Improved Annotation of Echinoderm Genomic Features

汇总计算2 棘皮动物基因组特征注释的改进 棘球蛋白数据库是最完整和最准确的基因组组合的集中资源， 存在于棘皮动物门物种的注释和转录数据。的有效性。 棘皮动物研究社区直接受到棘皮库数据质量的影响。一个 最近的调查确定了基因组组装和基因注释的改进，包括捕获基因 作为Echinobase用户社区的首要任务。 鉴于棘皮动物基因组水平相对较高，组装棘皮动物基因组在历史上一直具有挑战性 多态和重复序列在这些基因组中普遍存在。技术和技术的最新进展 用于基因组测序和组装的算法允许显著改善邻接性和 在我们的护理下，棘皮动物基因组的准确性，这个组成部分解决了如何实现这一点。 升级的基因组组合，以及棘皮动物转录组数据集的洪流，保证了 重新注释基因模型，并改进对同源关系的识别，这两者之间 棘皮动物以及该门以外的物种。这是对棘球虫的一个重大增强， 因为确定的直系同源将有助于将棘皮动物的研究与更广泛的社区联系起来 发育生物学家。 Echinobase还将作为一个场所，轻松地合成从高通量获得的信息 棘皮动物发育的分析，包括转录组和功能基因组数据集，以及 基因组中非编码调控元件的注释。这些努力将i)导致 在组装大的多态基因组时产生最佳方法的建议，这 仍然是一个难题；二)促进涉及棘皮动物基因组的生物信息学分析；三)使 基因组浏览器中转录(特别是单细胞)数据集的可视化 物种。 这些努力将增强棘皮动物界进行基因组研究的能力，以及 增加这项研究的整体影响。GRN研究尤其如此，它必须借鉴 所有这些类型的证据都支持节点和联系。因此，通过启用GRN研究，这一组成部分， 支持这一门在发育生物学方面最有影响力的研究。注解和展示的努力 这种跨越多种类型数据集和多种物种的数据不太可能由个人承担 调查人员，因此，只有这里提议的有重点的努力，作为整个棘球数据库的一部分，才能提供 这种有影响力的资源。

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.