Open Access Highly Accessed Research article

De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes

Hamid Ashrafi1*, Theresa Hill1, Kevin Stoffel1, Alexander Kozik2, JiQiang Yao13, Sebastian Reyes Chin-Wo12 and Allen Van Deynze1

Author Affiliations

1 Seed Biotechnology Center, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA

2 Genome Center, University of California, Davis, 1 Shields Ave, Davis, CA, 95616, USA

3 Present address: Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA

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BMC Genomics 2012, 13:571  doi:10.1186/1471-2164-13-571

Published: 30 October 2012

Additional files

Additional file 1:

Ashrafi et al. 2012 Pepper Annotation Supp 05072012. A Microsoft-Word 2007 file with 16 figures comparing the results of Blast2GO for GeneChip (Sanger-EST) and transcriptome assemblies of pepper as well as the IGA transcriptome assembly procedure flow chart.

Format: DOCX Size: 2.8MB Download file

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Additional file 2:

Ashrafi et al. Pepper Assembly Supp 05072012. A Microsoft-Excel 2007 file with 2 tables (worksheet) corresponding to Annotation results of the Sanger-EST and IGA transcriptome assemblies of pepper.

Format: XLSX Size: 13.1MB Download file

Open Data

Additional file 3:

Ashrafi et al. Pepper Assembly Supp 05072012. A Microsoft-Excel 2007 file with 13 tables corresponding to SSR and SNP lists identified in both the Sanger-EST and IGA transcriptome assemblies of pepper. It also includes identified SSR motifs and list of diversity panel (adapted from Hill et al. [11]).

Format: XLSX Size: 8.3MB Download file

Open Data