Take the lead in the mining of primate genome “mineral deposits”

In the early morning of June 2, Science published 8 papers online in the form of a special research issue and 2 papers in Science Advances, focusing on the phased breakthroughs of the primate genome project initiated and led by Chinese scientists. The program is jointly led by the Kunming Institute of Zoology, Chinese Academy of Sciences (hereinafter referred to as the Kunming Institute of Zoology) and the Research Center for Life Evolution of Zhejiang University.

The Primate Genome Project was launched in 2018 and expanded to establish the International Primate Research Consortium. This time, we submitted a total of 12 papers, of which 10 papers can be published together, which is really not easy! Wu Dongdong, one of the initiators of the program and a researcher at the Kunming Institute of Zoology, couldn’t help but sigh.

He said that these scientific breakthroughs have important guidance and practical significance for the conservation of primate diversity, the development and utilization of genetic resources, and also provide important genetic materials and candidate molecular targets for the origin, development and disease medical research of human special traits.

“The UK has the Darwin Tree of Life Project and the US has the Mammal Genome Project, and from a national strategic point of view, the collection of species genome resources is of great significance.” Zhang Guojie, another initiator of the Primate Genome Project and a professor at the Life Evolution Research Center of Zhejiang University, said frankly, “It’s like whoever first generates a large amount of data has a ‘mineral deposit’ and has the priority and dominance of mining these data.” ”

Cover of the special issue of Science. Photo courtesy of Zhang Guojie’s team

Why study primates?

Studies have shown that primates are one of the most diverse groups of mammals, including more than 520 species in 16 families, 82 genera, second only to pterodonts and rodents, and new species are still being discovered.

Why do scientists study primates? Wu Dongdong explained to reporters that the evolution of primates has gone through more than 65 million years, and many changes have taken place from nocturnal ancestors who live alone to today’s highly developed human society. In addition, some primates are also natural animal models for studying human origin and evolution, disease pathogenesis, transmission of virulent infectious diseases, and vaccine development.

At present, analyzing and reconstructing the genomic variation map from primate ancestors to modern human evolution is an indispensable part of our understanding of human evolutionary biology, and it is also a hot issue in the field of research.

“The richness and population size of primate species is being challenged more severely than ever due to human activities, and there are still considerable gaps in comparative genomics studies covering the vast majority of primate clades.” Wu Dongdong said that these studies are expected to reveal the evolution of human-specific phenotypic variation and the stepwise change of diversity between primate lineages, especially those taxa located at the base of the primate phylogenetic tree lack systematic comparative studies.

At the same time, as the research deepened, the research team realized that the traditional socio-ecological model had encountered a big bottleneck. Wu Dongdong gave an example: “It is difficult to explain why species living in the same environment exhibit different social system structures. ”

Although the latest study has found that the social evolution of primates is influenced by phylogenetic signals, that is, inherited from a common ancestor, and gradually evolved as species diverge, which means that the evolution of animal social systems has a genetic basis, “little is known about the genomic mechanisms of the diversity of primate social systems.”

In order to fill the above research gaps and carry out research on primate diversity protection, the primate genome project led by Kunming Animal has attracted many research units at home and abroad to join.

Wu Dongdong introduced that the research team has newly generated high-quality reference genomes from 27 primate species in 26 genera in 11 families, and integrated the reference genomes of 23 other published species to carry out the largest and most complete primate comparative genomics study to date.

What did the research team do?

Wu Dongdong first introduced the flagship paper published in Science, “Systematic Genomics Research Revealing Primate Evolution”, in which the research team used systematic genomics methods to reconstruct the evolutionary history of primate genomes and identify a series of key candidate genes and structural variants related to the evolution of complex human phenotypes and the phenotypic diversity of different lineages of primates.

Zhang Guojie, one of the corresponding authors of the paper and a researcher at the Kunming Institute of Zoology, told China Science News: “Our study of the high-quality long-reading long-reading three-generation reference genome of 27 key branches of primates assembled and released is of great significance for future biomedical research and the development, utilization and protection of primate genetic resources.” ”

In order to explore the genomic mechanism of primate social system diversity, Wu Dongdong, professors Qi Xiaoguang and Li Baoguo of Northwest University and Cyril C. Grueter, professor of the University of Western Australia, formed a joint research team to use Asian langurs as a research model to comprehensively analyze the origin, evolution and formation mechanism of Asian langur heavy society from multiple dimensions such as behavior, ecology and genetics, providing an important research paradigm for the social evolution of primates. The research was published in Science.

Hybridization between two species allows the formation of a third species, the hybrid, without altering chromosomal ploidy, which is common in lower animals and plants. But existing studies have found that crossbreeding is rare in mammalian groups, let alone non-human primates that are most closely related to humans.

Wu Dongdong, Zhang Guojie and Kunming Institute of Zoology researcher Zheng Yongtang and others found an interesting phenomenon in the research process: hybrid recombination caused the cynomolgus monkey species group (rhesus macaque, cynomolgus monkey, Taiwanese macaque and Japanese macaque) to produce new reproductive traits, such as genital morphology, sexual skin characteristics, etc. just between the two parents, and genetically, the genes related to reproduction have obvious traces of recombination and are subject to positive selection.

“We have identified hybridization events for the first time in macaque taxa, and the results of this study were published in Science Advances.” Zhang Guojie said.

In fact, in the course of primate evolutionary history, hybrid breeding events have occurred more than once. Wu Dongdong’s team collaborated with Yunnan University researcher Yu Li’s team and others to report in Science that another group of primates, the snub-nosed monkey, also has ancient hybrid breeding events, that is, the Qianjin snub-nosed monkey is a hybrid between the ancestor of the Sichuan golden snub-nosed monkey and the Nujiang golden snub-nosed monkey, and the Sichuan golden snub-nosed monkey itself is also a hybrid species.

What are the implications of these achievements?

Talking about the significance of these results, Wu Dongdong said that these studies reveal the evolutionary history and laws of primates from different perspectives and fields, and they are of great significance to the rational development, utilization and integration of primate resources, as well as the conservation of species diversity and life medicine research.

“The reason why it can become the lead unit is mainly because the genomic data provided by Kunming animals can be used as basic reference data and play a key role in related research.” Wu Dongdong believes that these data promote the study of genomic diversity of primates, the construction of genetic variation profiles of humans and non-human primates, and the construction and analysis of dynamic maps of incomplete lineage sorting of primates.

“Although we have data, the useful information in the data needs to be deeply mined and analyzed, which requires a lot of computing power, and we have mobilized multiple supercomputing resources across the country for this purpose.” Wu Dongdong revealed that the current study only covers 10% of primate species, and the source of samples for species still faces great challenges because these species are distributed all over the world.

Zhang Guojie told China Science News that at present, the United States, Britain, Germany, Australia and other countries have various large-scale genomics programs operated by state-level organizations. Not long ago, Science published a number of papers from the Mammalian Genome Project led by the Massachusetts Institute of Technology, Harvard University and other institutions in the form of a research issue, which analyzed the largest 240 mammalian genetic sequences to date.

“The reason why European and American countries take biological genome information as an important national strategic resource is because comparison with other species is an important way to understand the uniqueness of human beings. Starting from the overall picture of the evolution process of life and looking at the past of human beings from the perspective of evolutionary biology, we can better understand the current and future development trends of human beings. Zhang Guojie explained.

Wu Dongdong, Zhang Guojie and others hope that more domestic and foreign research units and teams will join in the future to share resources and achieve mutual benefit. (Source: China Science News, Shen Chunlei, Hu Minqi)

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