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BAC-end Sequence Analysis and a Draft Physical Map of the Common Bean (Phaseolus vulgaris L.) Genome

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Abstract

Common bean (Phaseolus vulgaris L.) is a legume that is an important source of dietary protein in developing countries throughout the world. Utilizing the G19833 BAC library for P. vulgaris from Clemson University, 89,017 BAC-end sequences were generated giving 62,588,675 base pairs of genomic sequence covering approximately 9.54% of the genome. Analysis of these sequences in combination with 1,404 shotgun sequences from the cultivar Bat7 revealed that approximately 49.2% of the genome contains repetitive sequence and 29.3% is genic. Compared to other legume BAC-end sequencing projects, it appears that P. vulgaris has higher predicted levels of repetitive sequence, but this may be due to a more intense identification strategy combining both similarity-based matches as well as de novo identification of repeats. In addition, fingerprints for 41,717 BACs were obtained and assembled into a draft physical map consisting of 1,183 clone contigs and 6,385 singletons with ~9x coverage of the genome.

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Acknowledgments

The authors would like to thank all of the collaborators in this project for their work and additions to this manuscript. We would also like to acknowledge the technical staff at the AGI BAC/EST Resource, Sequencing and Bioinformatics Centers for their contributions to this project. The project was supported by the USDA Cooperative State Research, Education and Extension Service—National Research Initiative—Plant Genome Program Grant number 06-35300-17266.

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Authors and Affiliations

  1. Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA

    Jessica A. Schlueter, Navdeep Gill, Jer-Young Lin & Scott A. Jackson

  2. Arizona Genome Institute, Department of Plant Sciences & BIO5, University of Arizona, Tucson, AZ, 86721, USA

    Jose Luis Goicoechea, Kristi Collura, Yeisoo Yu, Dave Kudrna, Andrea Zuccolo & Rod A. Wing

  3. Department of Horticultural Sciences, University of Florida, Gainesville, FL, 32611, USA

    C. Eduardo Vallejos

  4. International Center for Tropical Agriculture, Cali, Colombia

    Monica Muñoz-Torres, Matthew W. Blair & Joe Tohme

  5. Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA

    Monica Muñoz-Torres & Jeff Tomkins

  6. Department of Plant Sciences, North Dakota State University, Fargo, ND, 58105, USA

    Phillip McClean

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  1. Jessica A. Schlueter
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Correspondence to Scott A. Jackson.

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Jessica A. Schlueter, Jose Luis Goicoechea, and Kristi Collura, are the Co-first authors.

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Schlueter, J.A., Goicoechea, J.L., Collura, K. et al. BAC-end Sequence Analysis and a Draft Physical Map of the Common Bean (Phaseolus vulgaris L.) Genome. Tropical Plant Biol. 1, 40–48 (2008). https://doi.org/10.1007/s12042-007-9003-9

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