title: miRVine: a microRNA expression atlas of grapevine based on small RNA sequencing.
abstract: BACKGROUND
  miRNAs are the most abundant class of small non-coding RNAs, and they are involved in post-transcriptional regulations, playing a crucial role in the refinement of genetic programming during plant development. Here we present a comprehensive picture of miRNA regulation in Vitis vinifera L. plant during its complete life cycle. Furthering our knowledge about the post-transcriptional regulation of plant development is fundamental to understand the biology of such an important crop.
  
  
  RESULTS
  We analyzed 70 small RNA libraries, prepared from berries, inflorescences, tendrils, buds, carpels, stamens and other samples at different developmental stages. One-hundred and ten known and 175 novel miRNAs have been identified and a wide grapevine expression atlas has been described. The distribution of miRNA abundance reveals that 22 novel miRNAs are specific to stamen, and two of them are, interestingly, involved in ethylene biosynthesis, while only few miRNAs are highly specific to other organs. Thirty-eight miRNAs are present in all our samples, suggesting a role in key regulatory circuit. On the basis of miRNAs abundance and distribution across samples and on the estimated correlation, we suggest that miRNA expression define organ identity. We performed target prediction analysis and focused on miRNA expression analysis in berries and inflorescence during their development, providing an initial functional description of the identified miRNAs.
  
  
  CONCLUSIONS
  Our findings represent a very extensive miRNA expression atlas in grapevine, allowing the definition of how the spatio-temporal distribution of miRNAs defines organ identity. We describe miRNAs abundance in specific tissues not previously described in grapevine and contribute to future targeted functional analyses. Finally, we present a deep characterization of miRNA involvement in berry and inflorescence development, suggesting a role for miRNA-driven hormonal regulation.
authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. kullan@sun.ac.za.
authors.forename: Jayakumar
authors.initials: J
authors.lastname: Belli Kullan
authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. d.lopespaimpinto@sssup.it.
authors.forename: Daniela
authors.initials: D
authors.lastname: Lopes Paim Pinto
authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. e.bertolini@sssup.it.
authors.forename: Edoardo
authors.initials: E
authors.lastname: Bertolini
authors.affiliation: Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. marianna.fasoli@univr.it.
authors.forename: Marianna
authors.initials: M
authors.lastname: Fasoli
authors.affiliation: Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. sara.zenoni@univr.it.
authors.forename: Sara
authors.initials: S
authors.lastname: Zenoni
authors.affiliation: Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. giovannibattista.tornielli@univr.it.
authors.forename: Giovanni Battista
authors.initials: GB
authors.lastname: Tornielli
authors.affiliation: Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. mario.pezzotti@univr.it.
authors.forename: Mario
authors.initials: M
authors.lastname: Pezzotti
authors.affiliation: Department of Plant and Soil Sciences, University of Delaware, 15 Innovation Way, 19711, Newark, DE, USA. meyers@dbi.udel.edu.
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
authors.affiliation: Department of Computer, Control and Management Engineering, University of Rome "La Sapienza", Via Ariosto 25, 00185, Rome, Italy. farina@dis.uniroma1.it.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Farina
authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. marioenrico.pe@sssup.it.
authors.forename: Mario Enrico
authors.initials: ME
authors.lastname: Pè
authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. erica.mica@entecra.it.|Genomics Research Centre, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Via S. Protaso 302, 29017, Fiorenzuola d'Arda (PC), Italy. erica.mica@entecra.it.
authors.forename: Erica
authors.initials: E
authors.lastname: Mica
mesh_terms: D016000:Cluster Analysis; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D056626:Inflorescence / Q000235:genetics / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D025341:Principal Component Analysis; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D027843:Vitis / Q000235:genetics*
chemical_list: D035683:MicroRNAs