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.

几乎所有的基因序列（基因组序列草案）已经确定了几个养殖和伴侣动物，包括牛，猪，鸡，火鸡，狗和马。绵羊、鸭和鲑鱼等其他几个物种的基因组序列草案也将很快完成。构成这些基因组序列的数十亿个碱基的字符串（用四个字母A、C、G、T表示）对生物研究科学家来说并不是立即有用的。用基因的编码和调控部分以及物种内个体之间不同的碱基（遗传变体）等特征注释这些基因组序列草图极大地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动物物种（包括人类、小鼠和最近养殖的伴侣动物）复杂基因组的强大而有效的手段。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。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，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系统注释关键养殖和伴侣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。Ensembl系统中最近开发的功能可以分析和可视化相同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。我们将从动物遗传学研究社区获得的序列和基因型数据填充合奏动物变异数据库。可视化这些变异数据并使其可供科学界和动物育种业使用，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现代生物科学研究的重要生物信息学资源。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。

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

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

The sheep genome illuminates biology of the rumen and lipid metabolism.

• DOI: 10.1126/science.1252806
• 发表时间: 2014-06-06
• 期刊: Science (New York, N.Y.)
• 作者: Jiang Y;Xie M;Chen W;Talbot R;Maddox JF;Faraut T;Wu C;Muzny DM;Li Y;Zhang W;Stanton JA;Brauning R;Barris WC;Hourlier T;Aken BL;Searle SMJ;Adelson DL;Bian C;Cam GR;Chen Y;Cheng S;DeSilva U;Dixen K;Dong Y;Fan G;Franklin IR;Fu S;Guan R;Highland MA;Holder ME;Huang G;Ingham AB;Jhangiani SN;Kalra D;Kovar CL;Lee SL;Liu W;Liu X;Lu C;Lv T;Mathew T;McWilliam S;Menzies M;Pan S;Robelin D;Servin B;Townley D;Wang W;Wei B;White SN;Yang X;Ye C;Yue Y;Zeng P;Zhou Q;Hansen JB;Kristensen K;Gibbs RA;Flicek P;Warkup CC;Jones HE;Oddy VH;Nicholas FW;McEwan JC;Kijas J;Wang J;Worley KC;Archibald AL;Cockett N;Xu X;Wang W;Dalrymple BP
• 通讯作者: Dalrymple BP

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