Open Access Highly Accessed Research article

Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

José Blanca, Joaquín Cañizares, Cristina Roig, Pello Ziarsolo, Fernando Nuez and Belén Picó*

Author Affiliations

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

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BMC Genomics 2011, 12:104  doi:10.1186/1471-2164-12-104

Published: 10 February 2011

Additional files

Additional file 1:

Cucurbita unigenes. The fasta sequence of the 49,610 Cucurbita unigenes assembled from 454 ESTs is included.

Format: ZIP Size: 9.6MB Download file

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Additional file 2:

Annotation of ORFs and introns. Unigene length and predicted position of ORFs and introns is indicated for the whole Cucurbita unigene collection.

Format: XLSX Size: 3.6MB Download file

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Additional file 3:

Blast Hits and GO terms. Descriptions build from the blast hit obtained by a sequential blast search of 3 protein databases [60-62] and GO annotations for the whole Cucurbita unigene collection are compiled.

Format: XLS Size: 5.2MB Download file

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Additional file 4:

Arabidopsis and melon orthologs. Orthologs found by reciprocal search with Arabidopsis and melon databases [12,61] are indicated.

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Additional file 5:

Genes potentially encoding pathogen resistance, flowering, fruit and root traits. Genes were identified in the Cucurbita data set by comparison with the Arabidopsis and melon databases [12,61]. A brief description and the corresponding Arabidopsis and melon locus are given for each unigene.

Format: XLSX Size: 16KB Download file

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Additional file 6:

Cucurbita SSRs. The table provides the list of SSRs identified from the Cucurbita unigene dataset, their length, motif sequences, position in the unigene, and scores.

Format: XLSX Size: 101KB Download file

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Additional file 7:

Validated Cucurbita SSRs. The table provides the list of Cucurbita SSRs experimentally validated using a collection of C. pepo. Primers used for validation, number of alleles, and polymorphism detected between the sequenced genotypes, within subspecies, and within the zucchini morphotypes are included. Also transference to C. moschata is indicated.

Format: XLSX Size: 14KB Download file

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Additional file 8:

Cucurbita SNPs and INDELs. The file provides the list of SNPs and INDELs (SNVs) identified from the Cucurbita unigene dataset, their position, the nucleotide change (or I or D for insertion and deletion in INDELs), the quality of the polymorphic base, and additional information about allele number and frequency. The different filters applied for the in silico selection of the SNVs are also indicated: VKS (is not an SNPs, is an INDEL), HVR4 (SNV is in a region with more than 4 SNVs per 100 bp), CS60 (SNV is closer than 60 bp to another SNV), I60 (SNV is located closer than 60 bp to an intron), CL60 (SNV is closer than 60 bp to the sequence end), NVSM1 (SNV is variable within UPV196, or not sequenced in this genotype), NVSM2 (SNV is variable within MU16, or not sequenced in this genotype), CEF (SNV does not alter a restriction target and cannot be detected as a CAPS). The VCF (Variant Call Format) version 4.0 has been used for this file [108].

Format: VCF Size: 2.1MB Download file

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Additional file 9:

Cucurbita SNPs validated as CAPS. The table provides the list of SNPs that affected restriction targets and were validated via CAPS, their position, location, primers used for validation and the occurrence of polymorphism between the two sequenced varieties.

Format: XLSX Size: 13KB Download file

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Additional file 10:

Annotation results in GFF3. All the annotation results (ORFS, introns, descriptions, GO terms, Arabidopsis and melon orthologs, SNVs and SSRs) are provided also in the standard format GFF3 of The Sequence Ontology Resources [100] that facilitate annotations uploading, representation and analysis.

Format: ZIP Size: 3.9MB Download file

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