RNA-seq of centrarchid species
Total RNA was extracted from one retina of each fish using the standard TRIzol chloroform protocol described by Bertinetti et al. (2024). The RNA yield and integrity were assessed using a Qubit 4 fluorometer. RNA (200 ng) was used for poly(A) selection, and the resulting mRNA was used to generate RNA-Seq libraries using the CORALL RNA-Seq V2 Library Prep Kit (Lexogen, Austria) following the manufacturers guidelines. The fragment size and concentration of the generated libraries were quantified using Bioanalyzer 2100 (Agilent, CA, USA) at the Genomics and Bioinformatics Core Facility of the University of Notre Dame. Samples were pooled at equimolar ratios and paired-end sequenced on a DNBSEQ 400 platform (PE150, Innomics Inc., CA, USA).