Subterranean Fishes of the World

5617

2022

AIM 2022

24

The crucible of evolution has naturally shaped troglomorphic traits over a relatively short span of time in Astyanax mexicanus fishes. Understanding the structural basis of this adaptive process genome-wide has broad applications for a basic understanding of mechanisms of genetic adaptation. Comparatively diverse species, such as Astyanax mexicanus cavefish, have evolved physiological phenotypes that mimic some aspects of human diseases, but intriguingly, they do not exhibit the same underlying pathophysiological consequences. To evaluate genomic structural variation (SV) that differentiates independently evolved cavefish populations and is perhaps associated with these observed trait modifications, we long-read sequenced and assembled the genomes of Molino, Tinaja and a surface fish. Using HiFi sequencing technology we achieve high base accuracy and contiguity for all assemblies. For Molino, Tinaja and a surface fish we estimate N50 contig lengths of 13.6, 27.1, and 52.7 Mb, respectively. Redundant contigs were purged and sample specific HiC mapping data was used to scaffold each to chromosome levels of contiguity. In Molino, Tinaja and surface fish assemblies we observe N50 scaffold lengths of 34.5, 45.6, and 51.9 for the 25 known chromosomes of A. mexicanus. Overall, we observe good synteny with dot plots derived from pairwise whole-genome alignments. In addition, a preliminary estimation of SVs found in a comparison of the surface and Molino genomes using Assemblytics shows deletions present in Molino totaling 18,252 that occupies 6.7Mb at a size range of 50-10,000 bp. Our new high-quality genome references will continue to significantly advance trait dissection and a natural resilience concept of genetic adaptation in this model.

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