Building a genome analytic resource for the lepidopteran community

为鳞翅目动物群落建立基因组分析资源

• 批准号: BB/K020161/1
• 负责人: Mark Blaxter
• 金额: $ 68.1万
• 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: 2013
• 资助国家: 英国
• 起止时间: 2013 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FK020161%2F1
• 关键词: Building; genome; analytic; resource; lepidopteran

Genome sequencing, and large-scale, population genomic analysis, has suddenly become affordable. The explosion of data presents tremendous opportunity for ground-breaking research based on integration of data from independently-organized, community-driven genome projects, but this in turn requires shared database resources. For model organisms, genome databasing efforts grew with the research communities, and there are mature portals for deep investigation across many large scale datasets - the databases themselves have become a substrate for (meta-) research of high impact. For communities new to genomic (and population genomic) approaches, the need for accessible databases is even more pressing, as researchers are less likely to be fluent in the peculiar languages of genomics and in high-throughput bioinformatics. Here we propose the founding of a community database for lepidopteran genomics, LepBase, to meet the needs of the growing community of researchers using genomics to understand Lepidoptera as crop pests, as potentially invasive species, as developmental models, and as key taxa for understanding the interplay between ecology, genomics, evolution and speciation. While initially focussed on the available lepidopteran genomes the project will meet the challenge of future genomic riches (over 20 genomes 'in the pipeline') by building a platform that focuses on the needs of the lepidopteran research community.The challenge of integrating newly developed genomic resources across taxa is not a new one, and several computational frameworks exist to support such endeavors (such as the ENSEMBL project, and the GMOD ecosystem of tools). Central, aggregative database efforts, such as ENSEMBL Genomes, provide an effective and powerful, one-size-fits-all solution to genome warehousing. Coordinating with smaller research communities to directly implement clade-specific resources is overwhelming the resources of institutions that have a mandate to generate integrated genomic databases. ENSEMBL now advocates a multi-tiered approach to the aggregation, integration, and dissemination of the rapidly increasing wealth of genomic information arising from community-driven genome projects so that species-level genomic resources can flow 'upstream' into the pan-genome database.The goals of our project are: to develop a community-wide, comparative database for the Lepidoptera using the ENSEMBL platform; to institute effective tools for ongoing community annotation of emerging genomes; to forge close links with ENSEMBL Genomes to ensure upload of lepidopteran genomes into the global resource; to implement new modes of data visualisation and analysis in the ENSEMBL framework to meet community needs; and to provide training in genomics to the community of lepidopteran researchers. The LepBase database will also be a working model of community-driven databases that drive not only clade-specific research programmes but also enable the flow of knowledge from species-specific genome projects into a comprehensive framework.The project will be based in the Blaxter bioinformatics and genomics group in Edinburgh, in association with the GenePool Genomics Facility (currently engaged in sequencing butterfly and moth species), with project partners in the Jiggins Heliconius research group in Cambridge and Dasmahapatra in York, and the support of lepidopteran researchers worldwide. Initial focus will be on the genus Heliconius, for which a complete genome sequence and abundant annotation, transcriptome and resequencing data already exist. The database will be rapidly extended into silkmoth, Bicyclus, Danaus and other species. The resource will be overseen by a Scientific Advisory Board drawn from across the range of lepidopteran researchers, and will aim for financial sustainability beyond the tenure of the award through development of a 'subscription' model of funding from research partners.

基因组测序和大规模的群体基因组分析突然变得负担得起。数据的爆炸为基于独立组织的社区驱动的基因组项目的数据整合的突破性研究提供了巨大的机会，但这反过来又需要共享数据库资源。对于模式生物，基因组数据库的工作随着研究社区的发展而发展，并且在许多大规模数据集上有成熟的门户进行深入研究-数据库本身已成为高影响力（Meta）研究的基础。对于基因组学（和人口基因组学）方法的新社区，对可访问数据库的需求更为迫切，因为研究人员不太可能精通基因组学和高通量生物信息学的特殊语言。在这里，我们提出了一个鳞翅目基因组学，LepBase社区数据库的建立，以满足日益增长的社区的研究人员使用基因组学的需求，了解鳞翅目作物害虫，作为潜在的入侵物种，作为发展模式，并作为关键类群了解生态，基因组学，进化和物种形成之间的相互作用。虽然最初的重点是现有的鳞翅目基因组的项目将满足未来的基因组财富的挑战通过建立一个专注于鳞翅目研究社区需求的平台，整合新开发的跨分类群基因组资源并不是一个新的挑战，并且存在几个计算框架来支持这种努力（例如ENSEMBL项目和GMOD工具生态系统）。集中的聚合数据库工作，如ENSEMBL Genomes，为基因组仓储提供了一个有效而强大的通用解决方案。与较小的研究团体协调，直接实施分支特定的资源是压倒性的机构，有一个任务，以产生综合基因组数据库的资源。ENSEMBL现在提倡一种多层次的方法来聚合、整合和传播来自社区驱动的基因组计划的快速增长的基因组信息，以便物种水平的基因组资源可以“上游”进入泛基因组数据库。为正在进行的新兴基因组的社区注释制定有效的工具;与ENSEMBL基因组建立密切的联系，以确保将鳞翅目基因组上传到全球资源中;在ENSEMBL框架内实施新的数据可视化和分析模式，以满足社区需求;并为鳞翅目研究人员提供基因组学方面的培训。LepBase数据库还将成为社区驱动的数据库的工作模式，不仅推动特定分支的研究计划，而且使特定物种基因组项目的知识流入一个全面的框架。（目前从事蝴蝶和蛾类物种的测序工作），与剑桥的Jiggins Heliconius研究小组和约克的Dasmahapatra的项目合作伙伴，以及全世界鳞翅目研究人员的支持。最初的重点将是属Heliconius，其中一个完整的基因组序列和丰富的注释，转录组和重测序数据已经存在。该数据库将迅速扩展到蚕蛾，Bicyclus，Danaus和其他物种。该资源将由一个科学咨询委员会监督，该委员会来自鳞翅目研究人员的各个领域，并将通过开发研究合作伙伴的“订阅”资助模式，致力于在该奖项的任期之外实现财务可持续性。

项目成果

A supergene determines highly divergent male reproductive morphs in the ruff.

• DOI: 10.1038/ng.3443
• 发表时间: 2016-01
• 期刊: NATURE GENETICS
• 影响因子: 30.8
• 作者: Kuepper, Clemens;Stocks, Michael;Risse, Judith E.;dos Remedios, Natalie;Farrell, Lindsay L.;Mcrae, Susan B.;Morgan, Tawna C.;Karlionova, Natalia;Pinchuk, Pavel;Verkuil, Yvonne I.;Kitaysky, Alexander S.;Wingfield, John C.;Piersma, Theunis;Zeng, Kai;Slate, Jon;Blaxter, Mark;Lank, David B.;Burke, Terry
• 通讯作者: Burke, Terry

The genome of the emerging barley pathogen Ramularia collo-cygni.

• DOI: 10.1186/s12864-016-2928-3
• 发表时间: 2016-08-09
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: McGrann GR;Andongabo A;Sjökvist E;Trivedi U;Dussart F;Kaczmarek M;Mackenzie A;Fountaine JM;Taylor JM;Paterson LJ;Gorniak K;Burnett F;Kanyuka K;Hammond-Kosack KE;Rudd JJ;Blaxter M;Havis ND
• 通讯作者: Havis ND

Badger--an accessible genome exploration environment.

• DOI: 10.1093/bioinformatics/btt466
• 发表时间: 2013-11-01
• 期刊: Bioinformatics (Oxford, England)
• 作者: Elsworth B;Jones M;Blaxter M
• 通讯作者: Blaxter M

A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana.

• DOI: 10.1093/gigascience/gix035
• 发表时间: 2017-07-01
• 期刊: GigaScience
• 影响因子: 9.2
• 作者: Nowell RW;Elsworth B;Oostra V;Zwaan BJ;Wheat CW;Saastamoinen M;Saccheri IJ;Van't Hof AE;Wasik BR;Connahs H;Aslam ML;Kumar S;Challis RJ;Monteiro A;Brakefield PM;Blaxter M
• 通讯作者: Blaxter M

An exploration of the parallel evolution of iridescent structural colour in Heliconius butterflies

蝴蝶虹彩结构色平行进化的探索

• 发表时间: 2018
• 作者: Curran Emma V.