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Expression of microRNAs during female inflorescence development in African oil palm (Elaeis guineensis Jacq.)

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Abstract

In African oil palm, the formation of fruit relies on the successful progression of a 2- to 3-year phase of development of inflorescences, in particular the female inflorescence. In this study, we investigated microRNA expression in female inflorescences at two stages of floral development corresponding to the emergence of floral meristems and to the formation of floral organs. High-throughput sequencing data from messenger RNA (mRNA), small RNA, and RNA degradome libraries were used to predict and quantify orthologous and oil palm-specific microRNAs (miRNAs) and their targets. The expression of selected miRNA candidates was validated by quantitative RT-PCR. From female inflorescences, we assembled a reference transcriptome, which allowed us to identify the miRNA precursor sequences and the putative mRNA targets in oil palm. As validated by degradome analysis, we confirmed the cleavage patterns of mRNA targets for oil palm miRNAs. We report here differential gene expression patterns of 18 orthologous miRNA families and their targets in oil palm female inflorescences. Of these, we identified two distinct subsets of orthologous miRNAs that showed inverse expression patterns in female inflorescence of oil palm. We also predicted 15 putative oil palm-specific miRNAs, of which three were validated using quantitative RT-PCR. In oil palm, distinct subsets of miRNAs were differentially expressed at the stage when the floral meristems emerge and at the stage when the floral organs form. These miRNAs are likely to act in concert with their mRNA targets to regulate the early phase of floral organ establishment.

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References

  • Achard P, Herr A, Baulcombe DC, Harberd NP (2004) Modulation of floral development by a gibberellin-regulated microRNA. Development 131:3357–3365

    Article  CAS  PubMed  Google Scholar 

  • Adam H, Jouannic S, Escoute J, Duval Y, Verdeil JL, Tregear JW (2005) Reproductive developmental complexity in the African oil palm (Elaeis guineensis, Arecaceae). Am J Bot 92:1836–1852

    Article  PubMed  Google Scholar 

  • Adam H, Jouannic S, Morcillo F, Richaud F, Duval Y, Tregear JW (2006) MADS box genes in oil palm (Elaeis guineensis): patterns in the evolution of the SQUAMOSA, DEFICIENS, GLOBOSA, AGAMOUS, and SEPALLATA subfamilies. J Mol Evol 62:15–31

    Article  CAS  PubMed  Google Scholar 

  • Adam H, Marguerettaz M, Qadri R, Adroher B, Richaud F, Collin M, Thuillet AC, Vigouroux Y, Laufs P, Tregear JW, Jouannic S (2011) Divergent expression patterns of miR164 and CUP-SHAPED COTYLEDON genes in palms and other monocots: implication for the evolution of meristem function in angiosperms. Mol Biol Evol 28:1439–1454

    Article  CAS  PubMed  Google Scholar 

  • Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol: CB 18:758–762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Allen E, Xie Z, Gustafson AM, Carrington JC (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207–221

    Article  CAS  PubMed  Google Scholar 

  • Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7(10):986–995

    CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beulé T, Camps C, Debiesse S, Tranchant C, Dussert S, Sabau X, Jaligot E, Syed Alwee SSR, Tregear JW (2011) Transcriptome analysis reveals differentially expressed genes associated with the mantled homeotic flowering abnormality in oil palm (Elaeis guineensis). Tree Genet Genomes 7:169–182

    Article  Google Scholar 

  • Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S (2014) Technical variations in low-input RNA-seq methodologies. Sci Rep 4:3678

    Article  PubMed  PubMed Central  Google Scholar 

  • Blazquez MA, Soowal LN, Lee I, Weigel D (1997) LEAFY expression and flower initiation in Arabidopsis. Development 124:3835–3844

    CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Boualem A, Laporte P, Jovanovic M, Laffont C, Plet J, Combier JP, Niebel A, Crespi M, Frugier F (2008) MicroRNA166 controls root and nodule development in Medicago truncatula. Plant J 54:876–887

    Article  CAS  PubMed  Google Scholar 

  • Brousse C, Liu Q, Beauclair L, Deremetz A, Axtell MJ, Bouche N (2014) A non-canonical plant microRNA target site. Nucleic Acids Res 42:5270–5279

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carra A, Mica E, Gambino G, Pindo M, Moser C, Pe ME, Schubert A (2009) Cloning and characterization of small non-coding RNAs from grape. Plant J 59:750–763

    Article  CAS  PubMed  Google Scholar 

  • Chen X (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303:2022–2025

    Article  CAS  PubMed  Google Scholar 

  • Chen X, Zhang Z, Liu D, Zhang K, Li A, Mao L (2010) SQUAMOSA promoter-binding protein-like transcription factors: star players for plant growth and development. J Integr Plant Biol 52:946–951

    Article  CAS  PubMed  Google Scholar 

  • Chi X, Yang Q, Chen X, Wang J, Pan L, Chen M, Yang Z, He Y, Liang X, Yu S (2011) Identification and characterization of microRNAs from peanut (Arachis hypogaea L.) by high-throughput sequencing. PLoS One 6:e27530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chuck G, Meeley R, Irish E, Sakai H, Hake S (2007) The maize tasselseed4 microRNA controls sex determination and meristem cell fate by targeting Tasselseed6/indeterminate spikelet1. Nat Genet 39:1517–1521

    Article  CAS  PubMed  Google Scholar 

  • Corley RHV (1976a) Germination and seedling growth. In: Corley RHV, Hardon JJ, Wood BJ (eds) Developments in crop science. Elsevier, Amsterdam

    Google Scholar 

  • Corley RHV (1976b) Inflorescence abortion and sex differentiation. In: Corley RHV, Hardon JJ, Wood BJ (eds) Developments in crop science. Elsevier, Amsterdam

    Google Scholar 

  • Corley RHV, Gray BS (1976) Growth and morphology. In: Corley RHV, Hardon JJ, Wood BJ (eds) Developments in crop. Elsevier, Amsterdam

    Google Scholar 

  • Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:W155–W159

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • De Smet I, Voss U, Jurgens G, Beeckman T (2009) Receptor-like kinases shape the plant. Nat Cell Biol 11:1166–1173

    Article  CAS  PubMed  Google Scholar 

  • Dransfield J, Uhl NW (1998) Palmae. In: Kubitzki K (ed) Families and genera of vascular plants, flowering plants: monocotyledons. Springer, Berlin

    Google Scholar 

  • Durand-Gasselin T, Noiret JM, Kouamé RK, Cochard B, Adon B (1999) Availability of quality pollen for improved oil palm (Elaeis guineensis Jacq.) seed production. Plantations, Recherche, Développement 6:264–276

    Google Scholar 

  • Fang L, Liang Y, Li D, Cao X, Zheng Y (2013) Dynamic expression analysis of miRNAs during the development process of oil palm mesocarp. Plant Sci J 31:304–312

    Article  CAS  Google Scholar 

  • 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 40:37–52

    Article  PubMed  Google Scholar 

  • German MA, Luo S, Schroth G, Meyers BC, Green PJ (2009) Construction of parallel analysis of RNA ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc 4:356–362

    Article  CAS  PubMed  Google Scholar 

  • Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33:D121–D124

    Article  CAS  PubMed  Google Scholar 

  • Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34:D140–D144

    Article  CAS  PubMed  Google Scholar 

  • Guo HS, Xie Q, Fei JF, Chua NH (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell 17:1376–1386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hausser J, Syed AP, Bilen B, Zavolan M (2013) Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. Genome Res 23:604–615

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429–3431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iwakawa HO, Tomari Y (2013) Molecular insights into microRNA-mediated translational repression in plants. Mol Cell 52:591–601

    Article  CAS  PubMed  Google Scholar 

  • Jacquemard JC (1995) Le palmier a’ huile. Maisonneuve & Larose, Paris

    Google Scholar 

  • Kidner CA, Martienssen RA (2005) The role of ARGONAUTE (AGO1) in meristem formation and identity. Dev Biol 280:504–517

    Article  CAS  PubMed  Google Scholar 

  • Kiefer E, Heller W, Ernst D (2000) A simple and efficient protocol for isolation of functional RNA from plant tissues rich in secondary metabolites. Plant Mol Biol Report 18:33–39

    Article  CAS  Google Scholar 

  • Kim JC, Laparra H, Calderon-Urrea A, Mottinger JP, Moreno MA, Dellaporta SL (2007) Cell cycle arrest of stamen initials in maize sex determination. Genetics 177:2547–2551

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kramer MF. 2011. Stem-loop RT-qPCR for miRNAs. Current protocols in molecular biology. Edited by Frederick M. Ausubel et al., Chapter 15: Unit 15 10

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Lee WS, Gudimella R, Wong GR, Tammi MT, Khalid N, Harikrishna JA (2015) Transcripts and microRNAs responding to salt stress in Musa acuminata Colla (AAA group) cv. Berangan roots. PLoS One 10:e0127526

    Article  PubMed  PubMed Central  Google Scholar 

  • Li S, Liu L, Zhuang X, Yu Y, Liu X, Cui X, Ji L, Pan Z, Cao X, Mo B, Zhang F, Raikhel N, Jiang L, Chen X (2013) MicroRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis. Cell 153:562–574

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li J, Reichel M, Millar AA (2014) Determinants beyond both complementarity and cleavage govern microR159 efficacy in Arabidopsis. PLoS Genet 10:e1004232

    Article  PubMed  PubMed Central  Google Scholar 

  • Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769–773

    Article  CAS  PubMed  Google Scholar 

  • Liu X, Huang J, Wang Y, Khanna K, Xie Z, Owen HA, Zhao D (2010) The role of floral organs in carpels, an Arabidopsis loss-of-function mutation in microRNA160a, in organogenesis and the mechanism regulating its expression. Plant J 62:416–428

    Article  PubMed  Google Scholar 

  • Liu H, Qin C, Chen Z, Zuo T, Yang X, Zhou H, Xu M, Cao S, Shen Y, Lin H, He X, Zhang Y, Li L, Ding H, Lubberstedt T, Zhang Z, Pan G (2014) Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing. BMC Genomics 15:25

    Article  PubMed  PubMed Central  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method. Methods 25:402–408

    Article  CAS  PubMed  Google Scholar 

  • Low ET, Rosli R, Jayanthi N, Mohd-Amin AH, Azizi N, Chan KL, Maqbool NJ, Maclean P, Brauning R, McCulloch A, Moraga R, Ong-Abdullah M, Singh R (2014) Analyses of hypomethylated oil palm gene space. PLoS One 9:e86728

    Article  PubMed  PubMed Central  Google Scholar 

  • Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu S, Peng S, Zhu X, Liu G, Liao X, Li Y, Yang H, Wang J, Lam T, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:18

    Article  PubMed  PubMed Central  Google Scholar 

  • Luo Y, Guo Z, Li L (2013) Evolutionary conservation of microRNA regulatory programs in plant flower development. Dev Biol 380:133–144

    Article  CAS  PubMed  Google Scholar 

  • Martin A, Troadec C, Boualem A, Rajab M, Fernandez R, Morin H, Pitrat M, Dogimont C, Bendahmane A (2009) A transposon-induced epigenetic change leads to sex determination in melon. Nature 461:1135–1138

    Article  CAS  PubMed  Google Scholar 

  • Matts JA, Sytnikova Y, Chirn G, Igloi GL, Lau NC (2014) Small RNA library construction from minute biological samples. Methods Mol Biol 1093:123–136

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Md Nasaruddin N, Harikrishna K, Othman RY, Lim SH, Harikrishna JA (2007) Computational prediction of microRNAs from oil palm (Elaeis guineensis Jacq.) expressed sequence tags. Asia Pac J Mol Biol Biotechnol 15:107–113

    Google Scholar 

  • Mehrpooyan F, Othman RY, Harikrishna JA (2012) Tissue and temporal expression of miR172 paralogs and the AP2-like target in oil palm (Elaeis guineensis Jacq.). Tree Genet Genomes 8:1331–1343

    Article  Google Scholar 

  • 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 20:3186–3190

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, Mardis ER, Sahinalp SC, Unrau PJ (2008) Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res 18:571–584

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ong-Abdullah M, Ordway JM, Jiang N, Ooi SE, Kok SY, Sarpan N, Azimi N, Hashim AT, Ishak Z, Rosli SK, Malike FA, Bakar NA, Marjuni M, Abdullah N, Yaakub Z, Amiruddin MD, Nookiah R, Singh R, Low ET, Chan KL, Azizi N, Smith SW, Bacher B, Budiman MA, Van Brunt A, Wischmeyer C, Beil M, Hogan M, Lakey N, Lim CC, Arulandoo X, Wong CK, Choo CN, Wong WC, Kwan YY, Alwee SS, Sambanthamurthi R, Martienssen RA (2015) Loss of karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525:533–537

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pant BD, Buhtz A, Kehr J, Scheible WR (2008) MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. Plant J 53:731–738

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J (2003) TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652

    Article  CAS  PubMed  Google Scholar 

  • Rogers K, Chen X (2013) Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell 25:2383–2399

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M (2009) SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol 5:e1000386

    Article  PubMed  PubMed Central  Google Scholar 

  • Sanchez Mde L, Costas C, Sequeira-Mendes J, Gutierrez C (2012) Regulating DNA replication in plants. Cold Spring Harb Perspect Biol 4

  • Sarpan N, Kok S, Chai S, Fitrianto A, Nuraziyan A, Zamzuri I, Ong-Abdullah M, Ooi S (2015) A model for predicting flower development in Elaeis guineensis Jacq. J Oil Palm Res 27:315–325

    Google Scholar 

  • Shearman JR, Jantasuriyarat C, Sangsrakru D, Yoocha T, Vannavichit A, Tragoonrung S, Tangphatsornruang S (2013) Transcriptome analysis of normal and mantled developing oil palm flower and fruit. Genomics 101:306–312

    Article  CAS  PubMed  Google Scholar 

  • Shu J, Xia Z, Li L, Liang ET, Slipek N, Shen D, Foo J, Subramanian S, Steer CJ (2012) Dose-dependent differential mRNA target selection and regulation by let-7a-7f and miR-17-92 cluster microRNAs. RNA Biol 9:1275–1287

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh R, Ong-Abdullah M, Low ET, Manaf MA, Rosli R, Nookiah R, Ooi LC, Ooi SE, Chan KL, Halim MA, Azizi N, Nagappan J, Bacher B, Lakey N, Smith SW, He D, Hogan M, Budiman MA, Lee EK, DeSalle R, Kudrna D, Goicoechea JL, Wing RA, Wilson RK, Fulton RS, Ordway JM, Martienssen RA, Sambanthamurthi R (2013) Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature 500:335–339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Somyong S, Poopear S, Sunner SK, Wanlayaporn K, Jomchai N, Yoocha T, Ukoskit K, Tangphatsornruang S, Tragoonrung S (2016) Acc oxidase and miRNA 159a, and their involvement in fresh fruit bunch yield (FFB) via sex ratio determination in oil palm. Mol Gen Genomics. doi:10.1007/s00438-016-1181-4

    Google Scholar 

  • Song Y, Tian M, Ci D, Zhang D (2015) Methylation of microRNA genes regulates gene expression in bisexual flower development in andromonoecious poplar. J Exp Bot 66:1891–1905

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spanudakis E, Jackson S (2014) The role of microRNAs in the control of flowering time. J Exp Bot 65:365–380

    Article  CAS  PubMed  Google Scholar 

  • Sun F, Guo G, Du J, Guo W, Peng H, Ni Z, Sun Q, Yao Y (2014) Whole-genome discovery of miRNAs and their targets in wheat (Triticum aestivum L.). BMC Plant Biol 14:142

    Article  PubMed  PubMed Central  Google Scholar 

  • Szittya G, Moxon S, Santos DM, Jing R, Fevereiro MP, Moulton V, Dalmay T (2008) High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics 9:593

    Article  PubMed  PubMed Central  Google Scholar 

  • Vaucheret H, Vazquez F, Crété P, Bartel DP (2004) The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev 18:1187–1197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang L, Feng Z, Wang X, Zhang X (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26:136–138

    Article  PubMed  Google Scholar 

  • Wang ZJ, Huang JQ, Huang YJ, Li Z, Zheng BS (2012) Discovery and profiling of novel and conserved microRNAs during flower development in Carya cathayensis via deep sequencing. Planta 236:613–621

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Huang J, Sun Z, Zheng B (2015) Identification of microRNAs differentially expressed involved in male flower development. Funct Integr Genomics 15:225–232

    Article  CAS  PubMed  Google Scholar 

  • Xian Z, Huang W, Yang Y, Tang N, Zhang C, Ren M, Li Z (2014) miR168 influences phase transition, leaf epinasty, and fruit development via SlAGO1 in tomato. J Exp Bot 65:6655–6666

    Article  CAS  PubMed  Google Scholar 

  • Xiao Y, Xia W, Yang Y, Mason AS, Lei X, Ma Z. 2013. Characterization and evolution of conserved microRNA through duplication events in date palm (Phoenix dactylifera). PLoS ONE, e71435.

  • Xin C, Liu W, Lin Q, Zhang X, Cui P, Li F, Zhang G, Pan L, Al-Amer A, Mei H, Al-Mssallem IS, Hu S, Al-Johi HA, Yu J (2015) Profiling microRNA expression during multi-staged date palm (Phoenix dactylifera L.) fruit development. Genomics 105(4):242–251

    Article  CAS  PubMed  Google Scholar 

  • Yaish MW, Sunkar R, Zheng Y, Ji B, Al-Yahyai R, Farooq SA (2015) A genome-wide identification of the miRNAome in response to salinity stress in date palm (Phoenix dactylifera L.). Frontiers in Plant Sci 6:946. doi:10.3389/fpls.2015.00946

    Google Scholar 

  • Zhang Z, Yu J, Li D, Liu F, Zhou X, Wang T, Ling Y, Su Z (2010) PMRD: plant microRNA database. Nucleic Acids Res 38:D806–D813

    Article  CAS  PubMed  Google Scholar 

  • Zhu QH, Upadhyaya NM, Gubler F, Helliwell CA (2009) Over-expression of miR172 causes loss of spikelet determinacy and floral organ abnormalities in rice (Oryza sativa). BMC Plant Biol 9:149

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank the Sime Darby Technology Centre Sdn Bhd for providing the additional oil palm female inflorescence materials. We also thank Alena Sanusi for her editorial assistance.

Author contributions

HH: experimental work, analysis of data, writing of manuscript; RG: analysis of data; MO and JAH: concept of project, analysis of data, writing of manuscript; all authors read and approved the final manuscript.

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Authors and Affiliations

  1. Centre for Research in Biotechnology for Agriculture (CEBAR) and Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia

    Huili Ho, Ranganath Gudimella & Jennifer Ann Harikrishna

  2. Breeding and Tissue Culture Unit, Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia

    Meilina Ong-Abdullah

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  1. Huili Ho
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  2. Ranganath Gudimella
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  4. Jennifer Ann Harikrishna
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Corresponding author

Correspondence to Jennifer Ann Harikrishna.

Ethics declarations

The conduct of this research was approved by the grant management committee of the University of Malaya, headed by the Director of Institute of Research Management and Monitoring, Professor Noorsaadah Abdul Rahman (noorsaadah@um.edu.my). This study does not involve the use of any human, animal, and endangered or protected plant species as materials.

Conflict of interest

The data presented resulted from a collaborative study between researchers at the University of Malaya and at the Malaysian Palm Oil Board. The Malaysian Palm Oil Board provided funding and materials to the project. The Malaysian Palm Oil Board staff jointly participated with the university staff and students in the study design, data collection, data analysis, and preparation of the manuscript, in the role of collaborating researchers. The Malaysian Palm Oil Board also was involved in the decision to publish, based solely on consideration of intellectual property protection and not on the potential effects of any publication of results on company business. There is no restriction on the publication of the data or information described in this manuscript.

Funding

This work was supported by the Ministry of Science, Technology and Innovation, Malaysia, grant number ABI (P)-1 55-02-03-1005, and the Postgraduate Research Fund (PS229-2008C and PS316-2010A) awarded by the University of Malaya. JAH is partially funded by the High Impact Research Chancellery Grant UM.C/625/1/HIR/MOHE/SCI/19 from the University of Malaya.

Data archiving statement

The collection of small RNA sequences generated in this study is available under NCBI’s BioProject accession PRJNA305816 and NCBI’s Sequence Read Archive (SRA) database (accession numbers SRR5189964 and SRR5189967), under BioSample accession numbers SAMN06240308 and SAMN06240309. FASTQ reads generated from transcriptome sequencing of +6 and +15 female inflorescences are available under NCBI’s SRA database (accession numbers SRR5189966 and SRR5189969). The consensus reference transcriptome generated from this Transcriptome Shotgun Assembly (TSA) project has been deposited at the DDBJ/ENA/GenBank under the accession GFDD00000000. The version described in this paper is the first version, GFDD01000000. The degradome short reads have been deposited in NCBI’s SRA database (accession numbers SRR5189965 and SRR5189968).

Additional information

Communicated by W. Ratnam

Electronic supplementary material

ESM 1

In-house Python script used for alignment of small RNA reads (TXT 1 kb)

ESM 2

Distribution of repeat-associated 24 nt sequences in +6 and +15 female inflorescences (JPEG 55 kb)

ESM 3

Differentially-expressed orthologous miRNAs in +6 and +15 female inflorescences. Green filled-circles indicate miRNAs that were more highly expressed in +6 female inflorescence (absolute log2 fold change ≥1 and FDR cutoff <0.05), red filled-circles indicate miRNAs that were more highly expressed in +15 female inflorescence (absolute log2 fold change ≥1 and FDR cutoff <0.05) and blue filled-circles indicate non-differentially expressed miRNAs. (JPEG 41 kb)

ESM 4

Differentially expressed miRNAs in +15 female inflorescence. The relative expression levels of orthologous and oil palm-specific miRNAs shown as the ratio of +15/+6 inflorescence RNA (absolute log2 fold change ≥1 or ≤−1 and FDR cutoff <0.05) and their corresponding targets (+15/+6) were calculated using the RNA-seq data. For the orthologous miRNAs, only the ones with TPM ≥100 in at least one of the small RNA libraries were shown. The numbers and letters refer to the predicted target(s) as shown in the bottom panel. White asterisk (*) indicates target for which cleavage products were identified in the degradome data. (JPEG 1972 kb)

ESM 5

Correlation analysis of miRNA expression profiles (log2 fold change) determined by RT-qPCR and RNA-seq (JPEG 271 kb)

ESM 6

(XLSX 14206 kb)

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Ho, H., Gudimella, R., Ong-Abdullah, M. et al. Expression of microRNAs during female inflorescence development in African oil palm (Elaeis guineensis Jacq.). Tree Genetics & Genomes 13, 35 (2017). https://doi.org/10.1007/s11295-017-1120-5

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