Abstract
Macaques are the most widely used non-human primates in biomedical research. The genetic divergence between these animal models is responsible for their phenotypic differences in response to certain diseases. However, the macaque single nucleotide polymorphism resources mainly focused on rhesus macaque (Macaca mulatta), which hinders the broad research and biomedical application of other macaques. In order to overcome these limitations, we constructed a database named MACSNVdb that focuses on the interspecies genetic diversity among macaque genomes. MACSNVdb is a web-enabled database comprising ~74.51 million high-quality non-redundant single nucleotide variants (SNVs) identified among 20 macaque individuals from six species groups (muttla, fascicularis, sinica, arctoides, silenus, sylvanus). In addition to individual SNVs, MACSNVdb also allows users to browse and retrieve groups of user-defined SNVs. In particular, users can retrieve non-synonymous SNVs that may have deleterious effects on protein structure or function within macaque orthologs of human disease and drug-target genes. Besides position, alleles and flanking sequences, MACSNVdb integrated additional genomic information including SNV annotations and gene functional annotations. MACSNVdb will facilitate biomedical researchers to discover molecular mechanisms of diverse responses to diseases as well as primatologist to perform population genetic studies. We will continue updating MACSNVdb with newly available sequencing data and annotation to keep the resource up to date. Database URL: http://big.cdu.edu.cn/macsnvdb/
Highlights
Introduction retrieving macaque genome single nucleotide variants (SNVs) genotyping data
193.13 million single nucleotide variants (SNVs) were detected from 20 macaque genomes, of which 116.81 million were homozygous and 76.32 million were heterozygous, represent 74.51 million nrSNVs, with a density of 28.24 SNVs/kb and an average length of SNV intervals of 33.5 bp
We mapped all nrSNVs to annotated macaque genes and found that 45.75 million (61.41%) nrSNVs were present in intergenic region, while 28.75 million (38.59%) nrSNVs were present in genic region
Summary
Introduction retrieving macaque genome SNV genotyping data. MACSNVdb enables users similarity with human, macaques have been widely used to search synonymous and non-synonymous SNVs within in biomedical research, in vaccine and drug disease-associated or drug-target genes. Understanding the SNVs locates in macaque disease-related and drug-targeted genes will improve utilization of macaques in the context of biomedical research and provide a valuable resource for pharmacogenomic studies.
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