Differential fates of vertebrate Kazald gene quartet, from ancestral roles in skeletogenesis and regeneration to putative innovations in fish and birds

Abstract

Salamanders are known for their incredible regenerative abilities, but translating findings to mammals is complicated by unannotated genes and unclear orthology. An example highlighting this difficulty was a discovery in the axolotl (Ambystoma mexicanum) of a regeneration-associated gene that has been identified as either Kazald1 or Kazald2. Since orthology inference of genes across species is crucial to identifying gains and losses of gene functions, and thus if gene usage is likely to be consistent across species, we investigated the evolution of the axolotl genes using an extensive cross-species analysis. Molecular phylogeny inference conclusively identified the regeneration-associated gene as Kazald2, but also revealed an undescribed four-member Kazald gene family in jawed vertebrates. Moreover, synteny comparisons demonstrated that this family originated in the ancestral two-rounds of whole genome duplication. Additionally, we performed vertebrate-wide comparisons of Kazald gene expression profiles, employing available RNA-Seq which we validated in whole tissues of axolotl, zebrafish, and sharks. This uncovered seemingly ancestral connections conserved over jawed vertebrate evolution, such as Kazald1 with skeletogenesis and odontogenesis and Kazald2 with regeneration. It also suggested novel putative roles within specific lineages, including Kazald3 in teleost fish skeletogenesis and Kazald4 within avian brains. Our study thus demonstrates the establishment of a Kazald gene quartet in the jawed vertebrate ancestor, and elucidates the asymmetry of gene fates of its members, including deeply ancestral roles and comparably recent innovations. This provides a comprehensive report of this formerly undescribed gene family, offering a solid foundation for future studies of these genes in diverse species.