Administrative Supplement: Genome Resources for Model Amphibians

项目总结 在母公司R24的奖励下，我们正在开发基础基因组和生物信息学 将更好地促进对紫杉醇(Ambystoma Micianum)的研究的资源。具体来说，我们 正在寻求各种方法来改进目前的墨西哥拟青霉基因组组装并产生 新的数据集，描述了Axolotl组织再生过程中的表观遗传学变化。至 改善当前的基因组组装，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，很大程度上反映了入侵和分离 将虎纹伊蚊DNA导入原代囊虫遗传储备中心 人口。为了应对这一挑战，我们正在进行紫杉醇的长读DNA测序- 虎鳗杂交种和大约10个AGSC Axolotls的基因组测序。 虽然长读DNA测序方法将解决组装间隙/错误，但整个 只需对10株墨西哥黑曲霉进行基因组测序，就能鉴定出一些中等到高度的 个体内和个体间分离的单核苷酸多态频率 AGSC，留下了许多SNPs未识别和中低频率SNPs未得到验证。这个 如果我们有一个专门的， MiSeq DNA测序仪，用于验证更多数量的SNP。通过靶向测序 数百个AGSC A.micianum，我们将产生数据来验证DNA变体，这些DNA变体可能 这可能会危及A。 墨西哥群落。MiSeq数据可能会被证明对墨西哥拟青霉的管理有用。 AGSC中的库存，并可能导致发现有助于 表型变异，包括墨西哥蘑菇品系内和品系间的变异性。此外，一个 专用DNA测序仪将加快芯片和序列抗体验证的进展 允许我们快速开发一种新的、尖端的方法--切割和运行--来表征 组织再生过程中的表观遗传学变化。购买一台高性能的DNA 测序机通过这一行政补充请求将加快、增强和进一步 创新资源开发以实现父R24奖项的目标。

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.