羅氏454測(cè)序系統(tǒng)新近解讀大西洋鱈魚(yú)基因組

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

羅氏454測(cè)序系統(tǒng)新近解讀大西洋鱈魚(yú)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(xiàn)發(fā)表的一項(xiàng)研究中，一個(gè)國(guó)際研究小組首次完成了大西洋鱈魚(yú)全基因組測(cè)序，并意外發(fā)現(xiàn)這個(gè)物種的獨(dú)特的免疫系統(tǒng)。由奧斯陸大學(xué)領(lǐng)導(dǎo)，由挪威的大學(xué)以及水產(chǎn)生物研究機(jī)構(gòu)，利用羅氏公司454測(cè)序系統(tǒng)完成了這一高度復(fù)雜的鱈魚(yú)的基因組的全新測(cè)序，而其所用測(cè)序方法的時(shí)間和成本比起傳統(tǒng)方法而言的只是一小部分。引人注目的是，研究人員發(fā)現(xiàn)，大西洋鱈魚(yú)的免疫系統(tǒng)丟失了許多被認(rèn)為對(duì)于免疫系統(tǒng)是非常重要的基因。這一調(diào)查結(jié)果對(duì)于所有的脊椎動(dòng)物免疫系統(tǒng)的進(jìn)化過(guò)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(xué)生態(tài)和進(jìn)化的合成研究中心Kjetill S. Jakobsen 教授說(shuō)：“我們的目標(biāo)是利用尖端的測(cè)序技術(shù)獲得的大西洋鱈魚(yú)整個(gè)基因組序列，我們?cè)静](méi)有預(yù)計(jì)會(huì)發(fā)現(xiàn)大西洋鱈魚(yú)的其免疫系統(tǒng)缺失一些對(duì)于于免疫而言的重要組成部分�！北M管缺少對(duì)于主要組織相容性復(fù)合體（MHC）II途徑的一些必要的基因，大西洋鱈魚(yú)通過(guò)增加的MHC I基因和Toll樣受體基因的數(shù)量來(lái)維持其正常的免疫功能。這一發(fā)現(xiàn)將幫助更有針對(duì)性的開(kāi)發(fā)疫苗研制，以協(xié)助大西洋鱈魚(yú)的疾病管理和馴化過(guò)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(cè)序工作完全由454測(cè)序系統(tǒng)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(yùn)用454 GS的De Novo序列拼接軟件（Newbler）繪制出了高質(zhì)量的草圖。該研究組計(jì)劃利用注釋后的基因組確定與水產(chǎn)養(yǎng)殖及野生的鱈魚(yú)重要性狀相關(guān)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(shuō)：“我們的研究很清楚地表明，只使用454系統(tǒng)已經(jīng)完成大基因組的測(cè)序以及優(yōu)質(zhì)的全新基因組拼接。我們發(fā)現(xiàn)長(zhǎng)讀長(zhǎng)數(shù)據(jù)對(duì)保證結(jié)果質(zhì)量是必不可少。我們的下一步是使用最近推出的GS FLX+系統(tǒng)的更長(zhǎng)的讀長(zhǎng)來(lái)提高鱈魚(yú)基因組序列的拼接。我們相信超過(guò)800bp的讀長(zhǎng)將會(huì)幫助我們完成鱈魚(yú)轉(zhuǎn)錄組測(cè)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(fā)部門(mén)的James Knight說(shuō)：“這是454測(cè)序系統(tǒng)又一次完成從測(cè)序、基因組拼接到基因注釋的實(shí)例。我們超長(zhǎng)讀長(zhǎng)，準(zhǔn)確的測(cè)序結(jié)果和優(yōu)化基因組拼接軟件可以幫助任何規(guī)模的實(shí)驗(yàn)室有效地開(kāi)展這種類(lèi)型的大的測(cè)序項(xiàng)目�！�

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