Phylogenetically informed curation of eukaryotic 18S rDNA

真核生物 18S rDNA 的系统发育学调控

• 批准号: 1545931
• 负责人: Matthew Brown
• 金额: $ 1.67万
• 依托单位: Mississippi State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-01 至 2017-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1545931&HistoricalAwards=false
• 关键词: Phylogenetically; informed; curation; eukaryotic; 18S

The diversity of eukaryotic organisms extends far beyond the familiar plants, animals, and fungi; the vast majority of eukaryotes are microbial. Eukaryotic microbes are important in ecological processes, and directly influence the biology and health of animals and plants as parasites, commensals, and symbionts. However, the extent of their diversity is still largely unknown because most eukaryotes have not yet been or cannot be cultured. The investigators will coordinate an initiative that brings together taxonomists with microbial ecologists and database experts to curate reference databases for diverse microbial lineages by incorporating knowledge of phylogenetic, morphological, and/or environmental contextual data. The curated reference database created during this workshop will serve as a community resource and enable a broad array of researchers to engage in studies of eukaryotic microbial ecology. All of the workshop products - curation pipeline and curated reference datasets - will be made publicly available upon project completion and will be shared with existing databases to improve these resources. The investigators aim to recruit a diverse pool of applicants by advertising broadly within the scientific community, through the initiative website, relevant societies, and specifically encourage applications from underrepresented groups.As most eukaryotic lineages are microbial, high-throughput environmental sequencing has greatly expanded our knowledge of eukaryotic diversity by revealing new lineages and their environmental distribution. However, the value of these data for cataloging the extent and distribution of eukaryotic biodiversity is critically dependent on the quality of reference databases used to annotate these environmental sequences. Existing databases struggle to keep pace with rapidly changing views on eukaryotic taxonomy, the influx of new data, and computational challenges related to assembling high quality alignments and trees that are necessary for accurate characterization of lineage diversity. The EukRef initiative will address these challenges by bringing together taxonomists with expertise in individual lineages that span the eukaryotic tree of life along with microbial ecologists that actively use environmental sequencing data. The investigators will integrate the individual efforts of working group members into a database spanning the eukaryotic tree of life consisting of curated sequences, flexible taxonomy, and phylogenetic trees, including their underlying sequence alignments. This reference database and associated taxonomic and contextual data will be shared with existing databases GenBank, PR2, and SILVA to improve eukaryotic annotations in general. The EukRef database will increase the power of sequencing studies to uncover fundamental patterns in microbial ecology and diversity.

真核生物的多样性远远超出了我们熟悉的植物、动物和真菌;绝大多数真核生物是微生物。真核微生物在生态过程中具有重要作用，它们作为寄生虫、寄生虫和共生体直接影响动植物的生物学和健康。然而，它们的多样性程度在很大程度上仍然是未知的，因为大多数真核生物还没有或不能培养。研究人员将协调一项倡议，将分类学家与微生物生态学家和数据库专家聚集在一起，通过整合系统发育，形态和/或环境背景数据的知识，为不同的微生物谱系策划参考数据库。本次研讨会期间创建的策展参考数据库将作为社区资源，使广泛的研究人员能够从事真核微生物生态学的研究。 所有研讨会产品----策展管道和策展参考数据集----将在项目完成后公开提供，并将与现有数据库共享，以改善这些资源。研究人员的目标是通过在科学界广泛宣传，通过该倡议的网站，相关的社会，并特别鼓励来自代表性不足的群体的申请，招募一个多元化的申请人池。由于大多数真核生物谱系是微生物，高通量环境测序通过揭示新的谱系及其环境分布大大扩展了我们对真核生物多样性的认识。然而，这些数据的价值编目的程度和分布的真核生物多样性是严重依赖于质量的参考数据库用于注释这些环境序列。现有的数据库努力跟上快速变化的真核生物分类学的观点，新数据的涌入，以及与组装高质量的比对和树相关的计算挑战，这些比对和树是准确表征谱系多样性所必需的。EukRef计划将通过汇集具有跨越真核生物生命树的各个谱系专业知识的分类学家沿着积极使用环境测序数据的微生物生态学家来应对这些挑战。研究人员将把工作组成员的个人努力整合到一个数据库中，该数据库涵盖了真核生物的生命树，包括策划序列、灵活的分类学和系统发育树，包括它们的基本序列比对。该参考数据库和相关的分类学和上下文数据将与现有数据库GenBank、PR 2和SILVA共享，以总体上改进真核生物注释。EukRef数据库将增加测序研究的力量，以揭示微生物生态学和多样性的基本模式。