Conservation genomics of the Red Roman, Chrysoblephus laticeps, across Marine Protected Areas (MPAs) and exploited regions along the South African coastline

This research utilises VCF files generated with BCFtools from whole-genome sequences of the Red Roman seabream, obtained through DNBSEQ sequencing technology. The goal was to conduct genomic analyses to support the conservation of the species across its distribution range, including Marine Protected Areas and exploited regions along the South African coastline.

The reference genome was assembled using Flye Assembler and subsequently polished with Polca and Polypolish. Structural annotation was performed using Braker3, while functional annotation was performed using a combination of BlastN, InterProScan, and EggNOG mapper. The ten sample VCF files correspond to ten Red Roman samples mapped to Chrysoblephus laticeps, Pagrus major, Sparus aurata, and Acanthopagrus latus for the comparison of genetic metric estimates.</p>