Administrative Supplement: Genome Resources for Model Amphibians

University Of Kentucky, Lexington KY

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Abstract

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.