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.

摘要计算2 改善了棘皮动物基因组特征的注释 Echinobase是最完整，最精确的基因组组件的集中资源， eChinodermata中物种存在的注释和转录组数据。有效性 棘皮动物研究界直接受到棘皮动物携带的数据质量的影响。一个 最近的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。 鉴于相对较高的水平相对较高 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和 基因组测序和组装算法允许对连续性和 棘皮动物基因组在我们的护理中的准确性，该组件解决了如何实现。 升级的基因组组件，以及棘皮动物转录组数据集的洪水 重新注册基因模型，并在整个中识别直系同源关系，既可以 棘皮动物以及门外的物种。这是棘皮动物酶的显着增强， 因为所确定的直系同源物将有助于将echinoderm研究与更广泛的社区相关 发展生物学家。 echinobase还将作为轻松合成从高通量获得的信息的场所 棘皮动物开发的测定，包括转录组和功能基因组学数据集， 整个基因组中非编码调节元件的注释。这些努力我会导致 在大型多态基因组组装中的最佳方法的建议生成，这 仍然是一个困难的问题； ii）促进涉及棘皮动物基因组的生物信息学分析； iii）启用 在多个基因组浏览器中的转录组（尤其是单细胞）数据集的可视化 物种。 这些努力将增强棘皮动物社区进行基因组询问的能力，以及 增加这项研究的总体影响。 GRN研究尤其如此，必须利用 所有这些类型的证据支持节点和联系。通过启用GRN研究，该组成部分因此 支持该门的发育生物学最有影响力的研究。注释和显示的努力 这些数据跨多种类型的数据集和多种物种不太可能由个人进行 调查人员，因此，作为整体echinobase的一部分，此处提出的重点努力可以提供 这种有影响力的资源。