羅氏454測序系統新近解讀大西洋鱈魚基因組

瀏覽次數：3627　發布日期：2011-8-18　來源：本站　本站原創，轉載請注明出處

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

羅氏454測序系統新近解讀大西洋鱈魚基因組

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.

最近《自然》雜志在線發表的一項研究中，一個國際研究小組首次完成了大西洋鱈魚全基因組測序，并意外發現這個物種的獨特的免疫系統。由奧斯陸大學領導，由挪威的大學以及水產生物研究機構，利用羅氏公司454測序系統完成了這一高度復雜的鱈魚的基因組的全新測序，而其所用測序方法的時間和成本比起傳統方法而言的只是一小部分。引人注目的是，研究人員發現，大西洋鱈魚的免疫系統丟失了許多被認為對于免疫系統是非常重要的基因。這一調查結果對于所有的脊椎動物免疫系統的進化過程提供了新的思路。

“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.

奧斯陸大學生態和進化的合成研究中心Kjetill S. Jakobsen 教授說：“我們的目標是利用尖端的測序技術獲得的大西洋鱈魚整個基因組序列，我們原本并沒有預計會發現大西洋鱈魚的其免疫系統缺失一些對于于免疫而言的重要組成部分。”盡管缺少對于主要組織相容性復合體（MHC）II途徑的一些必要的基因，大西洋鱈魚通過增加的MHC I基因和Toll樣受體基因的數量來維持其正常的免疫功能。這一發現將幫助更有針對性的開發疫苗研制，以協助大西洋鱈魚的疾病管理和馴化過程。

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.

這次完整的基因組的測序工作完全由454測序系統完成，使用了GS FLX Titanium的3 KB，8 KB和20 KB paired end shot gun方案。最終，研究人員獲得40倍的基因組的覆蓋面和運用454 GS的De Novo序列拼接軟件（Newbler）繪制出了高質量的草圖。該研究組計劃利用注釋后的基因組確定與水產養殖及野生的鱈魚重要性狀相關的基因及其變異。

“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.”

Kjetill S. Jakobsen 教授說：“我們的研究很清楚地表明，只使用454系統已經完成大基因組的測序以及優質的全新基因組拼接。我們發現長讀長數據對保證結果質量是必不可少。我們的下一步是使用最近推出的GS FLX+系統的更長的讀長來提高鱈魚基因組序列的拼接。我們相信超過800bp的讀長將會幫助我們完成鱈魚轉錄組測序及完整的基因組注釋。”

“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.”

454 Life Sciences研發部門的James Knight說：“這是454測序系統又一次完成從測序、基因組拼接到基因注釋的實例。我們超長讀長，準確的測序結果和優化基因組拼接軟件可以幫助任何規模的實驗室有效地開展這種類型的大的測序項目。”

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