This article is part of a special issue on plant genomics.

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The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color

Juan C Motamayor1*, Keithanne Mockaitis2, Jeremy Schmutz13, Niina Haiminen4, Donald Livingstone III15, Omar Cornejo6, Seth D Findley1, Ping Zheng7, Filippo Utro4, Stefan Royaert5, Christopher Saski8, Jerry Jenkins13, Ram Podicheti9, Meixia Zhao10, Brian E Scheffler11, Joseph C Stack1, Frank A Feltus8, Guiliana M Mustiga1, Freddy Amores12, Wilbert Phillips13, Jean Philippe Marelli14, Gregory D May15, Howard Shapiro1, Jianxin Ma10, Carlos D Bustamante6, Raymond J Schnell15, Dorrie Main7, Don Gilbert2, Laxmi Parida4 and David N Kuhn5

Author Affiliations

1 Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA

2 Department of Biology, and Center for Genomics and Bioinformatics, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA

3 HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, AL, 35806, USA

4 IBM T J Watson Research, Yorktown Heights, NY, 10598, USA

5 United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA

6 Department of Genetics, Stanford University, 300 Pasteur Dr, Stanford, CA, 94305, USA

7 Department of Horticulture, Washington State University, Johnson Hall, Pullman, WA, 99164, USA

8 Clemson University Genomics Institute, 105 Collings Street, Clemson, SC, 29634, USA

9 Center for Genomics and Bioinformatics and School of Informatics and Computing, Indiana University, 919 E 10th St, Bloomington, IN, 47408, USA

10 Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA

11 United States Department of Agriculture-Agriculture Research Service, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, MS, 38776, USA

12 Estación Experimental Tropical Pichilingue, Instituto Nacional Autónomo de Investigaciones Agropecuarias (INIAP), Código Postal 24, Km 5 vía Quevedo - El Empalme, Quevedo, Ecuador

13 Programa de Mejoramiento de Cacao, CATIE 7170, Turrialba, Costa Rica

14 Mars Center for Cocoa Science (MCCS), CP 55, Itajuipe, Bahia, 45630, Brazil

15 National Center for Genome Resources, 2935 Rodeo Park Drive E, Santa Fe, NM, 87505, USA

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Genome Biology 2013, 14:r53  doi:10.1186/gb-2013-14-6-r53

Published: 3 June 2013

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Additional file 1:

This PDF document contains Supplemental Tables S1 to S28, Supplemental Results and Supplemental Materials and methods.

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Additional file 2:

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