Transcriptome sequencing for SNP discovery across Cucumis melo
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
BMC Genomics 2012, 13:280 doi:10.1186/1471-2164-13-280Published: 24 June 2012
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.
Format: PPT Size: 10.2MB Download file
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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.
Format: TXT Size: 30KB Download file
Additional file 3:
Changes in number and quality of reads after processing with ngs_backbone.
Format: XLSX Size: 12KB Download file
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 , their MAFs and allelic frequency in each group, and the filters implemented for its selection are detailed.
Format: ZIP Size: 16MB Download file
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
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  is listed.
Format: CSV Size: 11MB Download file
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