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BMC Genomics. 2015 May 16;16:393. doi: 10.1186/s12864-015-1610-5.

miRVine: a microRNA expression atlas of grapevine based on small RNA sequencing.

Author information

1
Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. kullan@sun.ac.za.
2
Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. d.lopespaimpinto@sssup.it.
3
Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. e.bertolini@sssup.it.
4
Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. marianna.fasoli@univr.it.
5
Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. sara.zenoni@univr.it.
6
Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. giovannibattista.tornielli@univr.it.
7
Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy. mario.pezzotti@univr.it.
8
Department of Plant and Soil Sciences, University of Delaware, 15 Innovation Way, 19711, Newark, DE, USA. meyers@dbi.udel.edu.
9
Department of Computer, Control and Management Engineering, University of Rome "La Sapienza", Via Ariosto 25, 00185, Rome, Italy. farina@dis.uniroma1.it.
10
Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. marioenrico.pe@sssup.it.
11
Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. erica.mica@entecra.it.
12
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.

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.

PMID:
25981679
PMCID:
PMC4434875
DOI:
10.1186/s12864-015-1610-5
[Indexed for MEDLINE]
Free PMC Article

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