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 在母公司R24奖下，我们正在开发基础基因组和生物信息学 这将有助于更好地研究美西蝾螈（Ambystoma mexicanum）。我们特别 正在寻求方法来改善目前的A。mexicanum基因组组装和产生 新的数据集，表征蝾螈组织再生过程中的表观遗传变化。到 为了改善目前的基因组组装，我们需要解决由以下原因引起的差距/错误： 复杂的重复和多态区域，主要反映了渐渗和分离 曲霉虎纹蛙（虎蝾螈）DNA进入原钝口遗传库存中心 人口为了应对这一挑战，我们正在对美西螈进行长读段DNA测序， 虎蝾螈杂交种，并对大约10个AGSC蝾螈的基因组进行测序。 虽然长读段DNA测序方法将解决组装间隙/错误，但整体上， 基因组测序只有10个A. mexicanum将确定一些中度到高度 频率单核苷酸多态性分离内和之间的个人， AGSC，留下许多未识别的SNP和未验证的中低频SNP。的 如果我们有一个专门， MiSeq DNA测序仪验证更多的SNP。通过靶向测序， 几百个AGSC A。墨西哥，我们将生成数据来验证DNA变异， 潜在地损害了A. 墨西哥社区MiSeq数据可能会证明在A. mexicanum 在AGSC的股票，并可能导致发现的遗传因素，有助于 表型变异，包括A.墨西哥线。此外， 专用的DNA测序仪将加快验证ChIP-Seq抗体的进展， 使我们能够快速开发出一种新的尖端方法- Cut&Run， 组织再生过程中的表观遗传变化。购买高性能DNA 排序机通过这一行政补充要求将加快，加强和进一步 创新资源开发，以实现R24奖的目标。