A one-stop genomic information knowledge base for the monkey research community
Introduction
Rhesus macaque, as a non-human primate model animal widely distributed in China, poses a unique model to explore the law of human evolution with the advantages of controllable environmental factors, convenient sampling and detection, and similar genome, physiological and pathological characteristics to humans. Because key issues regarding this animal model remain poorly addressed -- the limited genomic annotation and gene structure, lack of functional genomics data, and immature information research platform, rhesus macaque only has been mainly used in preclinical drug research for a long time, but not serve as a high-precision molecular medical model to support in-depth functional and mechanism studies.
We defined the rhesus macaque reference genome and gene structure in detail, established a rhesus macaque population genetics research platform, supplemented a large number of convincing transcripts missed before (72% of rhesus macaque transcripts were missed by existing authoritative annotations), and cleared the errors found in about 30% rhesus gene structure annotations from genomics platforms Ensembl and others. The self-produced and public data deeply integrated accounts for nearly 30% of the international non-human primate omics data. The breadth and depth of annotations for some regulatory levels are comparable to that of human genome annotations, which greatly enriches the understanding of rhesus macaque functional modulation.
By further integrating 65 public databases and developing dozens of online interfaces, we built a one-stop genomic information knowledge base, RhesusBase, which integrates annotation information of genome, gene structure, population genetics, expression regulation, molecular evolution, drug development, etc., totally with 7.6 billion functional annotation records. Especially, we developed Molecular Evolution Gateway, an NGS-oriented genomic framework to access and visualize macaque annotations in reference to human orthologous genes and the associated regulations, and PopGateway, the first genome-wide effort to identify and visualize the population genetics profile in rhesus monkey. Overall, RhesusBase provides a basis for precise functional and mechanism studies using rhesus macaque as a characteristic model.
