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

Daniel Gonzalez-Ibeas,Miguel A Aranda,Livia Donaire,José Blanca,Jordi Garcia-Mas,Ana Cano-Delgado,Montserrat Saladié,Albert Mascarell-Creus,Cesar Llave

doi:10.1186/1471-2164-12-393

Abstract

BackgroundMelon (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.ResultsWe 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.ConclusionWe 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.

Highlights

Melon (Cucumis melo L.) is a commercially important fruit crop that is cultivated worldwide
Results cDNA libraries and sequencing of small RNAs We used high throughput sequencing data to analyze the composition of the small RNA transcriptome of melon and compare the results to data in publicly-available RNA and genomic databases
Targets in Arabidopsis defined by miRanda generally have a score ≥170, and using this value as cutoff we found 150 melon unigenes as potential miRNA targets, the best of which are summarized in Table 4

Summary

Introduction

Melon (Cucumis melo L.) is a commercially important fruit crop that is cultivated worldwide. Despite the importance of melon, not much was available in the way of genomic sequence information prior to the establishment of a functional genomics consortium in 2004, which developed a range of tools and accumulated more than 33,000 expressed sequence tags (ESTs) and ~17,000 tentative consensus sequences (unigenes) [5] This EST collection has been expanded recently with the addition of 94,000 new ESTs from full-length enriched cDNA and standard cDNA libraries from various melon tissues and cultivars in the framework of the International Cucurbit Genome Initiative [6]. A melon sequencing consortium has recently produced a high-quality draft of the melon genome (unpublished data) These resources provided significant advances in the analysis of melon gene expression, the small RNA (sRNAs) component of the melon transcriptome has not been studied in detail. These important molecules have been studied in other crop species and have been shown to fulfill a number of critical regulatory roles [9,10,11,12]

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