FlyAtlas2: a definitive, expanded NGS expression resource for the Drosophila community and beyond

现在人类和其他生物的许多基因组已经被测序，我们知道大多数动物是由大约15,000-25,000个基因组成的。也许令人惊讶的是，我们仍然不知道所有这些基因都有什么作用，我们仍然在发现全新的基因。要理解基因的作用，一个重要的工具就是简单地了解基因在哪里被使用(或“表达”)。然后我们可以在一个简单的模型生物体中突变基因，并观察这些组织中发生了什么变化--这被称为“反向遗传学”，是后基因组研究的关键部分。简单的果蝇果蝇是此类研究的优秀模型，因为它具有独特的强大遗传学，并被世界各地数以千计的实验室使用。除了本身是一种重要的生物，它还被证明是研究人类功能和疾病以及研究密切相关的害虫和疾病媒介的一个有价值的模型。2007年，我们使用当时尖端的Affymetrix微阵列技术制作了FlyAtlas.org，这是一个关于幼蝇和成虫多组织(脑、心脏、肠道、肌肉等)基因表达的在线图谱。有了这个资源，用户可以很快(通常在10秒内)得到这个问题的答案：我感兴趣的基因在生物体中何时何地表达？由于FlyAtlas省去了去做一系列昂贵的实验的需要，因此这个网站每次使用都节省了很多天的工作。这个数据库揭示了果蝇研究界内外对这样的数据的巨大需求，这些数据已经被来自世界各地的650多篇论文使用。然而，从那时起，这项技术就迅速发展了，而‘下一代测序(NGS)’使我们能够提供更完整的图像。特别是，我们不受Affymetrix芯片上打印的基因的限制，可以识别和测量任何基因的不同转录本的丰度。此外，我们将能够识别已知转录本的新变种，甚至是全新的基因。我们还将能够绘制出微小的“微型RNA”在多个组织中的表达。其结果将是我们能够进行后基因组研究的方式的一步改变。所有这些数据将被迅速地放在网上-在公共领域-以告知和加速世界各地的研究。我们还将努力将新的、扩展的FlyAtlas资源推广到果蝇社区和更远的地方。除了给科学家带来明显的好处外，这些数据还将使利用果蝇进行生物医学研究成为可能，因为许多研究人员现在正在成功地在果蝇身上模拟人类疾病。此外，这项工作将使工业受益，因为这些数据将有助于为寻找新的更安全、更绿色的杀虫剂提供信息。这一点很重要，因为昆虫是世界各地疾病的主要媒介，也是农作物的害虫。

Now that many genomes (of humans and other organisms) have been sequenced, we know that most animals are made with about 15 000 - 25 000 genes. Perhaps surprisingly, we still do not know what all these genes do, and we are still discovering entirely new genes. A vital tool to understanding what genes do is simply to see where the genes are being used (or "expressed"). Then we can mutate the genes in a simple model organism, and see what changes in those tissues - this is called 'reverse genetics', and is a key part of post-genomic research. The simple fruit fly Drosophila is an excellent model for such studies, because of its uniquely powerful genetics, and is used by many thousands of labs around the world. As well as being an important organism to study in its own right, it has proved a valuable model both for human function and disease, and for study of closely related insect pests and vectors of disease.In 2007, we produced FlyAtlas.org, an online atlas of gene expression across multiple tissues (brain, heart, gut, muscle etc) of both larval and adult flies, using the then cutting-edge technology of Affymetrix microarrays. With this resource, users could quickly (in typically 10 seconds) get an answer to the question "where and when in the organism is my gene of interest expressed?" As FlyAtlas saves the need to go off and do a series of expensive experiments, this website thus saves many days of work each time it is used. This database revealed a great hunger for such data, both in the Drosophila research community and beyond, and the data have already been used in over 650 papers from around the world. However, since then the technology has rapidly advanced, and 'next generation sequencing (NGS)' allows us to provide a much more complete picture. In particular, we are not constrained by the genes printed on the Affymetrix chips, and can identify and measure the abundance of different transcripts from any gene. In addition, we will be able to identify novel variants of known transcripts, or even entirely new genes. We will also be able to map out the expression of tiny, 'micro RNAs' across multiple tissues. The result will be a step-change in how we are able to perform post-genomic research.All these data will be placed rapidly online -in the public domain- to inform and accelerate research worldwide. We will also work to evanglise the new, extended FlyAtlas resource both to the Drosophila community and beyond. As well as obvious benefits to scientists, the data will enable biomedical research using Drosophila, as many researchers are now successfully modelling human diseases in flies. Additionally, the work will benefit industry, as the data will help to inform the search for new classes of safer, 'greener' insecticides. This is important, because insects are major vectors of disease, and pests of crops, around the world.