Improved Annotation of Echinoderm Genomic Features

棘皮动物基因组特征的改进注释

• 批准号: 10241294
• 负责人: Veronica Frances Hinman
• 金额: $ 14.06万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-20 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10241294
• 关键词: ATAC-seq; Address; Affect; Algorithms; Bioinformatics; Caring; ChIP-seq; Clustered Regularly Interspaced Short Palindromic Repeats; Communities; DNA; Data; Data Display; Data Set; Databases; Development; Developmental Biology; EchinoBase; Echinodermata; Effectiveness; Elements; Future; Generations; Genes; Genetic Polymorphism; Genome; Genomics; Goals; Guide RNA; Hybrids; Individual; MicroRNAs; Modeling; Nature; Oligonucleotides; Orthologous Gene; Paper; Pathway Analysis; Proteome; Reagent; Recommendation; Regulator Genes; Regulatory Element; Repetitive Sequence; Research; Research Personnel; Resources; Signal Transduction; Surveys; Technology; Untranslated RNA; contig; design; experimental study; functional genomics; genome resource; genome sequencing; genomic data; high throughput screening; improved; innovation; scaffold; tool; transcriptome; transcriptome sequencing; trend; usability

Computational Component 2: Improved Annotation of Echinoderm Genomic Features SUMMARY Echinobase serves as a centralized resource for the most complete and accurate genome assemblies and annotations for species in the phylum Echinodermata. The effectiveness of the echinoderm research community is directly impacted by the quality of the genome assembly and annotation data hosted on Echinobase. A recent survey identified improvements to genome assemblies and gene annotations, including capturing gene orthologues, 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 also result in the generation of recommendations for optimal approaches in the assembly of large polymorphic genomes, which remains a difficult problem, and for bioinformatic analyses involving echinoderm genomes. This will in turn enhance the capabilities of the echinoderm community to make genomic inquiries, as well as increase the overall impact of this research. The types of data housed in Echinobase are most impactful when considered as an ensemble rather than in isolation; integrating signals from datasets generated by multiple research groups, using orthogonal approaches, and across species magnifies the significance of any trends identified in a single dataset. 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.

计算部分2：棘皮动物基因组特征的改进注释 摘要 棘球蛋白数据库是最完整和准确的基因组组装的集中资源 标题棘皮动物门的种类注释。棘皮动物研究的有效性 社区直接受到托管的基因组组装和注释数据的质量的影响 棘球绦虫。最近的一项调查确定了基因组组装和基因注释的改进，包括 获取基因同源，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，因为它具有相对较高的多态和重复性 在这些基因组中共有的序列。基因组测序技术和算法的最新进展 和组装使得棘皮动物基因组的邻接性和准确性在我们的 CARE和这一构成部分涉及如何实现这一点。升级的基因组组件以及 棘皮动物转录组数据集的泛滥保证了对基因模型的重新注释，并使改进的 棘皮动物之间以及与门外物种的直系关系的鉴定。 这是对Echinobase的重大增强，因为识别的同源词将用于语境化 棘皮动物研究提供给更广泛的发育生物学家社区。Echinobase还将作为一个 用于轻松合成从棘皮动物发育的高通量分析中获得的信息的场所， 包括转录组和功能基因组数据集，以及非编码调控的注释 基因组中的所有元素。这些努力还将产生最佳的 组装大的多态基因组的方法，这仍然是一个困难的问题，并 棘皮动物基因组的生物信息学分析。这将反过来增强 对棘皮动物界进行基因组研究，以及增加本研究的整体影响。这个 Echinobase中存储的数据类型在被视为一个集合而不是 隔离；整合来自多个研究小组生成的数据集的信号，使用正交 方法，跨物种放大了在单个数据集中确定的任何趋势的重要性。这是 尤其是GRN研究，它必须利用所有这些类型的证据来支持节点和 联系。因此，通过启用GRN研究，该组成部分支持在以下方面最有影响力的研究 这个门的发育生物学。跨多种类型注释和显示此数据的工作 数据集和多个物种不太可能由个别研究人员承担，因此只有一个 作为整个棘库的一部分，这里提出的有重点的努力可以提供这种有影响力的资源。