栉孔扇贝(chlamys farreri)bac文库的构建及其基因组特征研究-construction and genomic characteristics of bac library of chla mys farreri.docx

的关键基因（CfTLR, CfMyd88, CfTRAF6, CfNFκB 和 CfIκB）进行染色体定位。结果显示，包含这些基因的 5 个 BAC 克隆定位在染色体上的位置单一。进一步 通过核型分析及共定位验证，这 5 个克隆被定位于 5 对不同的染色体上，表明 TLR 信号通路的 5 个关键基因在栉孔扇贝基因组中并不连锁。这些研究对探索 栉孔扇贝免疫系统机理有着积极的作用，并有利于细胞染色体分析等工作的开展。3. 栉孔扇贝基因组勘探测序及特征分析 本研究采用全基因组鸟枪法策略，依托于 Illumina solexa 高通量测序平台对栉孔扇贝基因组进行勘探测序，获得了 62.44 Gb 的有效数据，评估覆盖深度约为 50X。对所有短序列组装结果显示 contig N50 为 1,267bp，scaffold N50 为 1,517bp，获得 scaffold 总长约为 870Mb。通过 17-kmer 分析估计栉孔扇贝基因组 大小约为 971Mb，并预测该测序个体的杂合度约为 1.35%。对 scaffold 序列进行 初步分析，估计其覆盖真实基因组的 57.1% ，覆盖转录组的 88.7% 。运用 RepeatMasker 软件进行扫描，获得了 884,644 个散在重复序列，主要分为四种类 型：DNA 转座子、SINE 反转座子、LINE 反转座子和 LTR 反转座子。其中， DNA 转座子数目最多，其次是 SINE 反转座子、LINE 反转座子和 LTR 反转座 子。运用 SciRoKo 软件进行扫描，获得了 134,887 个微卫星序列，分为 437 种类 型，其中单碱基重复的微卫星数目最多。这些结果的获得将有利于对栉孔扇贝基 因组结构特征的探索，并为全基因组测序策略的选择及基因组学研究方向的确定 提供重要的参考信息。关键词：栉孔扇贝；BAC 文库；荧光原位杂交；全基因组测序BAC Libraries Construction and Genomic Analysis in Zhikong Scallop (Chlamys farreri)AbstractZhikong scallop (Chlamys farreri) is one of the most important economic aquiculture bivalves in China, but study on its genome is underdeveloped. In this study, we constructed three bacterial artificial chromosome (BAC) libraries of C.farreri as platform for genomic research, and harvested positive BAC clones containing target genes, which are relevant to growth and immune function of C.farreri. Additionally, we performed genome sequencing and comparative analysis of the C.farreri using next-generation sequencing technology, and thus made a preliminary assessment of the genome.Construction and characterization of BAC libraries in C.farreriWe constructed three bacterial artificial chromosome (BAC) libraries for C.farreri. The BAC libraries were generated based on three restriction enzymes, BamHI, HindIII and Sau3AI, respectively. The BamHI library consists of 34,560 clones, with an average insert size of 98 kb and no insert-empty clones. The HindIII library consists of 132,480 clones, with an average size of 106 kb, but approximately 1.67% of the clones don’t contain scallop nuclear DN