Improved Annotation of Echinoderm Genomic Features

简要说明. 2 棘皮动物基因组特征注释的改进 Echinobase作为最完整和准确的基因组组装的集中资源， 注释和转录组数据，存在于棘皮动物门的物种。的有效性 棘皮动物研究社区直接受到Echinobase上托管的数据质量的影响。一 最近的调查发现，基因组组装和基因注释的改进，包括捕获基因， 直向同源物，作为Echinobase用户社区的首要任务。 组装棘皮动物基因组在历史上一直具有挑战性，因为相对高水平的 多态性和这些基因组中常见的重复序列。技术的最新进展和 用于基因组测序和组装的算法允许显著改善邻近性， 在我们的护理棘皮动物基因组的准确性，这个组件解决了如何实现这一目标。 升级的基因组组装，沿着大量的棘皮动物转录组数据集，保证了 基因模型的重新注释，并使改进的直系亲属关系的鉴定， 棘皮动物以及门外的物种。这是Echinobase的显著增强， 因为鉴定的直系同源物将有助于将棘皮动物研究置于更广泛的社会背景中， 发育生物学家 Echinobase还将作为一个场所，可以轻松地合成从高通量 棘皮动物发育的分析，包括转录组和功能基因组学数据集，沿着 整个基因组的非编码调控元件的注释。这些努力将导致： 为大型多态性基因组组装的最佳方法提出建议， 仍然是一个难题; ii）促进涉及棘皮动物基因组的生物信息学分析;以及iii）使 在多个基因组浏览器中可视化转录组（特别是单细胞）数据集， 物种 这些努力将提高棘皮动物群体进行基因组调查的能力， 提高这项研究的整体影响力。GRN研究尤其如此，它必须借鉴 所有这些类型的证据来支持节点和联系。通过启用GRN研究，该组件因此， 支持了这一门最具影响力的发育生物学研究。注释和显示的努力 这种跨多种类型数据集和多个物种的数据不太可能由个人承担， 因此，只有像这里提出的那样，作为整个Echinobase的一部分， 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.