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The SMBE Satellite Meeting on Eukaryotic -Omics will bring together an interdisciplinary pool of researchers to discuss current efforts, challenges, and future directions for high-throughput sequencing approaches focused on microbial eukaryotes (environmental studies of non-model organisms). The meeting program will encompass investigations of eukaryote biodiversity, ecology, and evolution, using approaches such as rRNA marker genes, shotgun metagenomics, metatranscriptomics, and computational biology tools and software pipelines.
Microbial eukaryotes (typically, organisms <1mm, such as nematodes, protists, and fungi) are abundant and ubiquitous across every ecosystem on earth. Yet, there exists a well-recognized gap in the understanding of their global biodiversity. This unexplored diversity represents one of the major challenges in biology and limits our capacity to understand, mitigate and remediate the consequences of environmental change. Driven by fundamental advances in DNA sequencing, new high-throughput sequencing (HTS) platforms make it possible to explore biodiversity at a scale that allows for the discovery of virtually all of the of the organisms in an environmental sample. It is now possible to conduct en mass eukaryotic biodiversity assessment using traditional molecular loci (e.g. ribosomal rRNA) at a fraction of the time and cost required for traditional approaches. However, eukaryote-focused approaches are still in their infancy, especially compared to studies of bacteria/archaea where molecular methods have dominated research approaches for decades.
There are a number of reasons for promoting coordination of a distinct eukaryotic community: 1) The markers for eukaryotes are unique. To maximize the utility of phylogentically informative ribosomal gene regions (e.g. 18S), and to rapidly develop new additional markers (e.g. conserved protein-coding genes), the gene regions used by the community must be homologous. Realizing a truly global perspective for eukaryotic biodiversity will require dedication and coordination amongst research groups, 2) The biology/evolution of rRNA genes (intragenomic variants) and the applicability of additional loci (e.g. mitochondrial) are unique concerns within the eukaryotic community; both these aspects have a substantial impact on the computational analyses needed for HTS datasets, 3) The ability to physically isolate microbial eukaryotes allows for linking genetic data to morphologies and taxonomy; this empirical link is critical for ecological inferences (e.g. community feeding strategies). 4) Interpreting and combining eukaryotic sequence data is inherently difficult, due to sparse eukaryotic reference databases (comparative lack of rRNA and whole genome sequences), eukaryote-specific genome organization (larger size, presence of introns) and complex eukaryotic cellular/metabolic processes (unexplored metabolic pathways, significant numbers of proteins with unknown function), 5) We continue to lack the cyberinfrastructure and community coordination needed for effective interpretation of large HTS datasets, a problem made even more urgent by the rapidly increasing magnitude of HTS datasets.
Overcoming the most substantial challenges in eukaryotic -omics will require large-scale community mobilization: ultimately, the eukaryotic community must aim to coordinate the application and analysis of common genetic loci, facilitate data sharing and promote comparative analyses using existing resources in conjunction with new open-access database structures. The proposed workshop will strive towards this goal by cultivating a long-term, connected community of eukaryote-focused researchers, whilst promoting sustained interdisciplinary interactions.
***The meeting organizers would like to attribute Flickr users Antonio Guillén, the Goldstein Lab, and Derek Keats for Creative Commons-licensed images used to construct the meeting logo (please follow links to reach original images).***