878PubMedPubMedCentralCrossRefGoogle Scholar
  30. Kesari R, Trivedi PK, Nath P (2007) Ethylene-induced ripening in banana evokes expression of defense and stress related genes in fruit tissue. Postharvest Biol Technol 46:136–143CrossRefGoogle Scholar
  31. Kesari R, Trivedi PK, Nath P (2010) Gene expression of pathogenesis-related protein during banana ripening and after treatment with 1-MCP. Postharvest Biol Technol 56:64–70CrossRefGoogle Scholar
  32. Lakhwani D, Pandey A, Dhar YV, Bag SK, Trivedi PK, Asif MH (2016) Genome-wide analysis of the AP2/ERF family in Musa species reveals divergence and neofunctionalisation during evolution. Sci Rep 6:18878PubMedPubMedCentralCrossRefGoogle Scholar
  33. 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:R25PubMedPubMedCentralCrossRefGoogle Scholar
  34. Leung AKL, Sharp PA (2010) MicroRNA functions in stress responses. Mol Cell 40:205–215PubMedPubMedCentralCrossRefGoogle Scholar
  35. Li WC, Wu JY, Zhang HN, Shi SY, Liu LQ, Shu B, Liang QZ, Xie JH, Wei YZ (2014) De novo assembly and characterization of pericarp transcriptome and identification of candidate genes mediating fruit cracking in Litchi chinensis Sonn. Int J Mol Sci 15:17667–17685PubMedPubMedCentralCrossRefGoogle Scholar
  36. Liu YL, Wang L, Chen DJ, Wu XM, Huang D, Chen LL, Li L, Deng XX, Xu Q (2014) Genome-wide comparison of microRNAs and their targeted transcripts among leaf, flower and fruit of sweet orange. BMC Genomics 15:695PubMedPubMedCentralCrossRefGoogle Scholar
  37. Lohani S, Trivedi PK, Nath P (2004) Changes in activities of cell wall hydrolases during ethylene-induced ripening in banana: effect of 1-MCP, ABA and IAA. Postharvest Biol Technol 31:119–126CrossRefGoogle Scholar
  38. Lotfi A, Pervaiz T, Jiu S, Faghihi F, Jahanbakhshian Z, Ghadirzadeh F, Jinggui K, Seyed F, Seyedi M (2017) Role of microRNAs and their target genes in salinity response in plants. Plant Growth Regul 82:377–390CrossRefGoogle Scholar
  39. Luo X, Gao Z, Shi T, Cheng Z, Zhang Z, Ni Z (2013) Identification of miRNAs and their target genes in Peach (Prunus persica L.) using high-throughput sequencing and degradome analysis. PLoS ONE 8:e79090PubMedPubMedCentralCrossRefGoogle Scholar
  40. Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, Moulton V, Dalmay T (2008) Deep sequencing of tomato short RNAs identifies miRNAs targeting genes involved in fruit ripening. Genome Res 18:1602–1609PubMedPubMedCentralCrossRefGoogle Scholar
  41. Pandey A, Alok A, Lakhwani D, Singh J, Asif MH, Trivedi PK (2016) Genome-wide expression analysis and metabolite profiling elucidate transcriptional regulation of flavonoid biosynthesis and modulation under abiotic stresses in banana. Sci Rep 6:31361PubMedPubMedCentralCrossRefGoogle Scholar
  42. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20:3407–3425PubMedPubMedCentralCrossRefGoogle Scholar
  43. Reimand J, Kull M, Peterson H, Hansen J, Vilo J (2007) g : Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res 35:W193–W200PubMedPubMedCentralCrossRefGoogle Scholar
  44. Ruan MB, Zhao YT, Meng ZH, Wang XJ, Yang WC (2009) Conserved miRNA analysis in Gossypiumhirsutum through small RNA sequencing. Genomics 94:263–268PubMedCrossRefGoogle Scholar
  45. Rubio-Somoza I, Cuperus JT, Weige D, Carrington JC (2009) Regulation and functional specialization of small RNA-target nodes during plant development. Curr Opin Plant Biol 12:622–627PubMedCrossRefGoogle Scholar
  46. Sanchita TR, Asif MH, Trivedi PK (2018) Dietary plant miRNAs as an augmented therapy: cross-kingdom gene regulation. RNA Biol 15:1433–1439PubMedPubMedCentralCrossRefGoogle Scholar
  47. Sharma D, Tiwari M, Lakhwani D, Tripathi RD, Trivedi PK (2015) Differential expression of microRNAs by arsenate and arsenite stress in natural accessions of rice. Metallomics 7:174–187PubMedCrossRefGoogle Scholar
  48. Sharma D, Tiwari M, Pandey A, Bhatia C, Sharma A, Trivedi PK (2016) MicroRNA858 is a potential regulator of phenylpropanoid pathway and plant development. Plant Physiol 171:944–959PubMedPubMedCentralGoogle Scholar
  49. Si JN, Zhou T, Bo WH, Xu F, Wu RL (2014) Genome-wide analysis of salt-responsive and novel microRNAs in Populus euphratica by deep sequencing. BMC Genet 15:S6PubMedPubMedCentralCrossRefGoogle Scholar
  50. Singh R, Parihar P, Singh S, Singh MPVVB, Singh VP, Prasad SM (2017) Micro RNAs and nitric oxide cross talk in stress tolerance in plants. Plant Growth Regul 83:199–205CrossRefGoogle Scholar
  51. Song CNA, Wang C, Zhang CQ, Korir NK, Yu HP, Ma ZQ, Fang JG (2010) Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics 11:431PubMedPubMedCentralCrossRefGoogle Scholar
  52. Stauffer E, Maizel A (2014) Post-transcriptional regulation in root development. Wiley Interdiscip Rev RNA 5:679–696PubMedCrossRefGoogle Scholar
  53. Stocks MB, Moxon S, Mapleson D, Woolfenden HC, Mohorianu I, Folkes L, Schwach F, Dalmay T, Moulton V (2012) The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics 28:2059–2061PubMedPubMedCentralCrossRefGoogle Scholar
  54. Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK (2008) Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol 8:25PubMedPubMedCentralCrossRefGoogle Scholar
  55. Tiwari M, Sharma D, Trivedi PK (2014) Artificial microRNA mediated gene silencing in plants: progress and perspectives. Plant Mol Biol 86:1–18PubMedCrossRefGoogle Scholar
  56. Trivedi PK, Nath P (2004) MaExp1, an ethylene-induced expansin from ripening banana fruit. Plant Sci 167:1351–1358CrossRefGoogle Scholar
  57. Wang T, Chen L, Zhao M, Tian Q, Zhang WH (2011) Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. BMC Genomics 12:367PubMedPubMedCentralCrossRefGoogle Scholar
  58. Wu J, Wang DF, Liu YF, Wang L, Qiao X, Zhang SL (2014) Identification of miRNAs involved in pear fruit development and quality. BMC Genomics 15:953PubMedPubMedCentralCrossRefGoogle Scholar
  59. Xin CQ, Liu WF, Lin Q, Zhang XW, Cui P, Li FS, Zhang GY, Pan LL, Al-Amer A, Mei HL, Al-Mssallem IS, Hu SN, Al-Johi HA, Yu J (2015) Profiling microRNA expression during multi-staged date palm (Phoenix dactylifera L.) fruit development. Genomics 105:242–251PubMedCrossRefGoogle Scholar
  60. Zhang C, Zhang B, Ma R, Yu J, Guo S, Guo L, Korir NK (2016) Identification of known and novel microRNAs and their targets in Peach (Prunus persica) fruit by high-throughput sequencing. PLoS ONE 11:e0159253PubMedPubMedCentralCrossRefGoogle Scholar
  61. Zhu MK, Chen GP, Zhou S, Tu Y, Wang Y, Dong TT, Hu ZL (2014) A new tomato NAC (NAM/ATAF1/2/CUC2) transcription factor, SlNAC4, functions as a positive regulator of fruit ripening and carotenoid accumulation. Plant Cell Physiol 55:119–135PubMedCrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2020

Authors and Affiliations

  1. 1.CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI)LucknowIndia
  2. 2.Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
  3. 3.National Institute of Plant Genome ResearchNew DelhiIndia

Personalised recommendations