France, J. | bioRxiv Science

bioRxiv2024

Conserved gene content and unique phylogenetic history characterize the 'bloopergene' underlying Triturus' balanced lethal system

In a balanced lethal system, half the reproductive output succumbs. Triturus newts are the best-known example. Their chromosome 1 comes in two distinct versions and embryos carrying the same version twice experience developmental arrest. Those possessing two different versions survive, suggesting that each version carries something uniquely vital. With target capture we obtain over 7,000 nuclear DNA markers across the genus Triturus and all main lineages of Salamandridae (the family to which Triturus belongs) to investigate the evolutionary history of Triturus chromosome 1 versus other chromosomes. Dozens of genes are completely missing from either one or the other version of chromosome 1 in Triturus. Furthermore, the unique gene content of 1A versus 1B is remarkably similar across Triturus species, suggesting that the balanced lethal system evolved before Triturus radiated. The tree topology of chromosome 1 differs from the rest of the genome, presumably due to pervasive, ancient hybridization between Triturus ancestor and other newt lineages. Our findings accentuate the complex nature of Triturus chromosome 1 - the bloopergene driving the evolutionarily enigmatic balanced lethal system.

evolutionary biology↗

bioRxiv2024

NewtCap: an efficient target capture approach to boost genomic studies in Salamandridae (True Salamanders and Newts)

Salamanders have large and complex genomes, hampering whole genome sequencing. However, reduced representation sequencing provides a feasible alternative to obtain genome-wide data. We present NewtCap: a sequence capture bait set that targets c.7k coding regions across the genomes of all true salamanders and newts (the family Salamandridae, also known as salamandrids). We test the efficacy of NewtCap, originally designed for the Eurasian Triturus newts, in 30 species, belonging to 17 different genera, that cover all main Salamandridae lineages. We also test NewtCap in two other salamander families. We discover that NewtCap performs well across all Salamandridae lineages (but not in the salamander families Ambystomatidae and Hynobiidae). As expected, the amount of genetic divergence from the genus Triturus correlates negatively to capture efficacy and mapping success. However, this does not impede our downstream analyses. We showcase the potential of NewtCap in the contexts of; 1) phylogenomics, by reconstructing the phylogeny of Salamandridae, 2) phylogeography, by sequencing the four closely related species comprising the genus Taricha, 3) hybrid zone analysis, by genotyping two Lissotriton species and different classes of interspecific hybrids, and 4) conservation genetics, by comparing Triturus ivanbureschi samples from several wild populations and one captive-bred population. Overall, NewtCap has the potential to boost straightforward, reproducible, and affordable genomic studies, tackling both fundamental and applied research questions across salamandrids.

genomics↗