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

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 1, 2009
Publication Date: March 3, 2009
Citation: Simon, P.W., Cavagnaro, P.F., Chung, S., Szklarczyk, M., Grzebelus, D., Senalik, D.A., Atkins, A.E. 2009. Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences. Molecular Genetics and Genomics. 281(3):273-288.

Interpretive Summary: The genetic code, or genome, of all organisms is very large, complex, and unique, so one way to simplify analysis is to break long regions of DNA into shorter pieces, called Bacterial Artificial Chromosomes, or BACs. The collection of BACs from one organism is a BAC lbrary. In this study we evaluated a BAC library for carrots. We found pieces of DNA unique for carrot, but we mainly found DNA sequence similar to other plants or, in some cases, animals and microbes. Overall the BAC analysis indicated the carrot is more similar to tomato than other plants for which BAC analysis has been done. This information will be of interest to genomics scientists, molecular biologists, and geneticists, as well as to seed companies and researchers evaluating carrot genetics.

Technical Abstract: A 17.3-fold redundant bacterial artificial chromosome (BAC) library has been synthesized for carrot, the most-economically important member of the family Apiaceae. The library consists of 92,160 clones with an average insert size of 121 kb and ~ 2 % organellar DNA content. To provide an overview of the composition and organization of the carrot nuclear genome we generated and analyzed 2,696 high quality BAC-end sequences (BES) from nearly 2000 random BACs, totaling 1.74 Mb of BES. Analysis of repeat DNA content revealed that 14 % of the BES consist of known repetitive elements, with transposable elements (mainly LTR retrotransposons) representing more than 80 % of this fraction. Eleven novel carrot repetitive elements were identified, covering ~ 8.5 % of the BES. Analysis of simple sequence repeats (SSRs) 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.