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.

计算组件 2：改进棘皮动物基因组特征的注释 概括 Echinobase 是最完整、最准确的基因组组装和分析的集中资源 棘皮动物门物种的注释。棘皮动物研究的有效性 社区直接受到基因组组装和注释数据质量的影响 刺碱。最近的一项调查发现了基因组组装和基因注释的改进，包括 捕获基因直系同源物是 Echinobase 用户社区的首要任务。组装棘皮动物 鉴于相对较高水平的多态性和重复性，基因组在历史上一直具有挑战性 这些基因组中常见的序列。基因组测序技术和算法的最新进展 和组装可以显着提高我们的棘皮动物基因组的连续性和准确性 护理和该组件解决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基因模型的重新注释并能够改进 鉴定棘皮动物之间以及门外物种的直系同源关系。 这是 Echinobase 的显着增强，因为确定的直向同源物将有助于上下文化 将棘皮动物研究推广到更广泛的发育生物学家群体。 Echinobase 还将作为 轻松合成从棘皮动物发育的高通量测定中获得的信息的场所， 包括转录组和功能基因组学数据集，以及非编码监管的注释 整个基因组的元素。这些努力还将产生最佳建议 组装大型多态性基因组的方法，这仍然是一个难题，并且对于 涉及棘皮动物基因组的生物信息分析。这将反过来增强 棘皮动物界进行基因组调查，并增加这项研究的整体影响。这 Echinobase 中存储的数据类型在被视为整体而不是被视为整体时最具影响力 隔离;使用正交整合来自多个研究小组生成的数据集的信号 方法，并且跨物种放大了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，该组件支持以下领域最具影响力的研究： 该门的发育生物学。跨多种类型注释和显示此数据的努力 数据集和多个物种不太可能由个体研究人员进行，因此只能 这里提出的集中工作，作为整个 Echinobase 的一部分，可以提供这种有影响力的资源。