Ensembl and enabling genetics and genomics research in farmed animal species

几乎所有的基因序列（基因组序列草图）已经确定了几种养殖动物和同伴动物，包括牛、猪、鸡、火鸡、狗和马。羊、鸭和鲑鱼等其他几种物种的基因组序列草图也将很快完成。构成这些基因组序列的数十亿个碱基（用A、C、G、T四个字母表示）并不能立即对生物研究科学家有用。用基因的编码和调控部分以及物种个体间的碱基差异（遗传变异）等特征对这些草图基因组序列进行注释，极大地提高了基因组序列的价值和实用性。以一种自由访问的方式将基因组序列可视化并完成注释，进一步提高了信息的价值。网络安装的Ensembl基因组浏览器、数据库和相关的注释工具已被证明是强大而有效的注释动物物种复杂基因组的手段，包括人类、小鼠和最近的养殖动物和伴侣动物。本项目旨在提高养殖动物和伴侣动物基因组注释的质量。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分析，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）。将这些分析的序列读数映射回相关的基因组序列，不仅为分析提供了一个全基因组框架，而且还为注释基因组序列本身提供了进一步的信息。因此，更新重要动物物种的基因组序列注释是一个反复出现的需求。我们将使用Ensembl系统对关键养殖动物和伴侣动物物种的基因组序列进行注释。由此产生的带注释的基因组序列将作为资源在万维网上免费提供。最近在Ensembl系统中开发的功能可以分析和可视化同一物种个体之间的遗传变异（即序列差异）。这种遗传变异解释了生长、产奶量和疾病易感性等性状的差异。我们将用从动物遗传学研究界获得的序列和基因型数据填充Ensembl-animal Variation数据库。将这些变异数据可视化，并使其可供科学界和动物育种行业使用，将有助于研究了解动物复杂性状的遗传控制和养殖动物的遗传改良。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重要生物信息学资源。这些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，该项目致力于为重要的养殖动物和伴侣动物物种提供高质量的最新注释参考基因组，以便对这些经济上或社会上重要的动物物种进行研究。

The sequence of almost all genes (a draft genome sequence) has been determined for several farmed and companions animals including cattle, pigs, chickens, turkeys, dogs and horses. Draft genome sequences for several other species such as sheep, ducks and salmon will be completed soon. 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 the coding and regulatory parts of genes, and 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 an 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 the so-called next generation sequencing technology, 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. Recently developed features within the Ensembl system enable the analysis and visualisation of genetic variation (i.e. sequence differences) between individuals of the same species. This genetic variation explains the differences in traits such as growth, milk yield and susceptibility to disease. We will populate the Ensembl-animal Variation databases with sequence and genotype data acquired from the animal genetics research community. Visualising these variation data and making them accessible to the scientific community and the animal breeding industry will facilitate research to understand the genetic control of complex traits in animals and genetic improvement of farmed animals. A high quality annotated reference genome sequence is a critical bioinformatics resource for the effective prosecution of contempary research in the biological sciences. 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.