Transcriptomics reveals orchestration of larval and juvenile development and metamorphosis in Southern Flounder Paralichthys lethostigma

Developmental transitions involve changes in the genetic programs governing molecular processes. Characterizing these genetic programs gives us insight into how genes work to orchestrate developmental transitions in morphology, physiology, or even behavior. One fascinating developmental transition, metamorphosis, bridges larval and juvenile periods. Southern Flounder, a flatfish, is an ideal model system to investigate these developmental states due to dramatic phenotypic changes during metamorphosis. Here, we use transcriptomics to investigate how genetic programs orchestrate larval development, metamorphosis, and juvenile development in Southern Flounder. Our analysis of Southern Flounder transcriptomes comprehensively describes distinct larval and juvenile genetic programs that overlap during metamorphosis. We also describe a third genetic program that peaks during metamorphosis. These results provide insight into molecular orchestration of flatfish and teleost metamorphosis and more generally into how the timing of genetic programs orchestrates metamorphosis. We also propose that these program trajectories can be used to pinpoint timing of metamorphosis in animals with less phenotypically distinct larval and juvenile forms. Overall design: Bulk RNA-seq profiling of the Southern Flounder (Paralichthys legostigma) at 8 post-hatch developmental time timepoints.