Genomic Analysis Of Chinese And Indian Macaque Populations

Non-human primates are very similar to human beings in both their evolutionary characteristics and physiological habits.The application of non-human primate species the clinical research of biomedicine and the development of new drugs can not only observe the response of primates to clinical treatment and the therapeutic effect of new drugs,but also avoid the related troubles of human ethics and morality.While the representative species of nonhuman primates —— Macaca mulatta,have similar biological characteristics as humans and can be used as disease models for detecting human gene mutations and disease correlations.In 1978,India banned the export of Macaca mulattas to breeding centers around the world,reducing the availability of Indian Macaca mulattas,followed by increased demand for Chinese Macaca mulattas in biomedical research.At present,a large number of scientific studies have been carried out on the evolutionary biology,population genetics and population genomics of Macaca mulatta species,revealing the evolutionary history,adaptive mechanism and scientific value of Macaca mulatta species.Population genomics has been used to identify disease-related genetic variants and identify macaque functional deletion mutations using population genome sequencing,which provides theoretical support for the establishment of valuable animal models of genetic diseases.The genome data of 20 Chinese Macaca mulatta individuals and 20 Indian Macaca mulatta individuals were downloaded from the NCBI(National Center for Biotechnology Information).The average depth of sequencing was 37.07×,and the genome coverage rate was 98.67%.All the data were adult Macaca mulattas,in order to avoid sex and age differences,the SNPs data of Macaca mulattas were analyzed in this study.In this study,40 G VCF files of Chinese Macaca mulattas and Indian Macaca mulattas were obtained for follow-up analysis.SNPs(Single Nucleotide Polymorphisms)and Indels(insertion-deletion)analysis were performed on the genome data of 40 individuals in the two groups,and 37,495,118 high-quality SNPs loci information and 30,339,415 autosomal Indels were obtained.Through the construction of phylogenetic trees,principal component analysis,population structure analysis,polymorphism index,linkage disequilibrium,systematic geographic history,and selective elimination analysis,genomics research was conducted to explore the susceptibility of macaque populations to the same disease in different habitats degree.Further genetic analysis showed that,due to the influence of geographical location and lifestyle,the Chinese Macaca mulatta and Indian Macaca mulatta populations have evolved into two independent branches.In addition,this study performed genome scanning on the two populations of Chinese Macaca mulattas and Indian Macaca mulattas,and extracted the regions affected by the selective elimination to obtain the gene?IDs of the two populations.Subsequently,using DAVID(Database for Annotation,Visualization,and Integrated Discovery)websites GO(Gene Ontology)and KEGG(Kyoto Encyclopedia of Genes and Genomes),these candidate genes were functionally classified and enriched,and a total of 309 were selected.There are large differences in the number and function of the selected genes between the two populations of Chinese Macaca mulattas and Indian Macaca mulattas.Among them,there are 34 selected genes in Chinese Macaca mulattas and 275 selected genes in Indian Macaca mulattas.For example,the HIVEP1 gene,which is selected only in the Indian population,is a transcription factor that plays an important role in the growth and development of organisms,such as participating in the regulation of HIV-1 gene expression.In the 1990 s,scientists synthesized a virus containing the HIV-1 gene to infect Macaca mulattas.During the study,the infected Macaca mulattas showed symptoms similar to AIDS.The appearance of this symptom provides a very ideal animal model for scientists to study vaccines with HIV-1 antigen as the core in the future.After infecting the synthetic virus strains with Chinese Macaca mulattas and Indian Macaca mulattas,Chinese Macaca mulattas and Indian Macaca mulattas have different responses to viral infections,that is,there are large differences in the susceptibility of Chinese Macaca mulattas and Indian Macaca mulattas to the same virus,and they also react differently.There may also be a certain degree of difference in the tolerance of the Macaca mulatta populations to the drugs,thus reminding the scientific research personnel to conduct targeted research and development in the development of new drugs,and truly "make medicines for the people".The wide distribution of Chinese Macaca mulattas and Indian Macaca mulattas and the comparison of their different habitat types,as well as their wide application in biomedical research,make them an important case study to analyze the local adaptation characteristics to different selection pressures.In this study,the selection of cynomolgus monkeys living in different environments is compared to determine the selection goals that are more in line with biological clinical research,so as to increase the chance of finding selection characteristics.In summary,this study selects Chinese and Indian Macaca mulatta populations as the research object.Based on the methods of evolutionary genetics and bioinformatics,the first comparative study of population genomics was conducted on the Macaca mulatta populations in two different habitats in China and India.Attempt to use population genomics analysis methods to study human disease model animals at the genomic level,screen out many candidate genes with important biological functions,and use population genomics data to reveal the genetic diversity and environmental impact of Chinese Macaca mulattas and Indian Macaca mulattas adaptive mechanism.Overall,these results indicate that the genomic structure of Macaca mulattas used in biomedical research and their geographic origin may strongly influence the results of biomedical experiments,which should be considered when using Macaca mulattas as animal models in clinical and neurobiological studies.