Ensembl - adding value to animal genomes through high quality annotation

Ensembl - 通过高质量注释为动物基因组增加价值

• 批准号: BB/S02008X/1
• 负责人: Alan Archibald
• 金额: $ 47万
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2019
• 资助国家: 英国
• 起止时间: 2019 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FS02008X%2F1
• 关键词: Ensembl; adding; value; animal; genomes

This project will deliver high quality up-to-date annotated genomes for key farmed and domesticated animals to enable research on these economically and socially important species.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. High quality annotated genome sequences are key resources to enable such research.The sequence of almost all genes (a reference genome sequence) has been determined for major farmed and domesticated animal species such as cattle, goats, sheep, pigs, chickens, ducks, turkeys, dogs and horses as well as 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 particularly useful or understandable on their own. Once a genome has been sequenced, it needs to be 'annotated' (i.e. explanatory notes need to be added to identify key features within the genome sequence) in order for research scientists to make sense of it.Annotating reference 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.Ensembl provides a means for researchers to look at or 'browse' the annotated genome information. The databases and tools provided by Ensembl have been shown to be a powerful and effective means of annotating the complex genomes of animal species including humans, mice and more recently farmed and domesticated animals.Enabled by advances in genome sequencing technologies and associated computational methods scientists around the world are generating more and better genome sequences. As the genome sequence of a single individual does not completely represent the genetic make-up of a species, scientists are also sequencing multiple individuals within a species. Individual research groups and international consortia are also generating sequence information that can be used in the annotation and analysis pipelines that we will run to identify both coding and regulatory sequences. We will use these data to annotate the genomes of farmed and domesticated animals, including aquaculture species. We will run comparative analyses to compare genomes both between species and between individuals within a species.These richly annotated genome sequences, which are in effect maps of where the coding gene content and regulatory sequences are located, will be made freely available to the scientific community and others via the Ensembl Genome Browser mounted on the World Wide Web as well as via an Application Programming Interface for power users. We will also provide between and within species comparative views.The annotated genomes that we will deliver are valuable not only to academic researchers, but also to scientists working in industry, including those in the animal breeding, animal health and pharmaceutical sectors. Keeping this information up-to-date, by characterising new genome sequences and integrating new data as it becomes available, is essential for reference genome sequences to remain current and useful.

该项目将为重要的养殖和驯养动物提供高质量的最新注释基因组，以使对这些经济和社会上重要物种的研究成为可能。家畜研究具有重要的社会经济影响，包括巩固和加速农业动物部门的改进，通过提供动物模型、改善动物健康和福利以及增进对自然和野生动物种群的了解，促进医学研究。高质量的注释基因组序列是实现此类研究的关键资源。已经确定了牛、山羊、绵羊、猪、鸡、鸭、火鸡、狗和马等主要养殖和驯养动物以及包括鳕鱼、虹鳟、鲑鱼和罗非鱼在内的几种重要鱼类的几乎所有基因的序列（参考基因组序列）。然而，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）本身并不是特别有用或容易理解。一旦基因组测序完成，就需要对其进行“注释”（即需要添加解释性注释以识别基因组序列中的关键特征），以便研究科学家能够理解它。在参考基因组序列上标注基因编码和调控部分的位置，以及物种内个体之间的碱基差异（遗传变异）等特征，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可视化基因组序列并完成注释，进一步提高了信息的价值。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。Ensembl提供的数据库和工具已被证明是一种强大而有效的注释动物物种复杂基因组的手段，包括人类，小鼠和最近的养殖和驯养动物。由于基因组测序技术和相关计算方法的进步，世界各地的科学家正在生成更多更好的基因组序列。由于单个个体的基因组序列并不能完全代表一个物种的基因组成，科学家们也在对一个物种内的多个个体进行测序。个别研究小组和国际联盟也在生成序列信息，这些信息可以用于我们将运行的注释和分析管道，以识别编码和调控序列。我们将使用这些数据对养殖和驯养动物（包括水产养殖物种）的基因组进行注释。我们将进行比较分析，比较物种之间和物种内个体之间的基因组。这些有丰富注释的基因组序列，实际上是编码基因内容和调控序列的位置图，将通过安装在万维网上的Ensembl基因组浏览器以及为高级用户提供的应用程序编程接口，免费提供给科学界和其他人。我们还将提供物种之间和物种内部的比较观点。我们将提供的带注释的基因组不仅对学术研究人员很有价值，而且对在工业界工作的科学家也很有价值，包括动物育种、动物保健和制药部门的科学家。通过描述新的基因组序列特征和整合可用的新数据，使这些信息保持最新，对于参考基因组序列保持最新和有用至关重要。

项目成果

Suina genomes and phylogenomics

Suina 基因组和系统发育组学

• 发表时间: 2019
• 作者: Eory L

Ensembl 2022.

• DOI: 10.1093/nar/gkab1049
• 发表时间: 2022-01-07
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Cunningham F;Allen JE;Allen J;Alvarez-Jarreta J;Amode MR;Armean IM;Austine-Orimoloye O;Azov AG;Barnes I;Bennett R;Berry A;Bhai J;Bignell A;Billis K;Boddu S;Brooks L;Charkhchi M;Cummins C;Da Rin Fioretto L;Davidson C;Dodiya K;Donaldson S;El Houdaigui B;El Naboulsi T;Fatima R;Giron CG;Genez T;Martinez JG;Guijarro-Clarke C;Gymer A;Hardy M;Hollis Z;Hourlier T;Hunt T;Juettemann T;Kaikala V;Kay M;Lavidas I;Le T;Lemos D;Marugán JC;Mohanan S;Mushtaq A;Naven M;Ogeh DN;Parker A;Parton A;Perry M;Piližota I;Prosovetskaia I;Sakthivel MP;Salam AIA;Schmitt BM;Schuilenburg H;Sheppard D;Pérez-Silva JG;Stark W;Steed E;Sutinen K;Sukumaran R;Sumathipala D;Suner MM;Szpak M;Thormann A;Tricomi FF;Urbina-Gómez D;Veidenberg A;Walsh TA;Walts B;Willhoft N;Winterbottom A;Wass E;Chakiachvili M;Flint B;Frankish A;Giorgetti S;Haggerty L;Hunt SE;IIsley GR;Loveland JE;Martin FJ;Moore B;Mudge JM;Muffato M;Perry E;Ruffier M;Tate J;Thybert D;Trevanion SJ;Dyer S;Harrison PW;Howe KL;Yates AD;Zerbino DR;Flicek P
• 通讯作者: Flicek P

An improved pig reference genome sequence to enable pig genetics and genomics research

• DOI: 10.1093/gigascience/giaa051
• 发表时间: 2020-06-01
• 期刊: GIGASCIENCE
• 影响因子: 9.2
• 作者: Warr, Amanda;Affara, Nabeel;Archibald, Alan L.
• 通讯作者: Archibald, Alan L.

Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor-A tutorial.

• DOI: 10.1002/humu.24298
• 发表时间: 2022-08
• 期刊: Human mutation
• 影响因子: 3.9
• 作者: Hunt SE;Moore B;Amode RM;Armean IM;Lemos D;Mushtaq A;Parton A;Schuilenburg H;Szpak M;Thormann A;Perry E;Trevanion SJ;Flicek P;Yates AD;Cunningham F
• 通讯作者: Cunningham F

RT2T: A Global Collaborative Project to Study Chromosomal Evolution in the Suborder Ruminantia

RT2T：研究反刍亚目染色体进化的全球合作项目

• DOI: 10.21203/rs.3.rs-3918604/v1
• 发表时间: 2024
• 作者: Kalbfleisch T