LAUSR

Simple Summary The Haplotilapiine lineage is a specific cichlid group that is widely distributed in the Nile River’s Egyptian sector, divided into 22 tribes with 3000 species, and constitutes one of the most diverse subclades. However, the systematics of Haplotilapiine and their evolutionary histories still suffer from knowledge gaps that should be resolved to increase their usefulness as a model system. Therefore, we sequenced, assembled, and characterized five complete mitochondrial genomes representing three Egyptian tilapiine fish species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. These mitogenomes have the typical circular mitogenome characteristics of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region. Our results indicate that the structure, nucleotide composition, synteny, and gene orders are the main conserved aspect of cichlids. The phylogenetic analyses using the maximum likelihood method indicate that species belonging to the Nile tilapiine appear paraphyletic and provide a further supplement to the scientific classification of fish. These results provide a comprehensive framework and worthy information for future research on this family. Abstract To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genomes of three Nile tilapiine species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. Our results showed that the general mitogenomic features were conserved among the Nile tilapiine species. The genome length ranged from 16,436 to 16,631 bp and a total of 37 genes were identified (two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and 1 control region). The ND6 was the only CDS that presented a negative AT skew and a positive GC skew. The most extended repeat sequences were in the D-loop followed by the pseudogenes (trnSGCU). The ND5 showed relatively high substitution rates whereas ATP8 had the lowest substitution rate. The codon usage bias displayed a greater quantity of NNA and NNC at the third position and anti-bias against NNG. The phylogenetic relationship based on the complete mitogenomes and CDS was able to differentiate the three species as previously reported. This study provides new insight into the evolutionary connections between various subfamilies within cichlids while providing new molecular data that can be applied to discriminate between Nile tilapiine species and their populations.