藥物基因組公司運用羅氏GS FLX+ 完成大麻基因組測序

 

Medicinal Genomics, a private company headquartered in Marblehead, USA and the Netherlands, announced today that it has sequenced the entire genomes of Cannabis sativa and Cannabis indica, representing two strains of the therapeutic plant. The genome assemblies, comprising over 131 billion bases of sequence, are the largest known gene collection of the Cannabis genomes and will be made publically available to the scientific community this fall. The genomic data is expected to aid in the advancement of research on the therapeutic benefits of the Cannabis plant for a wide range of health conditions, including cancer and inflammatory diseases.

 

藥物基因組公司是一家美國和荷蘭聯(lián)合經(jīng)營的私營公司，總部設(shè)在美國的Marblehead，該公司8月18日宣布已完成了大麻這一重要藥用植物兩個品系（Cannabis sativa和Cannabis indica）的全基因組測序。此次基因組測序結(jié)果包括超過1310億的堿基對序列，是現(xiàn)有最大的大麻基因組基因集合。該實驗數(shù)據(jù)將在今年秋天向?qū)W界公開。這些基因數(shù)據(jù)預(yù)計將有助于大麻在包括癌癥、炎癥等廣泛醫(yī)療應(yīng)用中作用機(jī)制的研究。

 

“Despite compelling evidence of the therapeutic benefits of Cannabis, very little genomics research has been performed in this area,” said Kevin McKernan, founder and head of scientific operations of Medicinal Genomics. “With the goal to sequence multiple Cannabis varieties, we initially took the approach of using short-read next generation sequencing technology on the C. sativa strain. We very quickly realized that this method was not going to provide a clear picture of the genome required to tease out the important biological pathways. This realization caused somewhat of a paradigm shift in the way we approached this project. At this point we moved to triple backcrossed cultivars and longer read technology.”

 

藥物基因組公司創(chuàng)始人兼科學(xué)運營總監(jiān)Kevin McKernan先生說：“盡管大麻的治療效果早已有許多令人信服的證據(jù)，但是其基因組信息的非常有限，我們目標(biāo)是完成多個大麻種系的測序。最初我們嘗試使用短讀長的新一代測序技術(shù)對C.sativa進(jìn)行測序。然而，我們很快地意識到，這種技術(shù)不能為我們提供一個清晰的基因組全貌，將很難從中找出有用的生物途徑信息。認(rèn)識到這一點后我們馬上改變了策略，開始使用更長讀長的測序技術(shù)對三次回交的品系進(jìn)行測序。”

 

Surprised in part by the finding that genomic variation between Cannabis strains is over 1%, a figure that is 10 times the variation of human genomes, the team at Medicinal Genomics turned to Roche’s 454 Sequencing Center in Branford, Connecticut to sequence the Cannabis indica strain on Roche’s new GS FLX+ System, the latest advance in long read next generation technology. The researchers obtained roughly 18x genome coverage with the 700-800 base pair long reads, enabling a high-quality draft assembly of this complex plant genome.

 

研究人員在測序過程中驚訝地發(fā)現(xiàn)大麻品系間基因組變異超過1％，是人類基因組間差異的10倍之多。研究組因此轉(zhuǎn)向了位于康涅狄格州Branford的羅氏454測序中心，該中心擁最新的新一代超長讀長測序儀羅氏GS FLX+系統(tǒng)。在那里，研究人員獲得了讀長為700-800堿基對，約18倍基因組覆蓋率的測序數(shù)據(jù)，從而完成了這個復(fù)雜植物基因組的高質(zhì)量基因組草案的繪制。

 

“I was stunned by the read quality and more impressively the length of the data coming off the GS FLX+ Instruments,” said McKernan. “With the long reads we can sort out the variation in the strain and phase alleles so that we can make biological sense of the sequencing data. We can assemble some key synthase genes into much longer phased blocks, allowing us to focus more on the biology and less on the computational concerns over collapsed polymorphic assemblies we were seeing with the shorter read systems.”

 

McKerna先生高興地表示：“GS FLX+的數(shù)據(jù)讀長的高質(zhì)量和超長長度讓我驚呆了。有這些長讀長數(shù)據(jù)的幫助，我們可以弄清楚基因組所發(fā)生的變異，理清相等位基因信息，發(fā)現(xiàn)其相關(guān)的生物學(xué)意義。我們可以將關(guān)鍵的合成酶基因拼接到更長的基因組片段中，我們可以更專注于生物學(xué)上研究，而不用像使用短讀長測序系統(tǒng)時那樣花大量時間在拼接高度多樣性片段的計算機(jī)運算上。”

 

“We are pleased to see an industry-renowned expert in the field of next generation sequencing recognize the value of the long reads offered with our new GS FLX+ System,” said Todd Arnold, Vice President of Development at 454 Life Sciences, a Roche Company. “This project along with other work on a variety of large plant and animal genomes confirm the power of long reads for high-quality assembly and, most importantly, for correlating sequence content with biological significance.”

 

“我們很高興作為新一代測序系統(tǒng)領(lǐng)域的權(quán)威人士McKernan先生能夠如此認(rèn)可GS FLX+系統(tǒng)所提供的長讀長數(shù)據(jù)的價值，”羅氏454 Life Sciences研發(fā)部副總裁Todd Armold先生說。 “這個項目以及其他復(fù)雜動植物基因組測序工作肯定了長讀長在獲取高質(zhì)量基因組拼接結(jié)果方面的優(yōu)勢，更重要的，他有助于將序列信息與其生物學(xué)意義更好的關(guān)聯(lián)起來�！�

 

Later this fall the company plans to release the raw sequence data of the Cannabis indica genome as well as a full genome annotation. With the genomes in hand, researchers can begin to identify non-psychoactive compounds or enzyme pathways to better elucidate the therapeutic benefits of Cannabis, including the plant’s anti-cancer properties. These pathways can be optimized in the plant or cloned into other hosts for more efficient biologic production. In addition, it may be possible through genome directed breeding to attenuate the psychoactive effects of Cannabis, while enhancing the medicinal aspects.

 

該公司計劃在今年秋天的晚些時候公布這次大麻基因組測序的原始數(shù)據(jù)，以及完整的基因組注釋。擁有了這些基因組信息以后，研究人員就著手確定大麻含有的無精神作用的化合物或酶的作用途徑，以更好地闡明大麻的效用機(jī)制，包括其在抗癌方面的特性。這些研究結(jié)果可以幫助在種植過程中優(yōu)化這些化合物或酶，或者將其克隆其他載體上，從而更有效地進(jìn)行生產(chǎn)。此外，有可能通過基因定向育種減弱大麻對神精系統(tǒng)的影響，同時加強(qiáng)治療效果及藥用價值。