الفهرس 
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Abstract
The great radiations of African cichlid fishes are the most diverse extant and provide a peculiar and powerful model system in speciation and adaptive radiation research. The great lakes provided a suitable environment for that spectacularly rapid sequence of speciation events that produced one of the most diverse endemic species assemblages, in terms of morphology, behavior, and ecology. Therefore, new species are identified annually, and many species stay undescribed. The current study focused on the Egyptian tilapiine fish species inhabiting and dominating the Nile River by studying the complete mitochondrial genome. The thesis work was done in two major sections, The thesis work was done in two major parts, the first was to report a newly assembled, annotated, and characterized complete mitogenome of Sarotherodon galilaeus. The second part compares the mitogenomes of the three Egyptian tilapiine species, including both newly sequenced sequences and those found in the GenBank database (NCBI).
For the first part, Sarotherodon galilaeus (Linné, 1758) is a member of the family Cichlidae, which is considered the most important aquaculture freshwater species endemic to Africa and the Middle East. The genetics and molecular biology of this species are rare. This requires more comprehensive mitochondrial genomes-based phylogenetics to enhance understanding of the relationship and delineate this species. Here, we assembled the complete mitogenome of S. galilaeus using Illumina high-throughput sequencing technology. The mango tilapia mitogenome was 16,631 bp in length with an AT composition of 53.4% and 46.4% GC content. It encodes 37 genes comprising two rRNAs, 22 tRNAs, and 13 PCGs) as well as the D-loop known as the control region. The phylogenetic tree was conducted to provide a relationship within the haplotilapiine lineage based on the maximum likelihood method, and the newly sequenced S. galilaeus was clustered with other Sarotherodon species. Our results provide a new perception of the genetic basis of S. galilaeus species for further research on systematics, evolution, population genetics, and molecular ecology.
For the second part, a comparative mitogenomic analysis of the Nile tilapiine species that belongs to the Cichlidae family has not received much attention. To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genome sequences of three true tilapiine species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. Our results showed that the general mitogenomic features (gene composition, gene arrangement, and codon usage) 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, of these, two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and control region. Most PCGs were initiated with the typical ATG codon and terminated with the TAA codon, and the incomplete termination codon could be detected in five PCGs in the three species. The majority of AT skew and GC skew values were negative, where the amplitude of the GC skew was greater than the AT skew. The ND6 was the only gene that presented AT skew negative 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 more quantity of NNA and NNC, at the third position and anti-bias against NNG. The phylogenetic relationship was constructed using the maximum Likelihood method based on the complete mitogenomes, CDS, the D-Loop region, and the intergenic regions (IGS), in which only the complete mitogenomes and CDS were able to differentiate the three species in accordance with the previous reports. This study provides new insight into the phylogenetic and evolutionary connections between the various subfamilies within cichlids while providing new molecular data that can be applied to discriminate between the studied species.