Improved Annotation of Echinoderm Genomic Features

棘皮动物基因组特征的改进注释

• 批准号: 10715583
• 负责人: Veronica Frances Hinman
• 金额: $ 19.21万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-22 至 2028-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10715583
• 关键词: ATAC-seq; Address; Algorithms; Bioinformatics; Caring; Cells; ChIP-seq; Clustered Regularly Interspaced Short Palindromic Repeats; Communities; Data; Data Display; Data Set; Development; Developmental Biology; EchinoBase; Echinodermata; Effectiveness; Elements; Future; Gene Expression; Generations; Genes; Genetic Polymorphism; Genome; Genomics; Guide RNA; Individual; Maps; Modeling; Oligonucleotides; Ontology; Orthologous Gene; Paper; Phenotype; Process; Proteome; Reagent; Recommendation; Regulatory Element; Repetitive Sequence; Research; Research Personnel; Resources; Source; Surveys; Technology; Untranslated RNA; Visualization; data visualization; design; experimental study; functional genomics; genome annotation; genome browser; genome sequencing; genomic data; high throughput screening; improved; indexing; multiple data types; single cell technology; transcriptome; transcriptome sequencing; transcriptomics

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.

总结计算2 棘皮动物基因组特征的改进注释 Echinobase 是最完整、最准确的基因组组装的集中资源， 棘皮动物门物种的注释和转录组数据。的有效性 棘皮动物研究社区直接受到 Echinobase 上托管数据质量的影响。一个 最近的调查发现了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。 鉴于棘皮动物水平相对较高，组装棘皮动物基因组历来都是一项挑战。 这些基因组中常见的多态性和重复序列。技术和技术的最新进展 基因组测序和组装算法可以显着改善连续性和 我们关心的是棘皮动物基因组的准确性，本部分讨论了如何实现这一目标。 升级的基因组组装以及大量的棘皮动物转录组数据集保证了 重新注释基因模型并能够改进直系同源关系的识别，两者之间 棘皮动物以及该门以外的物种。这是 Echinobase 的显着增强， 因为所确定的直向同源物将有助于将棘皮动物研究纳入更广泛的社区 发育生物学家。 Echinobase 还将作为轻松合成从高通量获得的信息的场所 棘皮动物发育分析，包括转录组和功能基因组学数据集，以及 整个基因组非编码调控元件的注释。这些努力将 i) 导致 生成大型多态性基因组组装最佳方法的建议，其中 仍然是一个难题； ii) 促进涉及棘皮动物基因组的生物信息分析； iii) 启用 跨多个基因组浏览器中转录组（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群体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。通过启用 GRN 研究，该组件因此， 支持该门发育生物学中最具影响力的研究。努力注释和展示 这些跨多种类型的数据集和多个物种的数据不太可能由个人承担 调查人员，因此只有这里提出的集中努力，作为整个 Echinobase 的一部分，才能提供 这个有影响力的资源。