Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences
Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences
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DOI：
10.1007/s00438-008-0411-9
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发表时间：
2009-03-01
影响因子：
3.1
通讯作者：
Simon, Philipp W.
中科院分区：
文献类型：
--
作者：
Cavagnaro, Pablo F.;Chung, Sang-Min;Simon, Philipp W.
胡萝卜是伞形科中在经济上最重要的成员，也是人类饮食中维生素A原类胡萝卜素的主要来源。然而，胡萝卜的分子资源相对不发达，阻碍了许多遗传学研究。在此，我们报道了胡萝卜细菌人工染色体（BAC）文库的构建和特性。该文库冗余度为17.3倍，由92160个克隆组成，平均插入片段大小为121kb。为了提供胡萝卜核基因组组成和结构的概况，我们从近2000个BAC中产生并分析了2696条BAC末端序列（BES），BES总长1.74Mb。该分析显示，14%的BES由已知的重复元件组成，其中转座元件占该部分的80%以上。鉴定出11种新的胡萝卜重复元件，占BES的8.5%。对微卫星的分析表明，这些元件在胡萝卜BES中的频率相对较低。将翻译后的BES与蛋白质数据库进行比较表明，胡萝卜基因组中约10%为编码序列。此外，在用于比较的8种双子叶植物中，胡萝卜的BES与番茄的蛋白质编码序列具有最高的同源性。这个高覆盖度的文库将有助于胡萝卜的育种和遗传学研究。
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.