FishPIE: A universal phylogenetically informative exon markers set for ray-finned fishes

Understanding the evolutionary history of the highly diverse ray-finned fishes has been challenging, and the development of more universal primers for phyloge-netic analyses may help overcoming these challenges. We developed FishPIE, a nested PCR primer set of 82 phylogenetically informative exon markers, and tested it on 203 species from 31 orders of Actinopterygii. We combined ortholo-gous sequences of the FishPIE markers obtained from published genomes and transcriptomes and constructed the phylogeny of 710 species belonging to 190 families and 60 orders. The resulting phylogenies had topologies comparable to previous phylogenomic studies. We demonstrated that the FishPIE markers could address phylogenetic questions across broad taxonomic levels. By incorpo-rating the newly sequenced taxa, we were able to shed new light on the phylog-eny of the highly diverse Cypriniformes. Thus, FishPIE holds great promise for generating genetic data for broad taxonomic groups and accelerating our under-standing of the fish tree of life.

Automated summary

This study developed the FishPIE primer set for phylogenetic analysis of ray-finned fishes. By testing it on 203 species and combining it with published genomes and transcriptomes, a phylogeny of 710 species was constructed, providing new insights into the fish tree of life.