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; 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.

计算成分2：改进的棘皮动物基因组特征的注释 概括 Echinobase是最完整，最准确的基因组组件的集中资源， echinodermata门中物种的注释。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的质量的影响 echinobase。最近的一项调查确定了基因组组件和基因注释的改进，包括 捕获基因直系同源物，作为Echinobase用户社区的首要任务。组装echinoderm 鉴于多态性和重复性相对较高，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 组装可以显着改善我们在我们的棘皮动物基因组中的连续性和准确性 护理和此组件解决了如何实现。升级的基因组组件以及 Echinoderm转录组数据集的泛滥值保证重新注册基因模型，并启用改进 在棘皮动物中以及门外物种之间的直系关系鉴定。 这是棘皮动物酶的重大增强 对更广泛的发育生物学家社区的棘皮动物研究。 echinobase也将作为 从棘皮动物开发的高通量测定中获得的综合信息的场地， 包括转录组和功能基因组学数据集，以及非编码调节的注释 整个基因组的元素。这些努力还将导致最佳的建议产生 大型多态基因组组装中的方法，这仍然是一个困难的问题，并且 涉及棘皮动物基因组的生物信息学分析。这反过来将增强 Echinoderm社区进行基因组询问，并增加这项研究的总体影响。这 当将echinobase中包含的数据类型视为合奏而不是在 隔离;使用正交的多个研究组生成的数据集集成信号 方法和整个物种都放大了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，必须利用所有这些类型的证据来支持节点和 链接。通过启用GRN研究，该组成部分支持了最有影响力的研究 该门的发育生物学。努力注释和显示多种类型的数据 数据集和多种物种不太可能由个别研究人员进行，因此只有一个 作为整体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。