Molecular Genetics and Genomics

, Volume 281, Issue 3, pp 273–288

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

  • Pablo F. Cavagnaro
  • Sang-Min Chung
  • Marek Szklarczyk
  • Dariusz Grzebelus
  • Douglas Senalik
  • Anne E. Atkins
  • Philipp W. Simon
Original Paper

DOI: 10.1007/s00438-008-0411-9

Cite this article as:
Cavagnaro, P.F., Chung, S., Szklarczyk, M. et al. Mol Genet Genomics (2009) 281: 273. doi:10.1007/s00438-008-0411-9

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.

Keywords

Daucus carotaBAC (bacterial artificial chromosome) libraryBAC-end sequencesTransposable elementsMicrosatellites

Supplementary material

438_2008_411_MOESM1_ESM.xls (20 kb)
Supplement 1 (XLS 20 kb)
438_2008_411_MOESM2_ESM.xls (36 kb)
Supplement 2 (XLS 36 kb)
438_2008_411_MOESM3_ESM.doc (102 kb)
Supplement 3 (DOC 102 kb)

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Pablo F. Cavagnaro
    • 1
    • 2
  • Sang-Min Chung
    • 3
  • Marek Szklarczyk
    • 4
  • Dariusz Grzebelus
    • 4
  • Douglas Senalik
    • 1
    • 5
  • Anne E. Atkins
    • 1
  • Philipp W. Simon
    • 1
    • 5
  1. 1.Department of HorticultureUniversity of WisconsinMadisonUSA
  2. 2.INTAMendozaArgentina
  3. 3.Department of Life ScienceDongguk UniversitySeoulSouth Korea
  4. 4.Department of Genetics, Plant Breeding and Seed ScienceAgricultural University of KrakowKrakowPoland
  5. 5.USDA-Agricultural Research Service, Vegetable Crops Research UnitUniversity of WisconsinMadisonUSA