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Open Access Research article

A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus

M Carmen Marques12, Hugo Alonso-Cantabrana13, Javier Forment1, Raquel Arribas1, Santiago Alamar14, Vicente Conejero1 and Miguel A Perez-Amador1*

Author Affiliations

1 Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia and Consejo Superior de Investigaciones Científicas (CSIC). Avenida de los Naranjos s/n, 46022 Valencia, Spain

2 Current address : Centro de Investigación Príncipe Felipe. Avenida Autopista del Saler 16, 46012 Valencia, Spain

3 Current address : Synergia Bionostra S.L. Ronda de Poniente 4, 28760 Tres Cantos, Madrid, Spain

4 Current address : Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Burjassot, Valencia, Spain

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BMC Genomics 2009, 10:428  doi:10.1186/1471-2164-10-428

Published: 11 September 2009

Abstract

Background

Interpretation of ever-increasing raw sequence information generated by modern genome sequencing technologies faces multiple challenges, such as gene function analysis and genome annotation. Indeed, nearly 40% of genes in plants encode proteins of unknown function. Functional characterization of these genes is one of the main challenges in modern biology. In this regard, the availability of full-length cDNA clones may fill in the gap created between sequence information and biological knowledge. Full-length cDNA clones facilitate functional analysis of the corresponding genes enabling manipulation of their expression in heterologous systems and the generation of a variety of tagged versions of the native protein. In addition, the development of full-length cDNA sequences has the power to improve the quality of genome annotation.

Results

We developed an integrated method to generate a new normalized EST collection enriched in full-length and rare transcripts of different citrus species from multiple tissues and developmental stages. We constructed a total of 15 cDNA libraries, from which we isolated 10,898 high-quality ESTs representing 6142 different genes. Percentages of redundancy and proportion of full-length clones range from 8 to 33, and 67 to 85, respectively, indicating good efficiency of the approach employed. The new EST collection adds 2113 new citrus ESTs, representing 1831 unigenes, to the collection of citrus genes available in the public databases. To facilitate functional analysis, cDNAs were introduced in a Gateway-based cloning vector for high-throughput functional analysis of genes in planta. Herein, we describe the technical methods used in the library construction, sequence analysis of clones and the overexpression of CitrSEP, a citrus homolog to the Arabidopsis SEP3 gene, in Arabidopsis as an example of a practical application of the engineered Gateway vector for functional analysis.

Conclusion

The new EST collection denotes an important step towards the identification of all genes in the citrus genome. Furthermore, public availability of the cDNA clones generated in this study, and not only their sequence, enables testing of the biological function of the genes represented in the collection. Expression of the citrus SEP3 homologue, CitrSEP, in Arabidopsis results in early flowering, along with other phenotypes resembling the over-expression of the Arabidopsis SEPALLATA genes. Our findings suggest that the members of the SEP gene family play similar roles in these quite distant plant species.