Wang Xubo, Zhang Quanqi, Sun Xiaohua, Chen Yanjie, Zhai Teng, Zhuang Wei, Qi Jie, Wang Zhigang
Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, People's Republic of China.
Mar Biotechnol (NY). 2009 Mar-Apr;11(2):236-42. doi: 10.1007/s10126-008-9137-2. Epub 2008 Sep 2.
Half-smooth tongue sole (Cynoglossus semilaevis: Pleuronectiformes) is a commercially important cultured marine flatfish in China and forms an important fishery resource, but the research of its genome is underdeveloped. In this study, we constructed a female C. semilaevis fosmid library and analyzed the fosmid end sequences to provide a preliminary assessment of the genome. The library consists of 49,920 clones with an average insert size of about 39 kb, amounting to 3.23 genome equivalents. Fosmid stability assays indicate that female C. semilaevis DNA was stable during propagation in the fosmid system. Library screening with eight microsatellite markers yielded between two and five positive clones, and none of those tested was absent from the library. End-sequencing of both 5' and 3' ends of 1,152 individual clones generated 2,247 sequences after trimming, with an average sequence length of 855 bp. BLASTN searches of the nr and EST databases of GenBank and BLASTX searches of the nr database resulted in 259 (11.53%) and 287 (12.77%) significant hits (E < e (-5)), respectively. Repetitive sequences analysis resulted in 5.23% of base pairs masked using both the Fugu and Danio databases, repetitive elements were composed of retroelements, DNA transposons, satellites, simple repeats, and low-complexity sequences. The fosmid library, in conjunction with the fosmid end sequences, will serve as a useful resource for large-scale genome sequencing, physical mapping, and positional cloning, and provide a better understanding of female C. semilaevis genome.
半滑舌鳎（Cynoglossus semilaevis：鲽形目）是中国一种具有重要商业价值的养殖海水鲽形鱼类，也是一种重要的渔业资源，但其基因组研究尚不完善。在本研究中，我们构建了一个雌性半滑舌鳎fosmid文库，并分析了fosmid末端序列，以对基因组进行初步评估。该文库由49,920个克隆组成，平均插入片段大小约为39 kb，相当于3.23个基因组当量。Fosmid稳定性分析表明，雌性半滑舌鳎DNA在fosmid系统中传代过程中是稳定的。用8个微卫星标记对文库进行筛选，得到2至5个阳性克隆，且所有检测的标记在文库中均未缺失。对1,152个单个克隆的5'和3'末端进行末端测序，修剪后产生2,247个序列，平均序列长度为855 bp。在GenBank的nr和EST数据库中进行BLASTN搜索，以及在nr数据库中进行BLASTX搜索，分别得到259个（11.53%）和287个（12.77%）显著匹配（E < e(-5)）。重复序列分析结果显示，使用河豚和斑马鱼数据库对碱基对进行掩膜的比例为5.23%，重复元件由反转录元件、DNA转座子、卫星序列、简单重复序列和低复杂性序列组成。该fosmid文库以及fosmid末端序列将成为大规模基因组测序、物理图谱构建和定位克隆的有用资源，并有助于更好地了解雌性半滑舌鳎基因组。
