近日,，Plos One發(fā)表了中國(guó)科學(xué)院海洋研究所實(shí)驗(yàn)海洋生物重點(diǎn)實(shí)驗(yàn)室相建海研究員團(tuán)隊(duì)的研究成果，他們?cè)诤ＫB(yǎng)殖動(dòng)物的基因組研究領(lǐng)域取得了突破性進(jìn)展,。團(tuán)隊(duì)成員張曉軍博士等成功構(gòu)建了櫛孔扇貝物理圖譜,，這是我國(guó)海水養(yǎng)殖動(dòng)物的第一個(gè)物理圖譜。
櫛孔扇貝(Chlamys farreri)是我國(guó)北方沿海一個(gè)非常重要的養(yǎng)殖貝類(lèi),，肉質(zhì)鮮美,，營(yíng)養(yǎng)豐富，經(jīng)濟(jì)價(jià)值很高,，其產(chǎn)量曾達(dá)到貝類(lèi)養(yǎng)殖總產(chǎn)量的80%,。由于生態(tài)環(huán)境惡化、病害爆發(fā),、種質(zhì)退化等原因,，近年來(lái)死亡情況持續(xù)發(fā)生，嚴(yán)重地制約了其養(yǎng)殖產(chǎn)業(yè)的發(fā)展,。我國(guó)科研人員一直在開(kāi)展櫛孔扇貝的免疫學(xué)和基因組學(xué)等基礎(chǔ)研究,，以期找到解決問(wèn)題的關(guān)鍵。
2007年,，相建海研究員獲得國(guó)家自然基金項(xiàng)目“櫛孔扇貝高密度物理圖譜建立及與遺傳圖譜的整合”的資助,。研究團(tuán)隊(duì)經(jīng)過(guò)三年多不懈的努力，克服了細(xì)菌人工染色體（BAC）文庫(kù)構(gòu)建,、BAC指紋制備和圖譜組裝等一系列難題,，成功構(gòu)建出櫛孔扇貝高密度物理圖譜。該圖譜主要由3,696 條contigs組成,，平均長(zhǎng)度為490 kb,，包含了63,641個(gè)BAC克隆，覆蓋扇貝基因組1.5倍,；同時(shí)圖譜上錨定有10,587個(gè)BAC末端序列和167個(gè)分子標(biāo)記,，其中27個(gè)標(biāo)記同時(shí)存在于櫛孔扇貝的遺傳連鎖圖譜上，初步實(shí)現(xiàn)了遺傳圖譜和物理圖譜的整合,；另外有6個(gè)與免疫有關(guān)的重要功能基因被定位到該物理圖譜上,。
物理圖譜是從事基因組學(xué)研究重要平臺(tái)，目前基于二代測(cè)序技術(shù)的全基因組測(cè)序已經(jīng)非常高效和經(jīng)濟(jì),，然而物理圖譜仍然是一些復(fù)雜基因組測(cè)序組裝工作的關(guān)鍵組成部分,。同時(shí)，物理圖和遺傳圖的整合也是實(shí)現(xiàn)數(shù)量性狀（QTL）定位和有效圖位克隆最經(jīng)濟(jì)有效的手段,。另外,，通過(guò)比較多種物理圖譜數(shù)據(jù)，可以發(fā)現(xiàn)相近物種間基因組的同線性(synteny)或共線性(collinearity)，這對(duì)闡明新基因的結(jié)構(gòu),、功能,，基因間的關(guān)系，以及不同物種分子系統(tǒng)進(jìn)化過(guò)程等具有重要的意義,。
櫛孔扇貝的物理圖譜構(gòu)建研究填補(bǔ)了我國(guó)水產(chǎn)動(dòng)物基因組研究的技術(shù)和知識(shí)空缺,，為加快我國(guó)水產(chǎn)動(dòng)物基因組和功能基因研究打下了堅(jiān)實(shí)的基礎(chǔ)。（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.
