The genome availability for cichlid species of the subfamily Pseudocrenilabrinae, including Oreochromis niloticus can help develop robust molecular tools to address questions related to the conservation and management of O. niloticus in its invasive range and O. mossambicus in its natural range. The objectives of this study include (1) identifying the best candidate orthologous genes among Pseudocrenilabrinae using gene ontology and a dedicated filtering strategy, (2) mining coding sequences for these candidate genes from O. niloticus reference genome, and (3) in-silico testing of the gene-capture custom panel for Pseudocrenilabrinae. Combining a literature survey and sequence mining from the Genbank database based on 14 ontologies, we identified 2,040 candidate genes. We excluded genes not annotated in the O. niloticus genome, without orthologue in the Human Genome, with exons smaller than 300 bp, that were on scaffolds that failed to map to a chromosome or presented gaps in the alignment. The coding sequence of remaining 247 genes was mined from the O. niloticus genome and transferability across available species of Pseudocrenilabrinae was successful (coverage ~99%). This panel represents an important molecular resource for the family and should open new perspectives for the assessment of introgressive hybridisation between O. niloticus and O. mossambicus.
