Ensembl genome portal for farm and companion animals

对驯养动物的研究具有重要的社会经济影响，包括支持和加速农业动物部门的改进，通过提供动物模型促进医学研究，改善动物健康和福利，并为了解自然和野生动物种群提供信息。对于这类研究来说，了解塑造农场动物和伴侣动物的基因是必不可少的，牛、山羊、绵羊、猪、鸡、鸭、火鸡、狗和马等主要农场动物和伴侣动物物种的几乎所有基因序列（基因组序列草图）都已确定。包括鳕鱼、虹鳟鱼、鲑鱼和罗非鱼在内的几种重要鱼类的基因组序列草案也已公布，或即将公布。然而，数十亿碱基的字符串（用四个字母A、C、G、T表示）对生物研究科学家来说并不立即有用。用诸如基因的编码和调控部分位于何处的特征来注释这些基因组序列草图，并且物种内个体之间不同的碱基（遗传变体）极大地提高了基因组序列的价值和实用性。以免费访问的方式可视化基因组序列并完成注释，进一步提高了信息的价值。网络安装的Ensembl基因组浏览器、数据库和相关注释工具已被证明是注释包括人类在内的动物物种复杂基因组的强大而有效的手段，小鼠和最近养殖和伴侣动物。该项目关注提高养殖和伴侣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测序，而且对每个感兴趣的物种的多个个体的基因组进行测序，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用于测定，例如，不同细胞或不同条件下的基因表达程度（转录组学）或基因组状态（表观基因组学）。将来自这些测定的序列读出映射回相关基因组序列不仅提供了用于分析的全基因组框架，而且还提供了用于注释基因组序列本身的进一步信息。因此，有一个经常需要更新的基因组序列注释的重要动物物种。我们将使用Ensembl系统注释的基因组序列的关键养殖和伴侣动物物种。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源和关键生物信息学资源。这些关键信息不仅对学术研究人员有价值，而且对在工业界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流通性。因此，该项目关注的是为主要养殖和伴侣动物物种提供高质量的最新注释参考基因组，以便对这些具有经济或社会重要性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.