Melogene: New genomic tools for Melon (Cucumis melo) breeding: transcriptome, SSR, SNP collections and high throughput genotyping platforms.
Melogene includes a new version of the melon transcriptome with of 49,741 unigenes generated at COMAV. These unigenes have been annotated, screened for SSR motifs and used to identify a large SNP collection suited for high-throughput mapping purposes. All the ESTs used for the assembly are described in Melon Transcriptome Characterization: Simple Sequence Repeats and Single Nucleotide Polymorphisms Discovery for High Throughput Genotyping across the Species. A new assembly of these ESTs was produced with iAssembler v1.3. They include:
- 125,908 Sanger ESTs produced in several international projects available at ICuGI from different libraries and 10 melon genotypes representing several botanic groups of the two C. melo subspecies (the inodorus Piel de sapo T111 and Piñonet, the inodorus TamDew, the cantalupensis Vedrantais, Dulce, Noy Israel, Charentais, and C35, and the exotic conomon PI161375 and Pat81).
- 689,054 454 ESTs produced with GS FLX and GS FLX Titanium from multi tissue libraries of 4 genotypes (T111, Piñonet, Vedrantais, and PI161375) (Blanca et al., 2011, available at the NCBI Sequence Read Archive (SRA) with code SRA050214.1).
All these ESTs along with a new collection of short reads produced by SOLiD (sequenced by Sistemas Genómicos S.L.) after resequencing the transcriptome of 8 pools including 67 melon genotypes, have been mapped to the new transcriptome to generate a large SNP collection (239,521) that will accelerate genetics and breeding of this crop.
PLEASE READ BEFORE ACCESSING THE DATA. This data is made available before its publication with the understanding that users will respect the rights of those who contributed to produce it. The users are allowed to use it, but they are not allowed to publish it without the authorization of the owers of this web site.
- MELOGEN: an EST database for melon functional genomics. BMC Genomics 2007, 8:306 doi:10.1186/1471-2164-8-306
- Melon Transcriptome Characterization: Simple Sequence Repeats and Single Nucleotide Polymorphisms discovery. José Miguel Blanca, Joaquín Cañizares, Pello Ziarsolo, Cristina Esteras, Gisela Mir, Fernando Nuez, Jordi Garcia-Mas, and María Belén Picó. 2011.
- Transcriptome Sequencing for SNP discovery across Cucumis melo. José Blanca, Cristina Esteras, Pello Ziarsolo, Daniel Pérez, Victoria Fernández, Carmen Collado, Raquel Rodríguez, Alida Ballester, Cristina Roig, Joaquín Cañizares and Belén Pico. 2012.
- SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium. Esteras C, Formisano G, Roig C, Díaz A, Blanca J, Garcia-Mas J, Gómez-Guillamón ML, López-Sesé AI, Lázaro A, Monforte AJ, Picó B. 2013