Phylogenetically informed curation of eukaryotic 18S rDNA

Mississippi State University, Mississippi State MS

Investigators

Abstract

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.