Open Access Highly Accessed Research article

Transcriptome sequencing for SNP discovery across Cucumis melo

José Blanca1, Cristina Esteras1, Pello Ziarsolo1, Daniel Pérez1, Victoria Fernández-Pedrosa2, Carmen Collado2, Raquel Rodríguez de Pablos2, Alida Ballester2, Cristina Roig1, Joaquín Cañizares1 and Belén Picó1*

Author Affiliations

1 Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain

2 Sistemas Genómicos S.L, Ronda G. Marconi 6, 46980, Paterna, Valencia, Spain

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BMC Genomics 2012, 13:280  doi:10.1186/1471-2164-13-280

Published: 24 June 2012

Additional files

Additional file 1:

Resequenced melon genotypes. Photographs of the fruits of the genotypes resequenced, in eight pools, using SOLiD are included. A. Pools 1–4. B. Pools 5–8.

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Additional file 2:

The configuration of the ngs_backbone pipeline used for processing raw reads generated with SOLiD, for mapping, SNV calling and filtering is included.

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Additional file 3:

Changes in number and quality of reads after processing with ngs_backbone.

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Additional file 4:

SNVs detected by mapping SOLiD sequences against melon genome. All SNVs detected in all eight resequenced pools are included, their position in the reference genome (scaffold or contig), referred to the whole genome draft version 3.5 available in MELONOMICS [36], their MAFs and allelic frequency in each group, and the filters implemented for its selection are detailed.

Format: ZIP Size: 16MB Download file

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Additional file 5:

SNVs detected by mapping SOLiD sequences against melon transcriptome. All SNVs detected in all eight resequenced pools are included, their position in the reference transcriptome available in http://melogene.net webcite, their allelic frequency in each group are detailed. Alleles in reads from genotypes previously sequenced with Sanger and 454 are also indicated.

Format: ZIP Size: 9.6MB Download file

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Additional file 6:

Location of SNVs in melon genes. Correspondence of the SNVs located in melon genes annotated in the melon genome version 3.5 available in MELONOMICS [36] is listed.

Format: CSV Size: 11MB Download file

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Additional file 7:

Validation of SNPs. Information about the SNPs selected for validation is included along with genotyping results obtained with Sequenom with 78 varieties. PIC for each SNP along with the MAF estimated by SOLiD and by genotyping is indicated.

Format: XLSX Size: 138KB Download file

Open Data