Building a genome analytic resource for the lepidopteran community

基因组测序和大规模的人口基因组分析突然变得负担得起了。数据的爆炸为基于来自独立组织的、社区驱动的基因组项目的数据集成的开创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增长，并且有成熟的门户网站，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的(元)研究的基础。对于新接触基因组(和种群基因组)方法的社区来说，对可访问数据库的需求更加迫切，因为研究人员不太可能熟练掌握基因组学和高通量生物信息学的特殊语言。在这里，我们建议建立鳞翅目昆虫基因组学群落数据库LepBase，以满足越来越多的研究人员使用基因组学来理解鳞翅目昆虫是作物害虫、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类群的需要。虽然最初的重点是现有的鳞翅目基因组，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来应对未来基因组丰富的挑战(超过20个基因组正在进行中)。整合新开发的跨类群基因组资源的挑战并不是一个新的挑战，已经存在几个计算框架来支持这种努力(如EnSembl项目和GMOD工具生态系统)。集中的、聚合的数据库工作，如EnSembl基因组，为基因组仓储提供了一个有效和强大的、一刀切的解决方案。与较小的研究社区协调，直接实施特定于支系的资源，正在压倒有权生成综合基因组数据库的机构的资源。EnSembl现在提倡一种多层次的方法来聚合、整合和传播由社区驱动的基因组项目产生的迅速增加的基因组信息，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：利用EnSembl平台开发一个社区范围的鳞翅目比较数据库；为正在出现的基因组建立有效的社区注释工具；与EnSembl基因组建立密切联系，以确保将鳞翅目基因组上传到全球资源中；在EnSembl框架中实施新的数据可视化和分析模式，以满足社区需求；并为鳞翅目昆虫研究人员提供基因组学培训。LepBase数据库也将是社区驱动的数据库的工作模型，这些数据库不仅驱动特定支系的研究计划，而且使特定物种基因组项目的知识能够流动到一个全面的框架中。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，与基因池基因组学设施(目前从事蝴蝶和蛾类物种测序)相关联，与剑桥的Jiggins Heliconius研究小组和纽约的Dasmahapatra项目合作伙伴，以及世界各地的鳞翅目研究人员的支持。最初的关注点将放在螺旋藻属上，该属的完整基因组序列以及丰富的注释、转录组和重新测序数据已经存在。该数据库将迅速扩展到蚕蛾、双叶猴、丹瑙斯等物种。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，并将通过发展研究合作伙伴的“订阅”资助模式，致力于在奖项有效期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.