Enabling the Endangered Mexican Axolotl for Biomedical Research

Salamanders are important vertebrate model organisms in several areas of biomedical research, including tissue regeneration, neural transmission, vision, olfaction, and aging. The Salamander Genome Project is developing resources to better enable research efforts using the Mexican axolotl (Ambystoma mexicanum), a critically endangered species with an incredibly large 30 GB genome. Current research efforts include genetic mapping to identify genes for pigment mutants and thyroid hormone-responsive QTL, which are famously associated with heterochronic changes in developmental timing. Also, we recently completed a rigorous 398 GeneChip microarray analysis of limb regeneration to establish Regenerome – a searchable database of gene expression profiles at Sal-Site (www.ambystoma.org). The expression estimates within this database provide a fine scale temporal framework for building integrative models of regeneration and generating new hypotheses for engineering regeneration of human tissues. Finally, our comparative mapping studies show the axolotl genome to be a mosaic of conserved chromosome segments that correspond to ancestral, vertebrate macro- and micro- chromosomes. Thus, even though the axolotl genome is incredibly large, gene orders are highly conserved with reptilian and mammalian genomes. We have initiated sequencing of this 30 GB genome using an approach that couples laser capture micro-dissection and amplification, to provide both chromosome scale scaffolding and local sequence assembly. Reads from single chromosome libraries map with high fidelity to expected linkage groups, thus enriching gene content and resolving chromosome structure relative to other model organisms. Most importantly, these results prove our method for obtaining the whole genome sequence for one of our most unique and valuable vertebrate model organisms.