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

驯养动物是经济和社会上重要的物种，每年仅养殖动物就为英国经济贡献了超过150亿英镑的产值。然而，特别是养殖动物，面临着许多挑战。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们正在通过开发改进的繁殖策略、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，作为更好地了解人类健康的生物医学模型，家养动物越来越被证明是无价的。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遗传变化的潜在影响，研究人员可以大大加快他们的研究。该项目的目的是创建非常详细的驯化动物物种基因组图，并使其免费提供给全球的研究人员。虽然已经为牛、山羊、绵羊、猪、鸡、鸭、火鸡、狗和马等家养动物以及几种重要的鱼类产生了参考基因组序列，但它们通常来自一种动物，通常不能代表物种的多样性。同样，如果不了解基因组的不同成分在不同组织和细胞以及不同生命阶段的作用，单凭基因组序列的作用是有限的。最近，测序技术的进步意味着产生高质量的基因组组装更容易，成本更低。不再是每个驯化动物物种都有一个具有代表性的基因组，而是正在为每个物种的品种和种群产生新的基因组。例如，除了最初的拳师犬基因组外，现在至少有三个新犬种的基因组组装。由于牛是一种经济上如此重要的牲畜物种，在未来三年内，至少有200多种来自不同牛品种的基因组组合正在生产。捕获所有这些基因组多样性很重要，因为它可以帮助确定繁殖和保护策略。然而，为了让科学家理解这些基因组，基因组的表达区和调控区需要被注释。了解驯化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，罗斯林的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其影响，这些信息需要以一种研究人员可以自由访问的方式提供。Ensembl为研究人员提供了一种查看或“浏览”注释基因组信息的方法。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，有效地研究带注释的基因组，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家养动物物种复杂基因组的强大而有效的手段，它们必须跟上大量新数据和正在产生的研究问题。

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.