Ensembl in a new era - deep genome annotation of domesticated animal species and breeds

驯养动物是重要的经济和社会物种，仅养殖动物的年产量就为英国经济带来了超过150亿英镑的收入。然而，特别是养殖动物，与许多挑战有关。例如，它们对气候变化的影响，作为人畜共患疾病的宿主，它们对有限资源的使用，以及与动物福利有关的问题。英国和全球的科学家正在通过制定改进的育种战略、减少甲烷排放的干预措施和先进的福利方法来应对这些挑战。此外，驯养动物越来越多地被证明是更好地了解人类健康的生物医学模型。在这些研究中，最重要的是获得高度注释的参考基因组。例如，通过更好地了解基因组中功能元件的位置和基因变化的潜在影响，研究人员可以极大地加快他们的研究。该项目的目的是创建非常详细的家养动物物种基因组图，并向全球的研究人员免费提供这些地图。虽然已经为牛、山羊、绵羊、猪、鸡、鸭、火鸡、狗和马等驯养动物物种以及几个重要的鱼类物种生成了参考基因组序列，但它们通常来自一种动物，通常不能很好地代表整个物种的多样性。同样，如果不了解基因组序列的不同成分在不同组织和细胞中以及不同生命阶段的作用，仅基因组序列的作用也是有限的。最近，测序技术的进步意味着更容易、更低成本地产生高质量的基因组组件。每个驯养动物物种不再只有一个代表性的基因组，而是每个物种内的品种和种群都产生了新的基因组。例如，除了原来的拳击手基因组外，现在至少有三个新品种的狗的基因组组装。由于牛是一种如此重要的经济牲畜物种，在接下来的三年里，来自不同牛品种的至少200多个基因组组合将被生产出来。捕捉所有这些基因组多样性是很重要的，因为它可以帮助确定育种和保护策略。然而，对于科学家来说，为了理解这些基因组，需要对基因组的表达和调控区域进行注释。了解驯养动物的基因组是如何表达和调控的，可以帮助研究人员了解基因组的哪些区域影响感兴趣物种的重要特征。例如，罗斯林研究人员比较了水牛和家牛的注释基因组组合，以更好地理解为什么一个物种比另一个物种更容易感染疾病。一旦新的基因组组合被注释，为了最大限度地发挥它们的影响，这些信息需要以研究人员可以自由获取的方式提供。EnSembl为研究人员提供了一种查看或“浏览”带注释的基因组信息的方法。作为该项目的一部分，我们将提供培训，以确保研究人员能够充分利用EnSembl资源，有效地研究注释基因组并解释其分析的功能相关性。EnSembl提供的数据库和工具已被证明是注释驯化动物物种复杂基因组的强大而有效的手段，它们必须与正在产生的大量新数据和研究问题保持同步。

Domesticated animals are economically and socially important species with annual farmed animals outputs alone worth over 15 billion pounds to the UK economy. However, farmed animals, in particular, are associated with a number of challenges. For example, their impact on climate change, as reservoirs of zoonotic diseases, their use of finite resources and also issues around animal welfare. Scientists in the UK and across the globe are meeting these challenges through developing improved breeding strategies, interventions that reduce methane emissions, and advanced welfare approaches. Moreover, domesticated animals are increasingly proving invaluable as biomedical models for better understanding human health. Fundamentally important across these studies is access to highly annotated reference genomes. By, for example, providing a better understanding of the location of functional elements in the genome and the potential impact of genetic changes, researchers can dramatically accelerate their research. The aim of this project is to create very highly detailed maps of the genomes of domesticated animal species and make them freely available to researchers across the globe. Although reference genome sequences have been generated for domesticated animal species such as cattle, goats, sheep, pigs, chickens, ducks, turkeys, dogs and horses, as well as for several important fish species, they have most often been derived from one animal, and generally poorly represent the diversity across the species. Likewise, the genome sequence alone is of limited use without understanding what different elements of it do in different tissues and cells and at different life stages.Recently, advances in sequencing technology have meant it is easier and less costly to generate high quality genome assemblies. Instead of one representative genome per domesticated animal species, new genomes for breeds and populations within each species are being generated. For example, there are now genome assemblies for at least three new dog breeds in addition to the original Boxer genome. As cattle are such an economically important livestock species at least two hundred more genome assemblies from different cattle breeds are being produced in the coming three years. Capturing all of this genomic diversity is important because it can help determine breeding and conservation strategies. However, for scientists to make sense of these genomes the expressed and regulatory regions of the genome need to be annotated. Understanding how the genome of a domesticated animal is expressed and regulated can help researchers understand which regions of the genome influence important characteristics of the species of interest. For example, Roslin researchers compared the annotated genome assemblies of water buffalo and domestic cattle to better understand why one species is more susceptible to disease than the other. Once new genome assemblies are annotated, to maximise their impact, this information needs to be provided in a way that researchers can access it freely. Ensembl provides a means for researchers to look at or 'browse' the annotated genome information. As part of this project, we will provide training to ensure that researchers can fully utilise Ensembl resources to investigate annotated genomes efficiently and interpret the functional relevance of their analysis. The databases and tools provided by Ensembl have been shown to be a powerful and effective means of annotating the complex genomes of domesticated animal species, and it is essential they keep pace with the large amounts of new data and research questions that are being generated.