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Comparative Skin Histology of Frogs Reveals High-elevation Adaptation of the Tibetan Nanorana parkeri

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Asian Herpetological Research 2019年第2期10卷 79-85页

作者： Chunhua YANG Tingting FU Xinqiang LAN Yun ZHANG Lotanna Micah NNEJI Robert W.MURPHY Yanbo SUN Jing CHE state key laboratory of genetic Resources and evolution Kunming Institute of ZoologyChinese Academy of Sciences650223 KunmingChina Institute of Physical Science and Information Technology Anhui University230601 HefeiChina Kunming College of Life Science University of Chinese Academy of SciencesKunming 650204China key laboratory of animal models and Human Disease Mechanisms The Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of Sciences650223 KunmingChina Centre for Biodiversity and Conservation Biology Royal Ontario Museum100 Queen’s ParkTorontoOnt.M5S 2C6Canada Center for Excellence in animal evolution and genetics Chinese Academy of Sciences650223 KunmingChina

Adaptations to extreme environmental conditions are intriguing. animal skin, which directly interacts with external environment, plays diverse and important roles in adaptive evolution. The thin and bare skin of amphibians is sensitive to external environmental conditions and, thus, it facilitates investigations into adaptations for living in extreme environments. Herein, we compare the structures of skin in four anuran species living at elevations ranging from 100 m to 4500 m to assess phenotypic innovations in the skin of Nanorana parkeri, which lives at extremely high elevations. Analyses reveal similar basic skin structures, but N. parkeri differs from the other species by having more epidermal capillaries and granular glands, which correlate highly with responses to hypoxia and/or ultraviolet(UV) radiation. Further intraspecific comparisons from frogs taken at ~4500 m and ~2900 m reveal that all of the changes are fixed. Changes occurring only in the higher elevation population, such as possessing more skin pigments, may represent local adaptations to coldness and/or UV radiation. These results provide a morphological basis for understanding further the molecular adaptations of these frogs.

关键词： Nanorana parkeri skin structure phenotypic innovation high-elevation adaptation

Dynamic expression of the LAP family of genes during early development of Xenopus tropicalis

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Science China(Life Sciences) 2011年第10期54卷 897-903页

作者： YANG QiuTan LV XiaoYan KONG QingHua LI ChaoCui ZHOU Qin MAO BingYu Core Facility of genetically Engineered Mice State Key Laboratory of Biotheropy West China Hospital Sichuan University Chengdu 610041 China CAS-Max Planck Junior Scientist Group State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China

The leucine-rich repeats and PDZ (LAP) family of genes are crucial for the maintenance of cell polarity as well as for epithelial homeostasis and tumor suppression in both vertebrates and *** members of this gene family are known:densin,erbin,scribble and ***,we identified the four members of the LAP gene family in Xenopus tropicalis and studied their expression patterns during embryonic *** Xenopus LAP proteins show a conserved domain structure that is similar to their homologs in other *** Xenopus embryos,these genes were detected in animal cap cells at the early gastrula *** later stages of development,they were widely expressed in epithelial tissues that are highly polar in nature,including the neural epithelia,optic and otic vesicles,and in the *** data suggest that the roles of the Xenopus LAP genes in the control of cell polarity and morphogenesis are conserved during early *** and lano show similar expression patterns in the developing head,suggesting potential functional interactions between the two molecules in vivo.

关键词： Xenopus tropicalis LAP gene family Densin Erbin Scrib Lano expression pattern

Characterization of tree shrew telomeres and telomerase

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Journal of genetics and Genomics 2021年第7期48卷 631-639页

作者： Jian Sun Wenjing Liu Yongbo Guo Hailin Zhang Dewei Jiang Ying Luo Rong Liu Ceshi Chen key laboratory of animal models and Human Disease Mechanisms of Chinese Academy of Sciences&Yunnan Province National Resource Center for Non-Human PrimatesKunming Primate Research CenterNational Research Facility for Phenotypic&Genetic Analysis of Model Animals(Primate Facility)Kunming Institute of ZoologyKunmingYunnan 650201China Kunming College of Life Sciences University of Chinese Academy SciencesKunmingYunnan 650204China state key laboratory of genetic Resources and evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China laboratory of Molecular genetics of Aging&Tumor Medical FacultyKunming University of Science and TechnologyKunmingYunnan 650500China

The use of tree shrews as experimental animals for biomedical research is a new *** recent studies suggest that tree shrews are suitable for studying cancers,including breast cancer,glioblastoma,lung cancer,and hepatocellular ***,the telomeres and the telomerase of tree shrews have not been studied to ***,we characterize telomeres and telomerase in tree *** telomere length of tree shrews is approximately 23 kb,which is longer than that of primates and shorter than that of mice,and it is extended in breast tumor tissues according to Southern blot and flow-fluorescence in situ hybridization(FISH)*** shrew spleen,bone marrow,testis,ovary,and uterus show high telomerase activities,which are increased in breast tumor tissues by telomeric repeat amplification protocol *** telomere length becomes shorter,and telomerase activity decreases with *** tree shrew TERT and TERC are more highly similar to primates than to *** findings lay a solid foundation for using tree shrews to study aging and cancers.

关键词： Tree shrews Telomere TERT TERC Breast cancer

Chromosomal level assembly and population sequencing of the Chinese tree shrew genome

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Zoological Research 2019年第6期40卷 506-521页

作者： Yu Fan Mao-Sen Ye Jin-Yan Zhang Ling Xu Dan-Dan Yu Tian-Le Gu Yu-Lin Yao Jia-Qi Chen Long-Bao Lv Ping Zheng Dong-Dong Wu Guo-Jie Zhang Yong-Gang Yao key laboratory of animal models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Center for Excellence in animal evolution and genetics Chinese Academy of SciencesKunming Yunnan 650223China Kunming College of Life Science University of Chinese Academy of SciencesKunming Yunnan 650204China Kunming Primate Research Center of the Chinese Academy of Sciences Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China KIZ–CUHK Joint laboratory of Bioresources and Molecular Research in Common Diseases Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China state key laboratory of genetic Resources and evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Yunnan key laboratory of animal Reproduction Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China

Chinese tree shrews (Tupaia belangeri chinensis) have become an increasingly important experimental animal in biomedical research due to their close relationship to primates. An accurately sequenced and assembled genome is essential for understanding the genetic features and biology of this animal. In this study, we used long-read single-molecule sequencing and high-throughput chromosome conformation capture (Hi-C) technology to obtain a high-qualitychromosome-scale scaffolding of the Chinese tree shrew genome. The new reference genome (KIZ version 2: TS_2.0) resolved problems in presently available tree shrew genomes and enabled accurate identification of large and complex repeat regions, gene structures, and species-specific genomic structural variants. In addition, by sequencing the genomes of six Chinese tree shrew individuals, we produced a comprehensive map of 12.8 M single nucleotide polymorphisms and confirmed that the major histocompatibility complex (MHC) loci and immunoglobulin gene family exhibited high nucleotide diversity in the tree shrew genome. We updated the tree shrew genome database (TreeshrewDB v2.0: http://***) to include the genome annotation information and genetic variations. The new high-quality reference genome of the Chinese tree shrew and the updated TreeshrewDB will facilitate the use of this animal in many different fields of research.

关键词： Tupaia belangeri Chromosomal level assembly genome Population sequencing Database

The distinct morphological phenotypes of Southeast Asian aborigines are shaped by novel mechanisms for adaptation to tropical rainforests

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National Science Review 2022年第3期9卷 85-95页

作者： Xiaoming Zhang Qi Liu Hui Zhang Shilei Zhao Jiahui Huang Tuot Sovannary Long Bunnath Hong Seang Aun Ham Samnom Bing Su Hua Chen state key laboratory of genetic Resources and evolution Kunming Institute of Zoology Chinese Academy of Sciences Center for Excellence in animal evolution and genetics Chinese Academy of Sciences CAS key laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences China National Center for Bioinformation School of Future Technology and Sino-Danish College University of Chinese Academy of Sciences Kunming College of Life Science University of Chinese Academy of Sciences Department of Geography and Land Management Royal University of Phnom Penh Capacity Development Facilitator for Handicap International Federation and Freelance Research

Southeast Asian aborigines, the hunter-gatherer populations living in tropical rainforests, exhibit distinct morphological phenotypes, including short stature, dark skin, curly hair and a wide and snub nose. The underlying genetic architecture and evolutionary mechanism of these phenotypes remain a long-term mystery. We conducted whole genome deep sequencing of 81 Cambodian aborigines from eight ethnic groups. Through a genome-wide scan of selective sweeps, we discovered key genes harboring Cambodian-enriched mutations that may contribute to their phenotypes, including two hair morphogenesis genes(TCHH and TCHHL1), one nasal morphology gene(PAX3) and a set of genes(such as ENTPD1-AS1) associated with short stature. The identified new genes and novel mutations suggest an independent origin of the distinct phenotypes in Cambodian aborigines through parallel evolution, refuting the long-standing argument on the common ancestry of these phenotypes among the worldwide rainforest hunter-gatherers. Notably, our discovery reveals that various types of molecular mechanisms, including antisense transcription and epigenetic regulation, contribute to human morphogenesis, providing novel insights into the genetics of human environmental adaptation.

关键词： Cambodian aborigines genomic polymorphism positive selection parallel evolution environmental adaptation morphogenesis

Rapid evolution of the Mammalian HILS1 Gene and the Nuclear Condensation Process during Mammalian Spermiogenesis

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Journal of genetics and Genomics 2013年第1期40卷 55-59页

作者： Yanhua Su Dongdong Wu Weiping Zhou David M.Irwin Yaping Zhang laboratory for Conservation and Utilization of Bio-Resources & key laboratory for Microbial Resources of the Ministry of Education Yunnan University state key laboratory of genetic Resources and evolution Kunming Institute of ZoologyChinese Academy of Sciences Department of laboratory Medicine and Pathobiology University of Toronto Banting and Best Diabetes Centre University of Toronto

Many genes associated with reproduction show rapid evolution across diverse animal groups, a result commonly due to adaptive evolution driven by positive selection （Swanson and Vacquier, 2002）. Different theories have been proposed to explain the elevated rates of evolution （Swanson and Vacquier, 2002）, including sperm competition, where sperm compete to fertilize eggs leading to the proteins in the sper- matozoa adaptively evolving to increase their ability to fertilize eggs; sexual conflict, where the egg experiences a loss of fitness when sperm are too abundant; sexual selection, where eggs bind sperm carrying adaptive alleles （Palumbi, 1999）; and cryptic female choice （reviewed in Swanson and Vacquier, 2002）.

关键词： Rapid evolution of the Mammalian HILS1 Gene and the Nuclear Condensation Process during Mammalian Spermiogenesis HILS gene

The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks

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Zoological Research 2021年第6期42卷 834-844页

作者： Min-Sheng Peng Jian-Bo Li Zheng-Fei Cai Hang Liu Xiaolu Tang Ruochen Ying Jia-Nan Zhang Jia-Jun Tao Ting-Ting Yin Tao Zhang Jing-Yang Hu Ru-Nian Wu Zhong-Yin Zhou Zhi-Gang Zhang Li Yu Yong-Gang Yao Zheng-Li Shi Xue-Mei Lu Jian Lu Ya-Ping Zhang state key laboratory of genetic Resources and evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650201China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China KIZ/CUHK Joint laboratory of Bioresources and Molecular Research in Common Diseases Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650201China state key laboratory for Conservation and Utilization of Bio-resources in Yunnan Yunnan UniversityKunmingYunnan 650091China state key laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing 100871China Molbreeding Biotechnology Co. Ltd.ShijiazhuangHebei 050035China key laboratory of animal models and Human Disease Mechanisms of the Chinese Academy of Sciences&Yunnan Province Kunming Institute of ZoologyKunmingYunnan 650201China CAS key laboratory of Special Pathogens and Biosafety Wuhan Institute of VirologyChinese Academy of SciencesWuhanHubei 430071China Center for Excellence in animal evolution and genetics Chinese Academy of SciencesKunmingYunnan 650201China

Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks.A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses(SC2r-CoVs).Here,we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species,and detected positive signals in muscles of four Manis javanica and,for the first time,one *** analysis of pangolin mitochondrial DNA traced their origins from Southeast *** in-solution hybridization capture sequencing,we assembled a partial pangolin SC2r-CoV(pangolin-CoV)genome sequence of 22895 bp(MP20)from the *** *** analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in *** seized by Guangxi Customs.A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was *** analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously *** the potential infectivity of pangolin-CoVs,the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.

关键词： SARS-CoV-2 Pangolin Recombination Diversity Sequencing mtDNA

Molecular mechanisms of adaptive evolution in wild animals and plants

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Science China(Life Sciences) 2023年第3期66卷 453-495页

作者： Yibo Hu Xiaoping Wang Yongchao Xu Hui Yang Zeyu Tong Ran Tian Shaohua Xu Li Yu Yalong Guo Peng Shi Shuangquan Huang Guang Yang Suhua Shi Fuwen Wei CAS key Lab of animal Ecology and Conservation Biology Chinese Academy of SciencesBeijing 100101China state key laboratory for Conservation and Utilization of Bio-Resources in Yunnan School of Life SciencesYunnan UniversityKunming 650091China state key laboratory of Systematic and evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China state key laboratory of genetic Resources and evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming 650201China Institute of evolution and Ecology School of Life SciencesCentral China Normal UniversityWuhan 430079China College of Life Sciences Nanjing Normal UniversityNanjing 210023China state key laboratory of Biocontrol Guangdong Key Lab of Plant ResourcesSchool of Life SciencesSun Yat-sen University Southern Marine Science and Engineering Guangdong laboratory(Guangzhou) Guangzhou 511458China

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution,an important strategy for species survival and *** the molecular mechanisms of adaptive evolution is the key to understanding species diversification,phenotypic convergence,and inter-species *** the genome sequences of more and more non-model organisms are becoming available,the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide *** this study,we reviewed the latest research advances in wild animals and plants,focusing on adaptive traits,convergent evolution,and ***,we focused on the adaptive evolution of morphological,behavioral,and physiological ***,we reviewed the phenotypic convergences of life history traits and responding to environmental pressures,and the underlying molecular convergence ***,we summarized the advances of coevolution,including the four main types:mutualism,parasitism,predation and ***,these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction,demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics ***,we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.

关键词： adaptive evolution adaptive trait coevolution comparative genomics convergent evolution genetic convergence molecular mechanism mutualism parasitism phenotype convergence

Phylogenetic relationships of the zokor genus Eospalax(Mammalia,Rodentia,Spalacidae)inferred from whole-genome analyses,with description of a new species endemic to Hengduan Mountains

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Zoological Research 2022年第3期43卷 331-342页

作者： Tao Zhang Meng-Long Lei Hao Zhou Zhong-Zheng Chen Peng Shi state key laboratory of genetic Resources and evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650204China Jiangsu key laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences Soochow UniversitySuzhouJiangsu 215123China Joint laboratory of animal models for Human Diseases and Drug Development Soochow University and Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education School of Ecology and EnvironmentAnhui Normal UniversityWuhuAnhui 241000China School of Future Technology University of Chinese Academy of SciencesBeijing 100049China Center for Excellence in animal evolution and genetics Chinese Academy of SciencesKunmingYunnan 650223China

Zokors in the genus Eospalax,which are endemic to northern and western China,are subterranean rodents that inhabit various niches,including grasslands,high-altitude meadows,forests,and *** species in Eospalax were described a century ago but their taxonomy and phylogeny remain *** this study,we performed high-depth whole-genome sequencing of 47 zokor samples,comprising all six previously described *** analyses revealed a reliable and robust phylogeny of Eospalax and supported the validity of the six named *** to the inferred phylogenetic relationships,Eospalax first divergent into two clades in the early Pliocene(ca.4.68 million years ago(Ma)),one inhabiting the highaltitude Qinghai-Xizang(Tibet)Plateau(QTP)and adjacent regions,and the another inhabiting the lowaltitude Loess Plateau and Qinling-Daba *** most recent divergences occurred between *** and *** and between *** and *** in the late Pliocene(ca.2.09 and 2.19 Ma,respectively).We also collected specimens of zokors in the southern Hengduan Mountains(Muli County,Sichuan Province),far from the known distributions of all other *** and molecular analyses strongly suggested that the specimens represent a new species,formally described here as Eospalax muliensis *** new species belongs to the high-altitude clade and diverged from closely related species(ca.4.22 Ma)shortly after the first divergence in ***,Eospalax muliensis *** more supposedly plesiomorphic characters,suggesting a possible origin of the genus in the Hengduan Mountains.

关键词： Zokor Eospalax Phylogenomic analyses New species Hengduan Mountains