Ensembl genome portal for farm and companion animals

对家养动物的研究具有重要的社会经济影响，包括支持和加速改进农业部门的动物，通过提供动物模型促进医学研究，改善动物健康和福利，并使人们了解自然和野生动物种群。对塑造农场和同伴动物的基因的了解对这种研究是至关重要的。主要养殖和同伴动物物种，如牛、山羊、绵羊、猪、鸡、鸭、火鸡、狗和马，几乎所有基因的序列(基因组草稿序列)已经确定。几种重要的鱼类物种，包括鳕鱼、虹鲑鱼、鲑鱼和罗非鱼，也有或很快就会有基因组序列草案。然而，组成这些基因组序列的数十亿个碱基(符号为A、C、G、T)的字符串对生物研究科学家并不是立即有用的。用诸如基因编码和调节部分位于哪里以及物种内个体之间不同的碱基(遗传变体)等特征来注释这些草拟的基因组序列大大提高了基因组序列的价值和实用性。以可自由访问的方式可视化完整的基因组序列和注释进一步提高了信息的价值。安装在网络上的EnSembl基因组浏览器、数据库和相关的注释工具已被证明是注释动物物种复杂基因组的强大而有效的手段，包括人类、小鼠和最近饲养的和同伴动物。该项目致力于提高饲养和同伴动物基因组的基因组注释质量。国际科学家联盟正在使用所谓的下一代测序技术，不仅对经济上更重要的物种的基因组进行排序，而且还对每个感兴趣的物种的多个个体的基因组进行排序，并改进或完成关键物种的参考基因组序列。这些新的测序技术也越来越多地被用于分析，例如，在不同细胞或不同条件下基因表达的程度(转录组学)或基因组状态(表观基因组学)。将从这些分析中读出的序列映射回相关的基因组序列不仅提供了全基因组范围的分析框架，而且还提供了进一步的信息来注释基因组序列本身。因此，经常需要更新重要动物物种的基因组序列注释。我们将使用EnSembl系统来注释关键养殖动物物种和伴生动物物种的基因组序列。由此产生的注释基因组序列将作为万维网上的资源免费提供。高质量的注释参考基因组序列是有效开展当代生物科学研究的关键信息来源和关键生物信息学资源。这一关键信息不仅对学术研究人员有价值，而且对在工业领域工作的科学家也有价值，包括动物育种、动物健康和制药部门的科学家。然而，这种生物信息学资源的价值和效用严重依赖于资源的货币。因此，该项目致力于为主要养殖和伴生动物物种提供高质量的最新注释参考基因组，以便能够对这些经济或社会重要的动物物种进行研究。

Research on domesticated animals has important socio-economic impacts, including underpinning and accelerating improvements in the animal sector of agriculture, contributing to medical research by providing animal models, improving animal health and welfare and informing understanding of natural and wild animal populations. Knowledge of the genes that shape farm and companion animals is essential for such research.The sequence of almost all genes (a draft genome sequence) has been determined for major farmed and companion animal species such as cattle, goats, sheep, pigs, chickens, ducks, turkeys, dogs and horses. Draft genome sequences are also available, or soon will be, for several important fish species, including cod, rainbow trout, salmon and tilapia. However, the strings of billions of bases (symbolised as four letters A, C, G, T) that constitute these genome sequences are not immediately useful to biological research scientists.Annotating these draft genome sequences with features such as where the coding and regulatory parts of genes are located, and the bases which differ between individuals within a species (genetic variants) greatly enhances the value and utility of the genome sequence. Visualising the genome sequences complete with annotations in a freely accessible manner further improves the value of the information.The web-mounted Ensembl genome browser, databases and associated annotation tools have been shown to be powerful and effective means of annotating the complex genomes of animal species including humans, mice and more recently farmed and companion animals.This project is concerned with improving the quality of genome annotation for farmed and companion animal genomes. International consortia of scientists are using so-called next generation sequencing technologies, not only to sequence the genomes of more economically important species, but also the genomes of multiple individuals for each species of interest and to improve or finish the reference genome sequences for key species. These new sequencing technologies are also being used increasingly in assays, for example, of the extent of gene expression in different cells or under different conditions (transcriptomics) or of the state of the genome (epigenomics). Mapping the sequence read-outs from these assays back to the relevant genome sequence not only provides a genome-wide framework for analysis but also provides further information with which to annotate the genome sequence itself. Thus, there is a recurring need to refresh the genome sequence annotation for important animal species.We will use the Ensembl system to annotate the genome sequences of key farmed and companion animal species. The resulting annotated genome sequences will be made freely available as resources mounted on the World Wide Web.A high quality annotated reference genome sequence is a key source of information and critical bioinformatics resource for the effective prosecution of contemporary research in the biological sciences. This key information is valuable not only to academic researchers, but also to scientists working in industry, including those in the animal breeding, animal health and pharmaceutical sectors. However, the value and utility of such bioinformatics resources are critically dependent upon the currency of the resource. Thus, this project is concerned with delivering high quality up-to-date annotated reference genomes for key farmed and companion animal species to enable research on these economically or socially important animal species.