Administrative Supplement: Genome Resources for Model Amphibians

行政补充：模型两栖动物基因组资源

• 批准号: 10806365
• 负责人: Jeramiah James Smith
• 金额: $ 12.49万
• 依托单位: UNIVERSITY OF KENTUCKY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-01 至 2024-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10806365
• 关键词: Address; Administrative Supplement; Ambystoma; Ambystoma mexicanum; Amphibia; Antibodies; Award; Biological; ChIP-seq; Communities; Complex; DNA; DNA Resequencing; DNA sequencing; Data; Data Set; Dedications; Disease; Embryonic Development; Epigenetic Process; Frequencies; Genetic; Genome; Health; Human; Hybrids; Individual; Modeling; Molecular Probes; Organ Model; Parents; Performance; Phenotype; Population; Postembryonic; R24; Research; Research Personnel; Resource Development; Resources; Running; Salamander; Single Nucleotide Polymorphism; Speed; Tigers; Translating; Variant; bioinformatics resource; design; genome resource; genome sequencing; improved; innovation; member; novel strategies; organ regeneration; segregation; targeted sequencing; tissue regeneration; tissue repair; whole genome

PROJECT SUMMARY Under the parent R24 award, we are developing fundamental genomic and bioinformatic resources that will better enable studies of the axolotl (Ambystoma mexicanum). Specifically, we are pursuing approaches to improve the current A. mexicanum genome assembly and generate new data sets that characterize epigenetic changes during axolotl tissue regeneration. To improve the current genome assembly, we need to resolve gaps/errors that are caused by complex repetitive and polymorphic regions that largely reflect the introgression and segregation of A. tigrinum (Tiger salamander) DNA into the primary Ambystoma Genetic Stock Center population. To address this challenge, we are performing long read DNA sequencing of axolotl- tiger salamander hybrids and sequencing the genomes of approximately 10 AGSC axolotls. While the long read DNA sequencing approach will resolve assembly gaps/errors, whole genome sequencing of only 10 A. mexicanum will identify some of the moderate to high frequency single nucleotide polymorphisms segregating within and among individuals in the AGSC, leaving many SNPs unidentified and moderate to low frequency SNPs unvalidated. The impact of our parent award project would be significantly enhanced if we had a dedicated, MiSeq DNA sequencer to validate a greater number of SNPs. Through targeted sequencing of several hundred AGSC A. mexicanum, we will generate data to validate DNA variants that could potentially compromise the design and function of molecular probes by members of the A. mexicanum community. MiSeq data will likely prove useful in the management of A. mexicanum stocks in the AGSC and may lead to the discovery of genetic factors that contribute to phenotypic variation, including variability within and among A. mexicanum lines. Additionally, a dedicated DNA sequencer would speed progress in validating antibodies for ChIP-Seq and allow us to rapidly develop a new, cutting-edge approach – Cut&Run - to characterize epigenetic changes during tissue regeneration. The purchase of a high-performance DNA sequencing machine via this administrative supplement request will speed, enhance and further innovate resource development to accomplish objectives of the parent R24 award.

项目摘要 根据父母R24奖，我们正在开发基本基因组和生物信息学 可以更好地研究Axolotl（墨西哥ambystoma）的资源。具体来说，我们 正在采取方法来改善当前的墨西哥基因组组件并产生 新的数据集，表征了在Axolotl组织再生过程中表观遗传变化的特征。到 改善当前的基因组组件，我们需要解决由 复杂的重复和多态区域，在很大程度上反映了渗入和隔离 tigrinum（老虎sal）DNA的植物 人口。为了应对这一挑战，我们正在执行axolotl-的长读DNA测序 老虎sal杂种和测序约10个AGSC轴突的基因组。 虽然长读取DNA测序方法将解决组装差距/错误，但整个 基因组测序仅10 A.墨西哥素可以识别一些中等至高 频率单核苷酸多态性在隔离内外 AGSC，使许多SNP未识别，并且中等至低频SNP未验证。这 如果我们有专门的，我们的父母奖项项目的影响将大大增强 Miseq DNA测序仪以验证更多的SNP。通过针对的测序 数百个AGSC A.墨西哥，我们将生成数据以验证DNA变体 可能损害A分子问题的设计和功能。 墨西哥社区。 Miseq数据可能会被证明可用于管理墨西哥曲霉 AGSC中的股票，可能导致发现有助于 表型变化，包括墨西哥曲霉内部和中间的变异性。另外， 专用的DNA测序仪将加快验证ChIP-Seq抗体和 允许我们快速开发一种新的，尖端的方法 - 切割和运行 - 以表征 组织再生过程中的表观遗传变化。购买高性能DNA 通过此管理补充请求进行测序机将加快，增强并进一步 创新资源开发以完成父级R24奖的对象。