Administrative Supplement: Genome Resources for Model Amphibians

PROJECT SUMMARY Under the parent 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 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 axolotls will only validate high frequency single nucleotide polymorphisms, leaving many moderate to low frequency SNPs unvalidated. The impact of our parent award project would be significantly enhanced if we had a dedicated, DNA sequencer to validate a greater number of SNPs and insertion/deletion candidates. 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-and-Run - to characterize epigenetic changes during tissue regeneration. The purchase of a high-performance DNA sequencing machine via this administrative supplement request will speed progress and diversify efforts to accomplish genome resource development objectives of the parent R24 award.