Wu et al. Zool. Res. 2022, 43(2): 147−149 https://doi.org/10.24272/j.issn.2095-8137.2022.001 Commentary Open Access Initiation of the Primate Genome Project A crucial step for understanding human evolution is to identify the last two years, NHPs have played critical roles in the study the genomic changes that occurred during primate evolution, of SAR-CoV-2 infection mechanisms and vaccine thus allowing investigators to reconstruct the ancestral states development (Chandrashekar et al., 2020; Mercado et al., preceding the human condition. In the past several decades, 2020). Therefore, current primate genome sequencing efforts the primate clade has been a research focus in genome have prioritized the great ape lineage, i.e., taxa closest to sequencing due to its unique phylogenetic position and key humans, and other biomedically relevant species (Carbone et importance. Comparative genomic analyses of several primate al., 2014; Gibbs et al., 2007; Gordon et al., 2016; Locke et al., lineages have radically expanded our knowledge on the tempo 2011; Scally et al., 2012; The Chimpanzee Sequencing and and mode of different features in primate genome evolution, Analysis Consortium, 2005; The Marmoset Genome revealing many genomic innovations contributing to the Sequencing and Analysis Consortium, 2014; Warren et al., development and evolution of human phenotypes. However, 2020), with 90% of primate species yet to be characterized. with less than 10% of primate species currently sequenced, a Due to anthropogenic interference, climate change, and other considerable gap remains regarding the evolutionary history of factors, some 60% of the world’s primate species are every base pair in human and non-human primate (NHP) threatened with extinction and 75% are experiencing genomes. To fill this gap, we propose to organize and population declines (Estrada et al., 2017), thus highlighting an establish the Primate Genome Project (PGP) to scale up the impending extinction crisis. Therefore, the phylogenomic study number of high-quality reference genome assemblies for of primates is critical for broadening our knowledge on the primate species using cutting-edge sequencing technologies. evolutionary and adaptive history of each species, and for We outline here the possible paths going forward and some of providing relevant information for conservation decisions going the major questions to be addressed within this ambitious forward. project. We anticipate that genomic comparisons, including Currently, the genomes of a dozen representative NHP broader taxon sampling of extant primate species, will species from 22 genera have been published (Ensembl v103), significantly contribute to our understanding of the evolution of with 72% of genera not yet sequenced. The PGP aims to human phenotypes and diseases and the genomic close this gap and generate long-read-based high-quality mechanisms of primate speciation and adaptation, which will reference genomes for at least one representative species in ultimately assist in primate conservation efforts. each primate genus in the next few years. Ultimately, we wish Worldwide, there are currently more than 500 primate to determine the genome sequences for all primate species. species from 80 genera and 16 families, with new primate These high-quality genomes will provide rapid information for species still being discovered in recent years (Fan et al., 2017; comparisons in the context of primate phylogeny to Nater et al., 2017; Roos et al., 2020). As our closest biological reconstruct the primate tree of life and clarify the genomic relatives, NHPs hold many clues for understanding the origin changes underlying the speciation and adaptation processes and evolution of human complex traits, behaviors, and of major primate lineages. We anticipate that a detailed diseases. NHPs are widely used as biomedical research evolutionary landscape will be disclosed for all genomic models for studying the genetic basis of human diseases (e.g., variations across primate lineages from chromosomal neurodegeneration, diabetes, cancer, and cardiovascular rearrangements to single base-pair substitutions. This disease), as well as models for reproduction, transplantation, landscape will inform the evolutionary patterns of structural and pharmacology (Rogers & Gibbs, 2014). Furthermore, over variations, segmental duplications, protein-coding genes, and non-coding regulatory elements. By integrating the meta- This is an open-access article distributed under the terms of the records of trait data, genomic information will enable us to Creative Commons Attribution Non-Commercial License (http:// creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted Received: 04 January 2022; Accepted: 06 January 2022; Online: 06 non-commercial use, distribution, and reproduction in any medium, January 2022 provided the original work is properly cited. Foundation items: This work was supported by the National Natural Copyright ©2022 Editorial Office of Zoological Research, Kunming Science Foundation of China (31822048) and Strategic Priority Institute of Zoology, Chinese Academy of Sciences Research Program of the Chinese Academy of Sciences (XDPB17) 5 investigate phylogeny, incomplete lineage sorting, and Shaanxi Key Laboratory for Animal Conservation, College of Life chromosomal evolution, and to map genetic changes Sciences, Northwest University, Xi’an, Shaanxi 710069, China associated with human-specific phenotypes (such as brain 6 State Key Laboratory for Conservation and Utilization of Bio- and cognitive ability), and phenotypic diversity among primate Resource in Yunnan, Yunnan University, Kunming, Yunnan lineages that may contribute to their adaptive evolution. 650091, China Due to the difficulties in collecting samples of all primate 7 CAS Key Laboratory of Animal Ecology and Conservation species, it may not be feasible to sequence all individual Biology, Institute of Zoology, Chinese Academy of Sciences, primate species within a short time. Nevertheless, depending Beijing 100101, China on sample availability, we will select certain genera as primary 8 Department of Biology, Duke University, Durham, NC 27708, sequencing targets and generate reference genomes and USA population sequences for all recorded species in those 9 genera. This will allow us to investigate the genetic basis of Gene Bank of Primates and Primate Genetics Laboratory, speciation and characterize the history and genomic outcomes German Primate Center, Leibniz Institute for Primate Research, of hybridization, as observed in major primate lineages Göttingen 37077, Germany 10 (Ayoola et al., 2021; de Manuel et al., 2016; Svardal et al., Faculty of Environmental Earth Science, Hokkaido University, 2017). Conservation genomic analyses of population data will Sapporo, Hokkaido 060-0810, Japan be highly informative regarding genomic diversity and recent 11 Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan demographic history, which are crucial parameters for 12 Human Genome Sequencing Center, Department of Molecular evaluating the conservation status of species (Orkin et al., and Human Genetics, Baylor College of Medicine, Houston, TX 2021). 77030, USA We expect that the PGP will generate a rich resource for 13 Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. primate lineage genomics over the next few years. Given the Aiguader 88, Barcelona 08003, Spain advances in sequencing technologies, it is important to initiate 14 Catalan Institution of Research and Advanced Studies (ICREA), interdisciplinary cooperation and joint data analysis by Passeig de Lluís Companys, 23, Barcelona 08010, Spain integrating expertise in primatology, conservation, 15 biomedicine, genomics, and evolutionary biology. Therefore, CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona we welcome researchers to join the consortium and contribute Institute of Science and Technology (BIST), Baldiri i Reixac 4, to this necessary and timely research. Barcelona 08028, Spain 16 Institut Català de Paleontologia Miquel Crusafont, Universitat COMPETING INTERESTS Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Cerdanyola del Vallès, Barcelona 08193, Spain The authors declare that they have no competing interests. 17 Key Laboratory of Animal Models and Human Disease AUTHORS' CONTRIBUTIONS Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ-CUHK Joint Laboratory of Bioresources and D.D.W. and G.Z. conceived the review and prepared the draft. Molecular Research in Common Diseases, Kunming Institute of All authors contributed to the discussions. All authors read and Zoology, Chinese Academy of Sciences, Kunming, Yunnan approved the final version of the manuscript. 650201, China 18 Dong-Dong Wu1,2,3,4,*, Xiao-Guang Qi5, Li Yu6, Ming Li4,7, Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China Zhi-Jin Liu7, Anne D. Yoder8, Christian Roos9, 19 10,11 12 Villum Centre for Biodiversity Genomics, Section for Ecology Takashi Hayakawa , Jeffrey Rogers , Tomas Marques- 13,14,15,16 and Evolution, Department of Biology, University of Copenhagen, Bonet , Bing Su1,4, Yong-Gang Yao2,17,18, Copenhagen DK-2100, Denmark Ya-Ping Zhang1,4,18, Guojie Zhang1,4,19,20,* 20 China National GeneBank, BGI-Shenzhen, Shenzhen, 1 State Key Laboratory of Genetic Resources and Evolution, Guangdong 518083, China Kunming Institute of Zoology, Chinese Academy of Sciences, *Corresponding authors, E-mail: wudongdong@mail.kiz.ac.cn; Kunming, Yunnan 650223, China guojie.zhang@bio.ku.dk 2 National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for REFERENCES Phenotypic & Genetic Analysis of Model Animals (Primate Ayoola AO, Zhang BL, Meisel RP, Nneji LM, Shao Y, Morenikeji OB, et al. Facility), Kunming Institute of Zoology, Chinese Academy of 2021. 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