药物基因组公司运用罗氏GS FLX+ 完成大麻基因组测序[创新技巧]

药物基因组公司8月18日宣布已完成了大麻这一重要药用植物两个品系（Cannabis sativa和Cannabis indica）的全基因组测序。此次基因组测序结果包括超过1310亿的碱基对序列，是现有最大的大麻基因组基因集合。该实验数据将在今年秋天向学界公开。这些基因数据预计将有助于大麻在包括癌症、炎症等广泛医疗应用中作用机制的研究。

药物基因组公司是一家美国和荷兰联合经营的私营公司，总部设在美国的Marblehead，该公司8月18日宣布已完成了大麻这一重要药用植物两个品系（Cannabis sativa和Cannabis indica）的全基因组测序。此次基因组测序结果包括超过1310亿的碱基对序列，是现有最大的大麻基因组基因集合。该实验数据将在今年秋天向学界公开。这些基因数据预计将有助于大麻在包括癌症、炎症等广泛医疗应用中作用机制的研究。

药物基因组公司创始人兼科学运营总监Kevin McKernan先生说：“尽管大麻的治疗效果早已有许多令人信服的证据，但是其基因组信息的非常有限，我们目标是完成多个大麻种系的测序。最初我们尝试使用短读长的新一代测序技术对C.sativa进行测序。然而，我们很快地意识到，这种技术不能为我们提供一个清晰的基因组全貌，将很难从中找出有用的生物途径信息。认识到这一点后我们马上改变了策略，开始使用更长读长的测序技术对三次回交的品系进行测序。”

研究人员在测序过程中惊讶地发现大麻品系间基因组变异超过1％，是人类基因组间差异的10倍之多。研究组因此转向了位于康涅狄格州Branford的罗氏454测序中心，该中心拥最新的新一代超长读长测序仪罗氏GS FLX+系统。在那里，研究人员获得了读长为700-800碱基对，约18倍基因组覆盖率的测序数据，从而完成了这个复杂植物基因组的高质量基因组草案的绘制。

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McKerna先生高兴地表示：“GS FLX+的数据读长的高质量和超长长度让我惊呆了。有这些长读长数据的帮助，我们可以弄清楚基因组所发生的变异，理清相等位基因信息，发现其相关的生物学意义。我们可以将关键的合成酶基因拼接到更长的基因组片段中，我们可以更专注于生物学上研究，而不用像使用短读长测序系统时那样花大量时间在拼接高度多样性片段的计算机运算上。”

“我们很高兴作为新一代测序系统领域的权威人士McKernan先生能够如此认可GS FLX+系统所提供的长读长数据的价值，”罗氏454 Life Sciences研发部副总裁Todd Armold先生说。 “这个项目以及其他复杂动植物基因组测序工作肯定了长读长在获取高质量基因组拼接结果方面的优势，更重要的，他有助于将序列信息与其生物学意义更好的关联起来。”

该公司计划在今年秋天的晚些时候公布这次大麻基因组测序的原始数据，以及完整的基因组注释。拥有了这些基因组信息以后，研究人员就着手确定大麻含有的无精神作用的化合物或酶的作用途径，以更好地阐明大麻的效用机制，包括其在抗癌方面的特性。这些研究结果可以帮助在种植过程中优化这些化合物或酶，或者将其克隆其他载体上，从而更有效地进行生产。此外，有可能通过基因定向育种减弱大麻对神精系统的影响，同时加强治疗效果及药用价值。

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Medicinal Genomics Sequences the Cannabis Genome Using Roche’s GS FLX+ System

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.

“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.”

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.

“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.”

“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.”

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.