title: Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon.
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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors: URGV Plant Genomics, Unité de Recherche en Génomique Végétale, UMR1165 ERL8196 INRA-UEVE-CNRS. 2, Rue Gaston Crémieux, 91057 Evry, France.
authors: Christian
authors: C
authors: Clepet
authors: Tarek
authors: T
authors: Joobeur
authors: Yi
authors: Y
authors: Zheng
authors: Delphine
authors: D
authors: Jublot
authors: Mingyun
authors: M
authors: Huang
authors: Veronica
authors: V
authors: Truniger
authors: Adnane
authors: A
authors: Boualem
authors: Maria Elena
authors: ME
authors: Hernandez-Gonzalez
authors: Ramon
authors: R
authors: Dolcet-Sanjuan
authors: Vitaly
authors: V
authors: Portnoy
authors: Albert
authors: A
authors: Mascarell-Creus
authors: Ana I
authors: AI
authors: Caño-Delgado
authors: Nurit
authors: N
authors: Katzir
authors: Abdelhafid
authors: A
authors: Bendahmane
authors: James J
authors: JJ
authors: Giovannoni
authors: Miguel A
authors: MA
authors: Aranda
authors: Jordi
authors: J
authors: Garcia-Mas
authors: Zhangjun
authors: Z
authors: Fei
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