罗氏454测序系统新近解读大西洋鳕鱼基因组[创新技巧]

最近《自然》杂志在线发表的一项研究中，一个国际研究小组首次完成了大西洋鳕鱼全基因组测序，并意外发现这个物种的独特的免疫系统。由奥斯陆大学领导，挪威的大学以及水产生物研究机构利用罗氏公司454测序系统完成了这一高度复杂的鳕鱼的基因组的全新测序，而其所用测序方法的时间和成本比起传统方法而言的只是一小部分。引人注目的是，研究人员发现，大西洋鳕鱼的免疫系统丢失了许多被认为对于免疫系统是非常重要的基因。这一调查结果对于所有的脊椎动物免疫系统的进化过程提供了新的思路。

奥斯陆大学生态和进化的合成研究中心Kjetill南教授雅各布森说：“我们的目标是利用尖端的测序技术获得的大西洋鳕鱼整个基因组序列，我们原本并没有预计会发现大西洋鳕鱼的其免疫系统缺失一些对于于免疫而言的重要组成部分。”尽管缺少对于主要组织相容性复合体（MHC）II途径的一些必要的基因，大西洋鳕鱼通过增加的MHC I基因和Toll样受体基因的数量来维持其正常的免疫功能。这一发现将帮助更有针对性的开发疫苗研制，以协助大西洋鳕鱼的疾病管理和驯化过程。

这次完整的基因组的测序工作完全由454测序系统完成，使用了GS FLX Titanium的3 KB，8 KB和20 KB paired end 以及shot gun方案。最终，研究人员获得40倍的基因组的覆盖面和运用454 GS的De Novo序列拼接软件（Newbler）绘制出了高质量的草图。该研究组计划利用注释后的基因组确定与水产养殖及野生的鳕鱼重要性状相关的基因及其变异。

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Kjetill S. Jakobsen 教授说：“我们的研究很清楚地表明，只使用454系统已经完成大基因组的测序以及优质的全新基因组拼接。我们发现长读长数据对保证结果质量是必不可少。我们的下一步是使用最近推出的GS FLX+系统的更长的读长来提高鳕鱼基因组序列的拼接。我们相信超过800bp的读长将会帮助我们完成鳕鱼转录组测序及完整的基因组注释。”

454 Life Sciences研发部门的James Knight说：“这是454测序系统又一次完成从测序、基因组拼接到基因注释的实例。我们超长读长，准确的测序结果和优化基因组拼接软件可以帮助任何规模的实验室有效地开展这种类型的大的测序项目。”

附英文原稿：

RAS Media News: Researchers Decode Genome of Atlantic Cod Using 454 Sequencing Systems

Aug 11, 2011

In a study published online this week in Nature, an international team of researchers report the first complete sequence of the Atlantic cod genome and an unexpected discovery of the unique immune system of this important fish species. Led by researchers from the University of Oslo, a consortium of Norwegian universities and aquaculture institutions turned to 454 Sequencing Systems from Roche (SIX: RO, ROG; OTCQX: RHHBY) to obtain a comprehensive de novo assembly of the highly complex cod genome at a fraction of the time and cost of traditional sequencing methods. Strikingly, the researchers found that Atlantic cod has lost genes that are essential for a critical component of its immune system. The findings call to question fundamental ideas on the evolution of the immune system in all vertebrate species.

 “The overall aim of this initiative was to obtain the entire genome sequence of the Atlantic cod utilizing cutting edge sequencing technology,” said study lead Professor Kjetill S. Jakobsen from the Centre for Ecological and Evolutionary Synthesis, University of Oslo. “We had not expected to find that the Atlantic cod had lost such a crucial component of its immune system.” Despite lacking genes essential for the function of the major histocompatibility (MHC) II pathway, the Atlantic cod appears to function normally and relies on an increased number of MHC I genes and Toll-like receptor genes for its immune response. This finding will potentially allow for the development of more targeted vaccine development – aiding disease management and the process of domestication of Atlantic cod.

The complete genome sequence was generated exclusively using 454 Sequencing Systems with a combination of GS FLX Titanium shotgun, 3 kb, 8 kb and 20 kb paired end reads. In the end, the researchers obtained 40x genome coverage and generated a high-quality draft assembly using the 454 GS De Novo Assembler Software (Newbler). The consortium plans to use the assembly and fully annotated genome to identify genes and genetic variations associated with important traits for cod aquaculture and wild stocks.

“Our study shows quite clearly that this approach solely using 454 Systems gives excellent results for large genome sequencing and de novo assembly projects. We found that the long reads were essential to obtaining the desired quality of results to achieve our research goals,” explained Jakobsen. “Our next step is to improve the cod assembly using read length improvements offered by the recently launched GS FLX+ System. We believe the extended 800 bp reads will be particularly powerful for transcriptome sequencing and further refinement of our cod genome annotation.”

“This is another example of how 454 Sequencing Systems have helped a group make the transition from sequence to assembly to biological understanding,” said James Knight, R&D Fellow at 454 Life Sciences. “With our long, accurate reads and optimized assembly software, laboratory of any size can effectively carry out this type of large-scale project.”