BUSCADOR RECOLECTA

[Description of methods used for collection/generation of data] ATACseq and RNAseq methodology in different developmental stages, Analysis of the transcriptomes and chromatin accessibility of multiple developmental stages of the indirect-developing hemichordate Ptychodera flava. After the individual analysis of each sample, integration of ATACseq and RNAseq data was performed in order to reconstruct genetic and regulatory networks. These data were also compared to other species, what could shed light on deuterostome evolution., Ministerio de Ciencia e Innovación (grant PID2022-141288NB-I00)., supp_data_01.xlsx supp_data_02.xlsx supp_data_03.xlsx supp_data_04.xlsx supp_data_05.xlsx supp_data_06.xlsx supp_data_07.xlsx supp_data_08.xlsx supp_data_09.bed supp_data_10.tsv supp_data_11.tsv.gz supp_data_12.tsv.gz supp_data_13.xlsx supp_data_14.xlsx supp_data_15.xlsx supp_data_16.xlsx, Peer reviewed

To investigate differences in gene expression during flatfish metamorphosis we selected three key stages in turbot development: pre-metamorphic stage (15 dpf); climax of metamorphosis (30dpf); and post-metamorphic stage (57dpf). These fish were reared under standard production conditions at 18ºC. The migrant and non-migrant eyes and their respective surrounding tissue were directed for each stage and RNA were extracted. Libraries were sequenced on a BGISEQ-500 platform and single-end reads of 50 base pairs length were generated per sample, Flatfish have evolved their visual system to meet the demands of their environment through a fascinating process of metamorphosis. This morphological transformation involves a significant change in lifestyle from pelagic to benthic, accompanied by changes in body structure to achieve an asymmetrical flat shape. However, the fundamental change lies in the migration of one eye from its original position to the opposite location on the body. Although the role of thyroid hormone in triggering flatfish metamorphosis is well established, the specific gene regulatory network responsible for this extraordinary eye migration is still unknown. Here we show a global view through the creation of a general map of gene expression during the metamorphic process, encompassing both migrant and non-migrant eyes. Our research uncovers significant differences between migrant and non-migrant eyes of turbot in the pre-metamorphic and climax phases, emphasizing genetic disparities crucial for benthic adaptation, MCIN/AEI/10.13039/501100011033 (AGL2017-89648P and PID2021-126511OB-100 to J.R.) and “ERDF A way of making Europe”, by the “European Union”, No

Additional file 1. Supplementary Figures S1-22 (.pdf)., Ghent University Special Research Fund H2020 Marie Skłodowska-Curie Actions European Joint Programme on Rare Diseases (EJP RD) Research Foundation Flanders (FWO) Foundation John W. Mouton Pro Retina & Marie-Claire Liénaert Ghent University Fund Alzheimer and Neurodegenerative Diseases Junta de Andalucía, Peer reviewed

Additional file 3. BED file with Hi-C boundaries in RPE/choroid (25 kb resolution)., Ghent University European Commission Research Foundation - Flanders Junta de Andalucía, Peer reviewed

Additional file 4. BED file with Hi-C CHESS regions with differential 3D topology between neural retina vs. RPE/choroid., Ghent University European Commission Research Foundation - Flanders Junta de Andalucía, Peer reviewed

Additional file 5. BEDPE file with Hi-C loops in neural retina., Ghent University European Commission Research Foundation - Flanders Junta de Andalucía, Peer reviewed

Additional file 6. BEDPE file with Hi-C loops in RPE/choroid., Ghent University European Commission Research Foundation - Flanders Junta de Andalucía, Peer reviewed

Ghent University European Commission Research Foundation - Flanders Junta de Andalucía, Peer reviewed

Additional file 9. Supplementary Tables S1-6 (.xlsx)., Ghent University European Commission Research Foundation - Flanders Junta de Andalucía, Peer reviewed

Additional file 10. BED file with stable and differential HiChIP loops in neural retina and RPE/choroid, with annotation of interacting cis-regulatory elements (CREs, from [4])., Ghent University European Commission Research Foundation - Flanders Junta de Andalucía, Peer reviewed