Transcriptome datasets and histological profiles of critical larval stages in gilthead seabream

The transcriptome of the seabream larvae farmed in different European commercial hatcheries was analysed during critical larval stages. The complementary data herein presented support the findings reported in the associated research article "Insights into core molecular changes associated with metamorphosis in gilthead seabream larvae across diverse hatcheries". Samples were collected from gilthead seabream (Sparus aurata) hatcheries in Greece (site Gr), Italy (site It), and France (site Fr). RNA was extracted from larvae with different weights, mainly at the flexion (23 and 25 dph) and mid-metamorphosis stages (43, 50, 52, 56, and 60 dph). RNA-seq libraries were sequenced using Illumina HiSeq xten. The paired-end sequenced raw reads were deposited in the NCBI-SRA database with the accession number PRJNA956882. Differential expression and function of genes were obtained by comparing transcriptome profiles of larvae at different developmental stages. The presented data can be used to improve marine-farmed fish larvae production during critical larval stages.