Improved Annotation of Echinoderm Genomic Features

汇总计算2

SUMMARY COMPUTATION 2 Improved Annotation of Echinoderm Genomic Features Echinobase serves as a centralized resource for the most complete and accurate genome assemblies, annotations, and transcriptomic data that exist for species in the phylum Echinodermata. The effectiveness of the echinoderm research community is directly impacted by the quality of the data hosted on Echinobase. A recent survey identified improvements to genome assemblies and gene annotations, including capturing gene orthologs, as top priorities for the Echinobase user community. Assembling echinoderm genomes has historically been challenging given the relatively high levels of polymorphism and repetitive sequence common in these genomes. Recent advances in technologies and algorithms for genome sequencing and assembly permit significant improvements to the contiguity and accuracy of echinoderm genomes in our care, and this component addresses how this will be achieved. Upgraded genome assemblies, along with the deluge of echinoderm transcriptome datasets, warrant the re-annotation of gene models and enable the improved identification of orthologous relationships, both among echinoderms and also to species outside of the phylum. This is a significant enhancement of Echinobase, because the orthologs identified will serve to contextualize echinoderm research to a broader community of developmental biologists. Echinobase will also serve as a venue for easily synthesizing information obtained from high-throughput assays of echinoderm development, including transcriptome and functional genomics datasets, along with annotations of noncoding regulatory elements throughout the genome. These efforts will i) result in the generation of recommendations for optimal approaches in the assembly of large polymorphic genomes, which remains a difficult problem; ii) facilitate bioinformatic analyses involving echinoderm genomes; and iii) enable the visualization of transcriptomic (particularly single-cell) datasets in genome browsers across multiple species. These efforts will enhance the capabilities of the echinoderm community to make genomic inquiries, and increase the overall impact of this research. This is especially the case for GRN studies, which must draw on all these types of evidence to support nodes and linkages. By enabling GRN studies, this component therefore, supports the most impactful research in developmental biology for this phylum. Efforts to annotate and display this data across multiple types of datasets, and multiple species, are unlikely to be undertaken by individual investigators and thus only a focused effort as proposed here, as part of the overall Echinobase, can provide this impactful resource.