Application of genomic markers generated for ray-finned fishes in chondrichthyan Phylogenomics

Reconstructing a well-supported phylogenetic relationship among species is a prerequisite for biological and evolutionary researches. Chondrichthyes (sharks, rays, skates and chimaeras) serves as an important clade of highly commercial, ecological, evolutionary, and conservation significance. Yet the genome-scale data of chondrichthyans are lacking, which largely restrict phylogeny, evolution, and conservation investigations of these species. Recently reported 1105 orthologous exon markers generated for ray-finned fishes are powerful tools for phylogenomics inferences. Given the relatively close relationship between cartilaginous and ray-finned fish species, we purposed to verify whether these 1105 genomic exon markers generated for ray-finned fishes were applicable for chondrichthyan phylogenomics. In this study, we collected publically available 10 genomes and 30 transcriptomes of chondrichthyans to conduct the phylogenomics analysis. Phylogenomics analyses based on the 1105 genomic exon markers and the Benchmarking Universal Single-Copy Orthologs (BUSCO) approach were performed to reconstruct phylogenetic relationships of investigated chondrichthyans. We also attempted to apply these exon markers for phylogeny of 26 jawed fish species. Our results revealed well-supported and almost identical phylogenetic relationships of chondrichthyans, confirming the applicability of genomic exon markers of ray-finned fishes in chondrichthyan phylogeny. Moreover, phylogenomics analyses of 26 jawed fish species further confirmed the application of these genomic exon markers in both cartilaginous and lobe-finned fish phylogeny. Our results highlighted the wide-ranging utility of genomic markers of ray-finned fishes in phylogenetic inference of cartilaginous and lobe-finned fish species and provided substantial and background information for the evolutionary biology and conservation of chondrichthyans and related fish species.