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Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences

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Abstract

Carrot is the most economically important member of the Apiaceae family and a major source of provitamin A carotenoids in the human diet. However, carrot molecular resources are relatively underdeveloped, hampering a number of genetic studies. Here, we report on the synthesis and characterization of a bacterial artificial chromosome (BAC) library of carrot. The library is 17.3-fold redundant and consists of 92,160 clones with an average insert size of 121 kb. To provide an overview of the composition and organization of the carrot nuclear genome we generated and analyzed 2,696 BAC-end sequences (BES) from nearly 2,000 BACs, totaling 1.74 Mb of BES. This analysis revealed that 14% of the BES consists of known repetitive elements, with transposable elements representing more than 80% of this fraction. Eleven novel carrot repetitive elements were identified, covering 8.5% of the BES. Analysis of microsatellites showed a comparably low frequency for these elements in the carrot BES. Comparisons of the translated BES with protein databases indicated that approximately 10% of the carrot genome represents coding sequences. Moreover, among eight dicot species used for comparison purposes, carrot BES had highest homology to protein-coding sequences from tomato. This deep-coverage library will aid carrot breeding and genetics.

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Authors and Affiliations

  1. Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA

    Pablo F. Cavagnaro, Douglas Senalik, Anne E. Atkins & Philipp W. Simon

  2. INTA, EEA La Consulta CC8, Mendoza, Argentina

    Pablo F. Cavagnaro

  3. Department of Life Science, Dongguk University, 3-26 Pil-dong, Chung-gu, Seoul, 100-715, South Korea

    Sang-Min Chung

  4. Department of Genetics, Plant Breeding and Seed Science, Agricultural University of Krakow, Al. 29 Listopada 54, 31-425, Krakow, Poland

    Marek Szklarczyk & Dariusz Grzebelus

  5. USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA

    Douglas Senalik & Philipp W. Simon

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  1. Pablo F. Cavagnaro
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  2. Sang-Min Chung
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  3. Marek Szklarczyk
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  4. Dariusz Grzebelus
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  6. Anne E. Atkins
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  7. Philipp W. Simon
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Correspondence to Philipp W. Simon.

Additional information

Communicated by R. Hagemann.

Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers FJ147695–FJ150390.

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Cavagnaro, P.F., Chung, SM., Szklarczyk, M. et al. Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences. Mol Genet Genomics 281, 273–288 (2009). https://doi.org/10.1007/s00438-008-0411-9

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