Analysis of codon usage pattern in two subspecies of cows using gene expression data

Today, cows are selected using genetic information at the level of the genome translation, transcriptome and proteome. In this regard, there is a high correlation between codon usage patterns at the genome level and the level of expression of genes in the genome level, which are related to the expression and translation of the genes, this indicator is the result of a balance between factors such as mutation, natural selection, GC content and gene expression level. This information is useful in evaluating the evolutionary process and changes in the genome and predicting gene expression levels within species. However, there is limited information on the study of codon usage in bulls. In the present study, the codon usage pattern between two Holstein )Bos Taurus(and cholistani)Bos indicus(cattle populations is evaluated using gene expression data with different expression and its relation with gene expression. For this purpose, in this study, RNA-Seq data were used to assemble 40 samples of Holstein)Bos Taurus) and 45 cholistani (Bos indicus) breeds. Finally, the codon usage pattern was calculated based on indices such as ENC, GC3S, CAI and GC for different expression genes between the two breeds using the CODON W software. Also, R 3.4.2 Statistical software was used to calculate the correlation between the desired indicators and the graphs. An analysis of codon usage for ORF regions with different expressions in both Holstein and cholistani breeds showed that there is a high correlation between the total GC and GC3S values, which indicates the effect of GC and mutation as an important factor in the creation of various codons; Also, the correlation between ENC and GC3S showed that mutation was the most important factor in the formation of codons. The correlation between the CAI indexes, which is mainly used to predict gene expression levels, with the ENC index indicates the association between the codon usage pattern and the gene expression. This is the first report to examine the codon biology between the two Holstein and cholistani breeds, which not only provide a new perspective for understanding the mechanisms of the codon preference model, but also provide useful clues for molecular genetics and evolutionary studies.