Ensembl and enabling genetics and genomics research in farmed animal species

养殖动物物种的集成和遗传学和基因组学研究

• 批准号: BB/I025506/1
• 负责人: Paul Flicek
• 金额: $ 33.08万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FI025506%2F1
• 关键词: Ensembl; enabling; genetics; genomics; research

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.

几乎所有基因（基因组序列草案）的序列已确定针对包括牛，猪，鸡，火鸡，狗和马在内的几种养殖和伴侣动物的序列。绵羊，鸭子和鲑鱼等其他几种物种的基因组序列将很快完成。构成这些基因组序列的数十亿个基础（象征为四个字母A，C，G，T）对生物学研究科学家并不有用。用基因的编码和调节部分等特征来注释这些草案基因组序列，以及一个物种中个体之间不同的基础（遗传变异）大大增强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基因组序列，进一步提高了信息的价值。已显示网络安装的Ensembl基因组浏览器，数据库和相关的注释工具被证明是强大而有效的方法，可以注释动物物种的复杂基因组，包括人类，小鼠以及最近养殖的动物和伴随动物。该项目涉及提高养殖和伴侣动物基因组的基因组注释质量。科学家的国际联盟正在使用所谓的下一代测序技术，不仅是为了对更经济重要的物种的基因组进行测序，而且还为每种感兴趣的种类的多个个体的基因组进行了，并改善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中，例如在不同细胞或不同条件下（转录组学）或基因组状态（表观基因组学）的基因表达程度。将这些测定法的序列读出映射到相关的基因组序列不仅提供了分析基因组的框架，而且还提供了进一步的信息来注释基因组序列本身。因此，需要反复出现对重要动物物种的基因组序列注释。我们将使用Ensembl系统注释关键养殖和伴随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安装在万维网上的资源免费提供。最近在Ensembl系统中开发的特征可以使同一物种个体之间的遗传变异分析和可视化（即序列差异）。这种遗传变异解释了生长，牛奶产量和疾病易感性等特征的差异。我们将使用从动物遗传学研究界获取的序列和基因型数据来填充Ensembl-Animal变异数据库。可视化这些变异数据并使它们可以被科学界和动物育种行业访问，将促进研究，以了解动物中复杂性状的遗传控制以及养殖动物的遗传改善。高质量注释的参考基因组序列是一种重要的生物信息学资源，可有效起诉生物科学中的当代研究。此类生物信息学资源的价值和效用在很大程度上取决于资源的货币。因此，该项目涉及为关键养殖和伴侣动物物种提供高质量的注释参考基因组，以便对这些经济或社会重要的动物物种进行研究。

项目成果

Ensembl 2015.

• DOI: 10.1093/nar/gku1010
• 发表时间: 2015-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Cunningham F;Amode MR;Barrell D;Beal K;Billis K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fitzgerald S;Gil L;Girón CG;Gordon L;Hourlier T;Hunt SE;Janacek SH;Johnson N;Juettemann T;Kähäri AK;Keenan S;Martin FJ;Maurel T;McLaren W;Murphy DN;Nag R;Overduin B;Parker A;Patricio M;Perry E;Pignatelli M;Riat HS;Sheppard D;Taylor K;Thormann A;Vullo A;Wilder SP;Zadissa A;Aken BL;Birney E;Harrow J;Kinsella R;Muffato M;Ruffier M;Searle SM;Spudich G;Trevanion SJ;Yates A;Zerbino DR;Flicek P
• 通讯作者: Flicek P

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species.

• DOI: 10.1038/ng.2657
• 发表时间: 2013-07
• 期刊: NATURE GENETICS
• 影响因子: 30.8
• 作者: Huang, Yinhua;Li, Yingrui;Burt, David W.;Chen, Hualan;Zhang, Yong;Qian, Wubin;Kim, Heebal;Gan, Shangquan;Zhao, Yiqiang;Li, Jianwen;Yi, Kang;Feng, Huapeng;Zhu, Pengyang;Li, Bo;Liu, Qiuyue;Fairley, Suan;Magor, Katharine E.;Du, Zhenlin;Hu, Xiaoxiang;Goodman, Laurie;Tafer, Hakim;Vignal, Alain;Lee, Taeheon;Kim, Kyu-Won;Sheng, Zheya;An, Yang;Searle, Steve;Herrero, Javier;Groenen, Martien A. M.;Crooijmans, Richard P. M. A.;Faraut, Thomas;Cai, Qingle;Webster, Robert G.;Aldridge, Jerry R.;Warren, Wesley C.;Bartschat, Sebastian;Kehr, Stephanie;Marz, Manja;Stadler, Peter F.;Smith, Jacqueline;Kraus, Robert H. S.;Zhao, Yaofeng;Ren, Liming;Fei, Jing;Morisson, Mireille;Kaiser, Pete;Griffin, Darren K.;Rao, Man;Pitel, Frederique;Wang, Jun;Li, Ning
• 通讯作者: Li, Ning

Avianbase: a community resource for bird genomics.

• DOI: 10.1186/s13059-015-0588-2
• 发表时间: 2015-01-29
• 期刊: Genome biology
• 影响因子: 12.3
• 作者: Eöry L;Gilbert MT;Li C;Li B;Archibald A;Aken BL;Zhang G;Jarvis E;Flicek P;Burt DW
• 通讯作者: Burt DW

Analyses of pig genomes provide insight into porcine demography and evolution.

• DOI: 10.1038/nature11622
• 发表时间: 2012-11-15
• 期刊: Nature
• 影响因子: 64.8

Ensembl 2014.

• DOI: 10.1093/nar/gkt1196
• 发表时间: 2014-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Flicek P;Amode MR;Barrell D;Beal K;Billis K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fitzgerald S;Gil L;Girón CG;Gordon L;Hourlier T;Hunt S;Johnson N;Juettemann T;Kähäri AK;Keenan S;Kulesha E;Martin FJ;Maurel T;McLaren WM;Murphy DN;Nag R;Overduin B;Pignatelli M;Pritchard B;Pritchard E;Riat HS;Ruffier M;Sheppard D;Taylor K;Thormann A;Trevanion SJ;Vullo A;Wilder SP;Wilson M;Zadissa A;Aken BL;Birney E;Cunningham F;Harrow J;Herrero J;Hubbard TJ;Kinsella R;Muffato M;Parker A;Spudich G;Yates A;Zerbino DR;Searle SM
• 通讯作者: Searle SM