Genome assembly. chromosomal organization and comparative genomics of multiple bird species: beyond "catalogues of genes"

想象一下，试图在一个城镇中导航，只有你的a - z索引来引导你，而不是街道地图。从本质上讲，这就是对新物种的基因组进行测序时所发生的事情。在用基因序列填补空白之前，使用老式技术先“勾勒出街道的轮廓”。新技术（即所谓的“下一代测序”）要便宜得多，速度也快得多，但在区分基因之间的关系方面却相当差。从本质上讲，下一代测序集只不过是基因的目录，整个基因组的结构很少。幸运的是，这个问题可以用一种叫做“FISH”的技术来纠正，这种技术可以从下一代测序项目中获取数据，并直接将基因可视化，因为它们出现在基因组中的正确位置。在这个项目中，我们打算用25-30个最近完成的鸟类基因组序列来做这件事。鸟类是最多样化的动物之一，大约有1万种。许多是人类疾病和发展的典范，对农业（肉类和蛋类）至关重要。其他鸟类受到威胁或濒临灭绝，随着全球变暖的迫近，研究生态学和保护鸟类的分子工具是必不可少的。也有可能比较一个基因组与另一个基因组的整体结构，有点像比较具有相似布局的城镇地图。我们已经开发了在线工具，可以一次直接可视化几种鸟类基因组之间的相似性和差异性。当然，这些鸟类基因组之间的差异来自于进化过程中发生的变化。这个项目的主要目的之一是找出这种情况是如何以及为什么发生的。我们有很多想法，比如我们认为在基因组中或多或少可能发生进化重排的地方可能存在不同的“基因特征”。我们认为整个过程可能与我们的基因在生殖细胞中重组的机制有关。我们还认为，“漂浮在”这些鸟类基因组周围的小片段DNA可能会发挥作用。最后，我们得到了来自世界各地众多实验室的大力支持，他们都对鸟类基因组学感兴趣，并希望使用我们的在线资源来提出他们自己的生物学问题。出于这个原因，我们认为这个项目不仅将帮助我们了解鸟类的进化，而且还将使英国成为这类工作的中心国际枢纽。

Imagine trying to navigate through a town with only the index from your A-Z to guide you and not the street map. In essence, this is what happens when the genome of a new species is sequenced. Old fashioned technology used to "sketch the outline of the streets" first before filling in the gaps with the gene sequence. The new technology (so called "Next Generation Sequencing") is much cheaper and quicker but is quite poor at sorting out where the genes are in relation to one another. Essentially, Next Generation Sequencing assemblies are little more than catalogues of genes with little structure of the overall genome apparent. Fortunately this problem can be rectified using a technique called "FISH" that can take the data from next generation sequencing projects and visualise directly the genes as they appear in their rightful place in the genome. In this project we intend to do this with 25-30 recently completed genome sequences from birds. Birds are among the most diverse animals with around 10,000 living species. Many are models for human disease and development and are critical to agriculture (both meat and eggs). Others are threatened or endangered and, with impending global warming, molecular tools for the study of ecology and conservation of birds are essential. It is also possible to compare the overall structure of one genome with another, somewhat like comparing the maps of towns with similar layouts. We have developed online tools that can directly visualize the similarities and differences between the genomes of several birds at a time. Of course the differences between these bird genomes came about through changes that happened during evolution. One of the main aims of this project is to find out how and why this occurred. We have a number of ideas such as we think there may be different "gene signatures" at the places in the genome where evolutionary rearrangements are more or less likely to occur. We think that the whole process may be related to the mechanisms by which our genes recombine in our germ cells. We also think there may be a role for small pieces of DNA that "float around" these bird genomes. Finally, we have received overwhelming support from numerous laboratories all over the world, all of whom are interested in bird genomics and who would wish to use our online resource to ask biological questions of their own. For this reason we feel that this project not only will help us understand evolution in birds but also establish the UK as a central international hub for work of this kind.