Open Access Highly Accessed Research article

Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon

Christian Clepet1, Tarek Joobeur102, Yi Zheng3, Delphine Jublot1, Mingyun Huang3, Veronica Truniger4, Adnane Boualem1, Maria Elena Hernandez-Gonzalez2, Ramon Dolcet-Sanjuan5, Vitaly Portnoy6, Albert Mascarell-Creus7, Ana I Caño-Delgado7, Nurit Katzir6, Abdelhafid Bendahmane18, James J Giovannoni39, Miguel A Aranda4, Jordi Garcia-Mas5 and Zhangjun Fei39*

Author Affiliations

1 URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS. 2, Rue Gaston Crémieux, 91057 Evry, France

2 Molecular and Cellular Imaging Center, The Ohio State University, OARDC, 1680 Madison Ave, Wooster, OH 44691, USA

3 Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA

4 Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain

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

6 Department of Vegetable Research, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel

7 Department de Genètica Molecular, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain

8 Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh Saudi Arabia

9 USDA Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY 14853, USA

10 Seminis Vegetable Seeds, 37437 State Highway 16 Woodland, CA 95695, USA

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BMC Genomics 2011, 12:252  doi:10.1186/1471-2164-12-252

Published: 20 May 2011

Abstract

Background

Melon (Cucumis melo), an economically important vegetable crop, belongs to the Cucurbitaceae family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as a model system for sex determination and vascular biology studies. However, genomic resources currently available for melon are limited.

Result

We constructed eleven full-length enriched and four standard cDNA libraries from fruits, flowers, leaves, roots, cotyledons, and calluses of four different melon genotypes, and generated 71,577 and 22,179 ESTs from full-length enriched and standard cDNA libraries, respectively. These ESTs, together with ~35,000 ESTs available in public domains, were assembled into 24,444 unigenes, which were extensively annotated by comparing their sequences to different protein and functional domain databases, assigning them Gene Ontology (GO) terms, and mapping them onto metabolic pathways. Comparative analysis of melon unigenes and other plant genomes revealed that 75% to 85% of melon unigenes had homologs in other dicot plants, while approximately 70% had homologs in monocot plants. The analysis also identified 6,972 gene families that were conserved across dicot and monocot plants, and 181, 1,192, and 220 gene families specific to fleshy fruit-bearing plants, the Cucurbitaceae family, and melon, respectively. Digital expression analysis identified a total of 175 tissue-specific genes, which provides a valuable gene sequence resource for future genomics and functional studies. Furthermore, we identified 4,068 simple sequence repeats (SSRs) and 3,073 single nucleotide polymorphisms (SNPs) in the melon EST collection. Finally, we obtained a total of 1,382 melon full-length transcripts through the analysis of full-length enriched cDNA clones that were sequenced from both ends. Analysis of these full-length transcripts indicated that sizes of melon 5' and 3' UTRs were similar to those of tomato, but longer than many other dicot plants. Codon usages of melon full-length transcripts were largely similar to those of Arabidopsis coding sequences.

Conclusion

The collection of melon ESTs generated from full-length enriched and standard cDNA libraries is expected to play significant roles in annotating the melon genome. The ESTs and associated analysis results will be useful resources for gene discovery, functional analysis, marker-assisted breeding of melon and closely related species, comparative genomic studies and for gaining insights into gene expression patterns.