Bioinformatics Study of mtDNA Genes in Two Subspecies of Holstein (Bos taurus) and Cholistani (Bos indicus) Cattle Using RNA-Seq Data

The advent of the new generation of transcriptome sequencing has helped to improve the overall accuracy of different gene expression predictions using short RNA-Seq sequences. This technology can provide a more comprehensive view of functional genomics in many species with a unique gene sequence. The aim of this study was to investigate the structural reasons for different expression of mitochondrial genes in two subspecies of Holstein and Cholistani cattle, including ND3, ND4, ND4L, ND5 and ND6 genes, which are involved in important processes such as energy metabolism against stress. Biological and non-biological as well as disease resistance are involved.

In this study, RNA-Seq data were used to integrate 40 samples from the University of Wisconsin Dairy Cattle Center (Bos taurus) and 45 Christian cows (Bos indicus) at the Gujaratpir farm in Bahawalpur, Punjab, Pakistan. IGB, MEGA6 and DnaSPV.5 software were used to investigate the level of transcriptome coverage and genetic differences among the five mitochondrial genes, which included polymorphic regions, deletion and addition regions, binding regions and the percentage of transitional and transversional nucleotide substitutions.

The highest deletion region and length in all studied genes was related to Holstein genome and the highest length and binding region was related to Cholistani cattle. The highest number of deletions in Holstein and Cleistani cows were related to ND4 gene with 74 and 66 points, respectively, and the lowest deletions were related to ND4L with 9 and 4 deletion sites, respectively. The ND4 and ND4L genes had no binding regions, but the ND5 and ND6 genes in the Holstein and Cleistian breeds with 1 and 2 binding regions increased the genome by 11 and 22 bp, respectively. The highest level of transcriptome coverage was observed in ND3 and ND4 genes and the lowest level was observed in ND6 gene locus. The number of polymorphic regions in ND5 locus was more than other genes and equal to 38 polymorphic regions. The results also showed that the percentage of transitional substitution in bases is higher than transversional substitution which can be the reason for the stability of changes during evolution. Therefore, some of the structural reasons for mitochondrial genes that were expressed differently in both Holstein and Cholistani subspecies could be related to deletion and addition, polymorphic regions, transcriptome coverage level, and type and amount of transitional and intersecting substitutions during the evolution of the two subspecies.

Intense selection for milk production in Holstein cows compared to the Cholistani breed has led to a reduction in the length of the mitochondrial genome and changes in the nucleotide structure of some mitochondrial genes, resulting in altered gene expression and different responses to different environmental conditions.