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Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon
Clepet, Christian (Institut national de la recherche agronomique (França). Unité de Recherche en Génomique Végétale)
Joobeur, Tarek (Ohio State University)
Zheng, Yi (Boyce Thompson Institute)
Jublot, Delphine (Institut national de la recherche agronomique (França). Unité de Recherche en Génomique Végétale)
Huang, Mingyun (Boyce Thompson Institute)
Truniger, Veronica (Centro de Edafología y Biología Aplicada del Segura)
Boualem, Adnane (Institut national de la recherche agronomique (França). Unité de Recherche en Génomique Végétale)
Hernandez Gonzalez, Maria Elena (Ohio State University)
Dolcet Sanjuan, Ramon (Centre de Recerca en Agrigenòmica)
Portnoy, Vitaly (Newe Ya'ar Research Center)
Mascarell Creus, Albert (Centre de Recerca en Agrigenòmica)
Caño Delgado, Ana I. (Centre de Recerca en Agrigenòmica)
Katzir, Nurit (Newe Ya'ar Research Center)
Bendahmane, Abdelhafid (Institut national de la recherche agronomique (França). Unité de Recherche en Génomique Végétale)
Giovannoni, Jame J. (Boyce Thompson Institute)
Aranda, Miguel A. (Centro de Edafología y Biología Aplicada del Segura)
Garcia Mas, Jordi (Centre de Recerca en Agrigenòmica)
Fei, Zhangjun (Boyce Thompson Institute)

Date: 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 relate species, comparative genomic studies and for gaining insights into gene expression patterns.
Rights: Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original. Creative Commons
Language: Anglès.
Document: article ; recerca ; publishedVersion
Published in: BMC genomics, Vol. 12 (2011) , art. 252, ISSN 1471-2164

DOI: 10.1186/1471-2164-12-252
PMID: 21599934

12 p, 726.6 KB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (scientific output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles

 Record created 2017-06-26, last modified 2019-11-05

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