Open Access Research article

A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6

Christopher A Saski1, Frank A Feltus1,2, Margaret E Staton1, Barbara P Blackmon1, Stephen P Ficklin1, David N Kuhn3, Raymond J Schnell3, Howard Shapiro4 and Juan C Motamayor3,4*

1 Clemson University Genomics Institute, Clemson University, 51 New Cherry Street, Clemson, SC 29634, USA

2 Department of Genetics and Biochemistry, Clemson University, 51 New Cherry Street, Clemson, SC 29634, USA

3 Subtropical Horticulture Research Station, USDA-ARS, 13601 Old Culter Road, Miami, FL 33158, USA

4 Mars, Inc., 800 High St., Hackettstown, NJ 07840, USA

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BMC Genomics 2011, 12:413 doi:10.1186/1471-2164-12-413

Published: 16 August 2011

Additional files

Additional file 1:

Genetic marker BAC hybridizations. Summary of anchoring the Matina 1-6 genetic map to the Matina 1-6 physical map.

Format: XLSX Size: 65KB Download file

Open Data

Additional file 2:

Integration of genetic map to physical map through overgo probe hybridization. Genetic markers, linkage groups, and respective recombination distances.

Format: XLSX Size: 50KB Download file

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Additional file 3:

Genetically anchored FPC contigs. Assembled physical map contigs that were genetically anchored, with corresponding lengths and number of BACs.

Format: XLSX Size: 41KB Download file

Open Data

Additional file 4:

Unanchored FPC contigs. Assembled physical map contigs that were not genetically anchored, with corresponding lengths and number of BACs.

Format: XLSX Size: 44KB Download file

Open Data

Additional file 5:

T. cacao physical map BES aligned to V. vinifera genome assembly. Alignment of the Matina 1-6 physical map to the Vitis genome.

Format: XLSX Size: 52KB Download file

Open Data

Additional file 6:

T. cacao physical map BES aligned to P. trichocarpa genome assembly. Alignment of the Matina 1-6 physical map to the Populus genome.

Format: XLSX Size: 58KB Download file

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Additional file 7:

T. cacao physical map BES aligned to A. thaliana genome assembly. Alignment of the Matina 1-6 physical map to the Arabidopsis genome.

Format: XLSX Size: 49KB Download file

Open Data

Additional file 8:

T. cacao physical map BES aligned to T. cacao (Criollo) genome assembly. Alignment of the Matina 1-6 physical map to the Criollo genome.

Format: XLSX Size: 53KB Download file

Open Data

Additional file 9:

LG prediction of unanchored FPC contigs based on collinearity with other genomes. Summary of incorporation of unanchored contigs.

Format: XLSX Size: 46KB Download file

Open Data