Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences.
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.
Cavagnaro
Pablo F
PF
Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA.
Chung
Sang-Min
SM
Szklarczyk
Marek
M
Grzebelus
Dariusz
D
Senalik
Douglas
D
Atkins
Anne E
AE
Simon
Philipp W
PW
D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D030561:Databases, Nucleic Acid; D018552:Daucus carota / Q000235:genetics*; D020224:Expressed Sequence Tags; D015723:Gene Library; D018598:Minisatellite Repeats; D013045:Species Specificity
D017931:DNA Primers; D018744:DNA, Plant