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：棘皮动物基因组特征的改进注释 总结 Echinobase作为最完整和准确的基因组组装的集中资源， 棘皮动物门的物种注释。棘皮动物研究的有效性 上托管的基因组组装和注释数据的质量直接影响社区。 海胆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 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 由于多态性和重复性水平相对较高，基因组历来具有挑战性 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 和组装允许显着改善的连续性和准确性棘皮动物基因组在我们的 护理和本组成部分涉及如何实现这一目标。升级的基因组组装沿着 棘皮动物转录组数据集的泛滥保证了基因模型的重新注释，并使改进的 确定棘皮动物之间以及棘皮动物与门外物种之间的亲缘关系。 这是对Echinobase的显著增强，因为所鉴定的直系同源物将用于情境化 棘皮动物研究的发展生物学家的更广泛的社区。Echinobase还将作为 用于容易地合成从棘皮动物发育的高通量测定获得的信息的场所， 包括转录组和功能基因组学数据集，沿着非编码调控的注释， 在整个基因组中。这些努力也将导致产生的建议， 大多态性基因组的组装方法，这仍然是一个困难的问题， 涉及棘皮动物基因组的生物信息学分析。这反过来又会增强 棘皮动物社区进行基因组查询，以及增加这项研究的整体影响。的 Echinobase中存储的数据类型在被视为整体而不是 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 方法和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 特别是GRN研究的情况，它必须利用所有这些类型的证据来支持节点， 联动因此，通过支持GRN研究，该组件支持最有影响力的研究， 发展生物学的研究注释和显示跨多种类型的 数据集和多个物种，不太可能由个人研究者承担，因此只有一个 作为整个Echinobase的一部分，这里提出的集中努力可以提供这种有影响力的资源。