Building a genome analytic resource for the lepidopteran community

基因组测序和大规模群体基因组分析突然变得负担得起。数据的爆炸式增长为基于独立组织、社区驱动的基因组计划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界的发展而发展，并且有许多成熟的门户网站可以在许多大规模数据集上进行深入研究-数据库本身已经成为高影响力（元）研究的基础。对于基因组学（和群体基因组学）方法的新社区来说，对可访问数据库的需求更加迫切，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。在此，我们建议建立一个鳞翅目基因组学社区数据库LepBase，以满足越来越多的研究人员利用基因组学来了解鳞翅目作为作物害虫、潜在入侵物种、发育模式以及理解生态学、基因组学、进化和物种形成之间相互作用的关键分类群的需求。虽然最初的重点是可用的鳞翅目基因组，但该项目将通过建立一个专注于鳞翅目研究界需求的平台，迎接未来基因组财富的挑战（超过20个基因组“在管道中”）。跨分类群整合新开发的基因组资源并不是一个新挑战，并且存在一些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、综合的数据库工作，如ENSEMBL基因组，为基因组仓库提供了一个有效的、强大的、一刀切的解决方案。与较小的研究团体协调，直接实施特定进化支的资源，这压倒了那些有责任生成综合基因组数据库的机构的资源。现在，ENSEMBL提倡采用多层次的方法来聚集、整合和传播由社区驱动的基因组计划产生的快速增长的基因组信息财富，以便物种水平的基因组资源可以“上游”流入泛基因组数据库。我们项目的目标是：使用ENSEMBL平台开发一个社区范围的鳞翅目比较数据库；为正在进行的新兴基因组的社区注释建立有效的工具；与ENSEMBL genomics建立紧密联系，确保鳞翅目基因组上传到全球资源；在ENSEMBL架构内推行新的数据显示和分析模式，以切合社会需要；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数据库的一个工作模式，它不仅推动特定进化支的研究项目，而且使来自特定物种基因组项目的知识流动成为一个综合框架。该项目将以爱丁堡的Blaxter生物信息学和基因组学小组为基础，与GenePool基因组学设施（目前从事蝴蝶和飞蛾物种测序）合作，与剑桥的Jiggins Heliconius研究小组和约克的Dasmahapatra研究小组的项目合作伙伴合作，并得到全球鳞翅目研究人员的支持。最初的重点将放在Heliconius属上，因为已经有了完整的基因组序列和丰富的注释、转录组和重测序数据。该数据库将迅速扩展到蚕蛾、双环蛾、丹参等物种。该资源将由一个从鳞翅目研究人员中抽取的科学顾问委员会监督，并将通过开发一种来自研究伙伴的“订阅”资助模式，力求在该奖项的任期之后实现财务可持续性。

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.