近日，Plos One发表了中国科学院海洋研究所实验海洋生物重点实验室相建海研究员团队的研究成果，他们在海水养殖动物的基因组研究领域取得了突破性进展。团队成员张晓军博士等成功构建了栉孔扇贝物理图谱，这是我国海水养殖动物的第一个物理图谱。
栉孔扇贝(Chlamys farreri)是我国北方沿海一个非常重要的养殖贝类，肉质鲜美，营养丰富，经济价值很高，其产量曾达到贝类养殖总产量的80%。由于生态环境恶化、病害爆发、种质退化等原因，近年来死亡情况持续发生，严重地制约了其养殖产业的发展。我国科研人员一直在开展栉孔扇贝的免疫学和基因组学等基础研究，以期找到解决问题的关键。
2007年，相建海研究员获得国家自然基金项目“栉孔扇贝高密度物理图谱建立及与遗传图谱的整合”的资助。研究团队经过三年多不懈的努力，克服了细菌人工染色体（BAC）文库构建、BAC指纹制备和图谱组装等一系列难题，成功构建出栉孔扇贝高密度物理图谱。该图谱主要由3,696 条contigs组成，平均长度为490 kb，包含了63,641个BAC克隆，覆盖扇贝基因组1.5倍；同时图谱上锚定有10,587个BAC末端序列和167个分子标记，其中27个标记同时存在于栉孔扇贝的遗传连锁图谱上，初步实现了遗传图谱和物理图谱的整合；另外有6个与免疫有关的重要功能基因被定位到该物理图谱上。
物理图谱是从事基因组学研究重要平台，目前基于二代测序技术的全基因组测序已经非常高效和经济，然而物理图谱仍然是一些复杂基因组测序组装工作的关键组成部分。同时，物理图和遗传图的整合也是实现数量性状（QTL）定位和有效图位克隆最经济有效的手段。另外，通过比较多种物理图谱数据，可以发现相近物种间基因组的同线性(synteny)或共线性(collinearity)，这对阐明新基因的结构、功能，基因间的关系，以及不同物种分子系统进化过程等具有重要的意义。
栉孔扇贝的物理图谱构建研究填补了我国水产动物基因组研究的技术和知识空缺，为加快我国水产动物基因组和功能基因研究打下了坚实的基础。（生物谷Bioon.com）
doi:10.1371/journal.pone.0027612
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A BAC-Based Physical Map of Zhikong Scallop (Chlamys farreri Jones et Preston)
Xiaojun Zhang, Cui Zhao, Chao Huang, Hu Duan, Pin Huan, Chengzhang Liu, Xiuying Zhang, Yang Zhang, Fuhua Li, Hong-Bin Zhang, Jianhai Xiang
Zhikong scallop (Chlamys farreri) is one of the most economically important aquaculture species in China. Physical maps are crucial tools for genome sequencing, gene mapping and cloning, genetic improvement and selective breeding. In this study, we have developed a genome-wide, BAC-based physical map for the species. A total of 81,408 clones from two BAC libraries of the scallop were fingerprinted using an ABI 3130xl Genetic Analyzer and a fingerprinting kit developed in our laboratory. After data processing, 63,641 (~5.8× genome coverage) fingerprints were validated and used in the physical map assembly. A total of 3,696 contigs were assembled for the physical map. Each contig contained an average of 10.0 clones, with an average physical size of 490 kb. The combined total physical size of all contigs was 1.81 Gb, equivalent to approximately 1.5 fold of the scallop haploid genome. A total of 10,587 BAC end sequences (BESs) and 167 markers were integrated into the physical map. We evaluated the physical map by overgo hybridization, BAC-FISH (fluorescence in situ hybridization), contig BAC pool screening and source BAC library screening. The results have provided evidence of the high reliability of the contig physical map. This is the first physical map in mollusc; therefore, it provides an important platform for advanced research of genomics and genetics, and mapping of genes and QTL of economical importance, thus facilitating the genetic improvement and selective breeding of the scallop and other marine molluscs.
