title: Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: 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.
authors.forename: Daniel
authors.initials: D
authors.lastname: Gonzalez-Ibeas
authors.forename: José
authors.initials: J
authors.lastname: Blanca
authors.forename: Livia
authors.initials: L
authors.lastname: Donaire
authors.forename: Montserrat
authors.initials: M
authors.lastname: Saladié
authors.forename: Albert
authors.initials: A
authors.lastname: Mascarell-Creus
authors.forename: Ana
authors.initials: A
authors.lastname: Cano-Delgado
authors.forename: Jordi
authors.initials: J
authors.lastname: Garcia-Mas
authors.forename: Cesar
authors.initials: C
authors.lastname: Llave
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Aranda
mesh_terms: D001483:Base Sequence; D019184:Carmovirus / Q000502:physiology; D018548:Cotyledon / Q000235:genetics / Q000254:growth & development / Q000276:immunology / Q000821:virology; D028463:Cucumis melo / Q000235:genetics* / Q000254:growth & development / Q000276:immunology / Q000821:virology; D060467:Disease Resistance / Q000235:genetics; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics; D010788:Photosynthesis / Q000235:genetics; D054817:Pollination / Q000235:genetics; D017800:Potyvirus / Q000502:physiology; D018749:RNA, Plant / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*; D013045:Species Specificity; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant; D058727:RNA, Small Untranslated