الفهرس 
REVIEW OF LITERATUREOnly 14 pages are availabe for public view
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Abstract
Nile tilapia is one of the most popular types of fish consumed worldwide, but it originates in African countries. The Nile tilapia lives in fresh water. It is characterized by rapid growth and adaptation to the most difficult environmental conditions possible, except for prolonged hypothermia, which makes it the focus of attention of fish producers in the world in general, and in Egypt in particular. It is commensurate with the consumer’s taste and financial ability compared to its counterparts from animal protein sources, in addition to its high nutritional importance represented in a group of vitamins and omega 3, as well as its high protein content.
As for the state of the genome of the Nile tilapia, which is primarily responsible for its aforementioned characteristics, its information is not complete yet. What is available for the Nile tilapia genome is 22 linkage groups of 42,646 genes that are somehow related but did not reach the chromosome level. The number of 550 regions on the genome is still unknown whose nucleotides are sequenced so far, and even the previously recorded genes, some of which have not yet been fully defined.
This is where the idea of the current study originated, in which we tried to fill in the blanks of the Nile tilapia genome image, based on the Egyptian version, whose source was Al-Sharkawiia canal in Egypt. The current study was built on two basic strategies:
I. The first strategy centered on studying the whole genome through the second generation of sequencing technology called “NGS that stands for Next Generation Sequencing”. This technology resulted in millions of small reads that were mapped on the reference genome of the Nile tilapia downloaded from the NCBI database, to finally obtain the genome draft of the Egyptian Nile tilapia. Single nucleotide polymorphism (SNP) analysis was performed and resulted in 751,816 variable nucleotides presented in our genome draft than the reference genome, which in turn affected the genes carrying it.
These mutated genes could be divided into four groups according to the type of selection to which they were subjected: I. genes that were subjected to purifying selection, II. Genes that were subjected to positive selection, and III. Genes that were subjected to neutral selection. As for the last group, it was difficult to distinguish the type of selection under which it is subjected. This group of genes showed a high KaKs ratio that is the rate of non-synonymous substitution divided by synonymous substitution.
When conducting a gene enrichment analysis, it was possible to know the biological pathways in which these genes participate. The functions of these genes were generally associated with pathways of energy production and catabolism, pathways of innate and induced immune response, pathways of cytotoxicity and cancers, pathways of metabolism, as well as pathways of development and growth.
Thus, a link can be made between the function of these genes and the causes of their mutation in the Egyptian environment, then the potential harms and their causes can be presented to the concerned authorities and help as researchers in solving them, which will benefit the Egyptian society, and even the global community that is interested in the cultivation and production of Nile tilapia.
II. The second strategy is an attempt to identify the gaps in the Nile tilapia genome in an innovative and unprecedented way in any other study. The general steps were randomly selecting a number of these gaps, amplifying them by polymerase chain reaction (PCR), sequencing of the successfully amplified gaps by automated Sanger method, and finally predicting and annotating the obtained sequences. Sequence analysis depended on two types of tools; the ab initio- based and homology-based. All the tools used were effective, but provided they were used together, not individually. In the current study, FGENESH and GENSCAN gene prediction programs proved higher efficiency than AUGUSTUS. BLAST, OFR finder, SWISS-MODEL, InterPro, and Promoter v.20 were also effective tools. MEME-SUIT was the most supportive tool in the final decision about studied sequence. This strategy resulted in the discovery of potential six new copies of six different genes, repetitive DNA sequence, gene spacer, and two introns (non-coding sequences located inside the gene) in already predicted genes that are recorded on databases.
The potential new copy genes are mucin 1-like, KLR, ncRNA, uncharacterized protein, DMBT1, and ASBT. These genes belonged to gap 1, gap 10, gap 16, gap 25, gap 30, and gap 31, respectively. The two discovered introns belonged to gap 2 and gap 24, which were included in TRPM7 and Grid2 genes, respectively. Gene spacer belonged to gap 29, while repetitive sequence belonged to gap 51. We hope that all these discoveries can support future genetic and genomic studies on Nile tilapia.