Open Access Open Badges Research article

Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing

Daniel Gonzalez-Ibeas1, José Blanca2, Livia Donaire3, Montserrat Saladié4, Albert Mascarell-Creus5, Ana Cano-Delgado5, Jordi Garcia-Mas4, Cesar Llave3 and Miguel A Aranda1*

Author affiliations

1 Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS) - CSIC, Apdo. correos 164, 30100 Espinardo (Murcia), Spain

2 Departamento de Biotecnología, Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV) - UPV, Camino de Vera s/n, 46022 Valencia, Spain

3 Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas (CIB) - CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain

4 IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 (Barcelona), Spain

5 Molecular Genetics Department, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 (Barcelona), Spain

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Citation and License

BMC Genomics 2011, 12:393  doi:10.1186/1471-2164-12-393

Published: 3 August 2011



Melon (Cucumis melo L.) is a commercially important fruit crop that is cultivated worldwide. The melon research community has recently benefited from the determination of a complete draft genome sequence and the development of associated genomic tools, which have allowed us to focus on small RNAs (sRNAs). These are short, non-coding RNAs 21-24 nucleotides in length with diverse physiological roles. In plants, they regulate gene expression and heterochromatin assembly, and control protection against virus infection. Much remains to be learned about the role of sRNAs in melon.


We constructed 10 sRNA libraries from two stages of developing ovaries, fruits and photosynthetic cotyledons infected with viruses, and carried out high-throughput pyrosequencing. We catalogued and analysed the melon sRNAs, resulting in the identification of 26 known miRNA families (many conserved with other species), the prediction of 84 melon-specific miRNA candidates, the identification of trans-acting siRNAs, and the identification of chloroplast, mitochondrion and transposon-derived sRNAs. In silico analysis revealed more than 400 potential targets for the conserved and novel miRNAs.


We have discovered and analysed a large number of conserved and melon-specific sRNAs, including miRNAs and their potential target genes. This provides insight into the composition and function of the melon small RNAome, and paves the way towards an understanding of sRNA-mediated processes that regulate melon fruit development and melon-virus interactions.