Genomic studies of piscine streptococci and genome assembly of Clariidae catfishes (Siluriformes) for aquaculture enhancement

Abstract This thesis presents integrated genomic research aimed at enhancing aquaculture productivity through two main contributions: (1) the generation of high-quality, haplotype-resolved genome assemblies of Clarias macrocephalus (bighead catfish) and its F1 hybrid with Clarias gariepinus, and (2) the genomic analysis of Streptococcus iniae, a bacterial pathogen causing severe losses in farmed fish. Using long-read (PacBio HiFi, Oxford Nanopore), short-read (Illumina), and proximity-ligation (Hi-C) sequencing, we assembled chromosome-scale genomes for both catfish taxa, enabling improved trait analysis, hybrid assessment, and comparative transposable element studies in Siluriformes. In parallel, five S. iniae isolates were sequenced and analyzed using pangenomics, variant calling, recombination detection, and reverse vaccinology pipelines. This work contributes essential genomic resources for selective breeding and disease control, promoting more sustainable and genetically informed aquaculture practices.