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A whole-genome association approach for large-scale interspecies traits

Science China(Life Sciences) 2021年第8期64卷 1372-1374页

作者： Huizhong Fan Lei Chen Yibo Hu Guohui Shi Yi Dai fuwen wei Qi Wu Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China JUniversity of Chinese Academy of Sciences Beijing I0010IChina ANorthwestern Polytechnical University Xi'an 710129China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

Dear Editor,The genetic mechanism of large-scale interspecies traits,including evolutionary novelties and the characteristics of high taxa,is a central issue in evolutionary *** present,genome-wide association studies(GWAS)are known as one of the most powerful and affordable tools for understanding the association between heritable variations and phenotypic changes in populations of single ***,it would be interesting to determine whether GWAS can be applied to study large-scale interspecies traits.

关键词： scale evolutionary interspecies

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Ailuropoda melanoleuca (Giant Panda)

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TRENDS IN GENETICS 2020年第1期36卷 68-69页

作者： wei, fuwen Fan, Huizhong Hu, Yibo Chinese Acad Sci Inst Zool CAS Key Lab Anim Ecol & Conservat Biol Beijing Peoples R China Univ Chinese Acad Sci Beijing Peoples R China Chinese Acad Sci Ctr Excellence Anim Evolut & Genet Kunming Yunnan Peoples R China

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A single nucleotide mutation in the dual-oxidase 2(DUOX2) gene causes some of the panda's unique metabolic phenotypes

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National Science Review 2022年第2期9卷 34-42页

作者： Agata M.Rudolf Qi Wu Li Li Jun Wang Yi Huang Jacques Togo Christopher Liechti Min Li Chaoqun Niu Yonggang Nie fuwen wei John R.Speakman State Key Laboratory of Molecular Development Institute of Genetics and Developmental Biology Chinese Academy of Sciences Institute of Zoology Chinese Academy of Sciences Institute of Microbiology Chinese Academy of Sciences Institute of Biological and Environmental Sciences University of Aberdeen Centre of Excellence for Animal Ecology and Genetics Chinese Academy of Sciences Shenzhen Key Laboratory of Metabolic Health Center for Energy Metabolism and Reproduction Shenzhen Institute of Advanced Technology Chinese Academy of Sciences

The giant panda(Ailuropoda melanoleuca) is an iconic bear native to China,famous for eating almost exclusively *** unusual dietary behavior for a carnivore is enabled by several key adaptations including low physical activity,reduced organ sizes and hypothyroidism leading to lowered energy *** adaptive phenotypes have been hypothesized to arise from a panda-unique single-nucleotide mutation in the dual-oxidase 2(DUOX2) gene,involved in thyroid hormone *** test this hypothesis,we created genome-edited mice carrying the same point mutation as the panda and investigated its effect on metabolic *** mice were 27% smaller than heterozygous and wild-type ones,had 13 % lower body mass-adjusted food intake,5 5 % decreased physical activity,lower mass of kidneys(11%) and brain(5%),lower serum thyroxine(T4:36%),decreased absolute(12%) and mass-adjusted(5%) daily energy expenditure,and altered gut *** with T4 reversed the effects of the *** work uses a state-of-the-art genome editing approach to demonstrate the link between a single-nucleotide mutation in a key endocrine-related gene and profound adaptive changes in the metabolic phenotype,with great importance in ecology and evolution.

关键词： giant panda DUOX2 mutation metabolic rate thyroid hormones DUOX2 mice and microbiota

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Seasonal shift of the gut microbiome synchronizes host peripheral circadian rhythm for physiological adaptation to a low-fat diet in the giant panda

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CELL REPORTS 2022年第3期38卷 110203-110203页

作者： Huang, Guangping Wang, Le Li, Jian Hou, Rong Wang, Meng Wang, Zhilin Qu, Qingyue Zhou, Wenliang Nie, Yonggang Hu, Yibo Ma, Yingjie Yan, Li wei, Hong wei, fuwen Chinese Acad Sci Inst Zool CAS Key Lab Anim Ecol & Conservat Biol Beijing 100101 Peoples R China Southern Marine Sci & Engn Guangdong Lab Guangzho Ctr Evolut & Conservat Biol Guangzhou 511458 Peoples R China Third Mil Med Univ Inst Immunol Chongqing 400038 Peoples R China Chengdu Res Base Giant Panda Breeding Chengdu 610081 Peoples R China Chinese Acad Sci China Ctr Excellence Anim Evolut & Genet Kunming 650223 Yunnan Peoples R China Third Mil Med Univ Coll Basic Med Sci Dept Lab Anim Sci Chongqing 400038 Peoples R China Huazhong Agr Univ Coll Anim Sci & Technol State Key Lab Agr Microbiol Wuhan 430070 Peoples R China

Characteristics of the gut microbiome vary synchronously with changes in host diet. However, the underlying effects of these fluctuations remain unclear. Here, we performed fecal microbiota transplantation (FMT) of diet-specific feces from an endangered mammal (the giant panda) into a germ-free mouse model. We demonstrated that the butyrate-producing bacterium Clostridium butyricum was more abundant during shoot eating season than during the leaf-eating season, congruent with the significant increase in host body mass. Following season-specific FMT, the microbiota of the mouse model resembled that of the donor, and mice transplanted with the microbiota from the shoot-eating season grew faster and stored more fat. Mechanistic investigations revealed that butyrate extended the upregulation of hepatic circadian gene Per2, subsequently increasing phospholipid biosynthesis. Validation experiments further confirmed this causal relationship. This study demonstrated that seasonal shifts in the gut microbiome affect growth performance, facilitating a deeper understanding of host-microbe interactions in wild mammals.

关键词： multi-omics microbiome metabolism circadian rhythm host-microbe interaction fecal microbiota transplantation wild mammals physiological response fat accumulation low-fat diet

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Ailurus fulgens (Himalayan Red Panda) and Ailurus styani (Chinese Red Panda)

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TRENDS IN GENETICS 2020年第8期36卷 624-625页

作者： Hu, Yibo Thapa, Arjun wei, fuwen Chinese Acad Sci Inst Zool CAS Key Lab Anim Ecol & Conservat Biol Beijing Peoples R China Univ Chinese Acad Sci Beijing Peoples R China Chinese Acad Sci Ctr Excellence Anim Evolut & Genet Kunming Yunnan Peoples R China

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Diet drives convergent evolution of gut microbiomes in bamboo-eating species

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Science China(Life Sciences) 2021年第1期64卷 88-95页

作者： Guangping Huang Xiao Wang Yibo Hu Qi Wu Yonggang Nie Jiuhong Dong Yun Ding Li Yan fuwen wei CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing100101China University of Chinese Academy of Sciences Beijing100049China Beijing Milu Ecological Research Center Beijing100076China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming650223China State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing100101China

Gut microbiota plays a critical role in host physiology and *** coevolution between the host and its gut microbes facilitates animal adaptation to its specific ecological *** factors such as host diet and phylogeny modulate the structure and function of gut ***,the relative contribution of each factor in shaping the structure of gut microbiota remains *** giant(Ailuropoda melanoleuca)and red(Ailurus styani)pandas belong to different families of order *** have evolved as obligate bamboo-feeders and can be used as a model system for studying the gut microbiome convergent ***,we compare the structure and function of gut microbiota of the two pandas with their carnivorous relatives using 16S rRNA and metagenome *** found that both panda species share more similarities in their gut microbiota structure with each other than each species shares with its carnivorous *** indicates that the specialized herbivorous diet rather than host phylogeny is the dominant driver of gut microbiome convergence within *** analysis revealed that the symbiotic gut microbiota of both pandas possesses a high level of starch and sucrose metabolism and vitamin B12 *** findings suggest a diet-driven convergence of gut microbiomes and provide new insight into host-microbiota coevolution of these endangered species.

关键词： gut microbiome metagenome convergent evolution starch and sucrose metabolism vitamin B12 giant panda red panda

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Ecological civilization: China's effort to build a shared future for all life on Earth

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National Science Review 2021年第7期8卷 8-12页

作者： fuwen wei Shuhong Cui Ning Liu Jiang Chang Xiaoge Ping Tianxiao Ma Jing Xu Ronald R.Swaisgood Harvey Locke CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Center for Evolution and Conservation Biology Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Ministry of Ecology and Environment of the People's Republic of China Chinese Research Academy of Environmental Sciences Endangered Species Scientific Commission of the People's Republic of China San Diego Zoo Global Beyond the Aichi Targets Task Force IUCN World Commission on Protected Areas Yellowstone to Yukon Conservation Initiative

After hundreds of years of technological revolution and rapid development, humanity has reached a moment of crisis in its relationship with nature [1]. To find better solutions to address global challenges, holistic thinking is required to integrate environmental goals with human activities. Some of these approaches include sustainable development (SD), the planetary boundaries (PB) and, in China,ecological civilization (EC) based on the unity of nature and man (UNM)[2].

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Development of short-target primers for species identification in biological studies of Carnivora

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ECOLOGY AND EVOLUTION 2023年第5期13卷 e10135页

作者： Liu, Huiwen Wang, Dan Zhang, Chenglin Pu, Tianchun Xiong, Lijuan wei, fuwen Hu, Yibo Chinese Acad Sci Inst Zool CAS Key Lab Anim Ecol & Conservat Biol Beijing Peoples R China Univ Chinese Acad Sci Beijing Peoples R China Beijing Zoo Beijing Peoples R China Guizhou Normal Univ Sch Life Sci Guiyang Peoples R China

Noninvasive genetic sampling greatly facilitates studies on the genetics, ecology, and conservation of threatened species. Species identification is often a prerequisite for noninvasive sampling-based biological studies. Due to the low quantity and quality of genomic DNA from noninvasive samples, high-performance short-target PCR primers are necessary for DNA barcoding applications. The order Carnivora is characterized by an elusive habit and threatened status. In this study, we developed three pairs of short-target primers for identifying Carnivora species. The COI279 primer pair was suitable for samples with better DNA quality. The COI157a and COI157b primer pairs performed well for noninvasive samples and reduced the interference of nuclear mitochondrial pseudogenes (numts). COI157a could effectively identify samples from Felidae, Canidae, Viverridae, and Hyaenidae, while COI157b could be applied to samples from Ursidae, Ailuridae, Mustelidae, Procyonidae, and Herpestidae. These short-target primers will facilitate noninvasive biological studies and efforts to conserve Carnivora species.

关键词： Carnivora COI noninvasive sample species identification

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Symbiotic bacteria mediate volatile chemical signal synthesis in a large solitary mammal species

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ISME JOURNAL 2021年第7期15卷 2070-2080页

作者： Zhou, Wenliang Qi, Dunwu Swaisgood, Ronald R. Wang, Le Jin, Yipeng Wu, Qi wei, fuwen Nie, Yonggang Chinese Acad Sci Inst Zool Key Lab Anim Ecol & Conservat Biol Beijing 100101 Peoples R China Chengdu Res Base Giant Panda Breeding Chengdu 610081 Peoples R China San Diego Zoo Global Inst Conservat Res San Diego CA 92027 USA Univ Chinese Acad Sci Beijing 100049 Peoples R China China Agr Univ Coll Vet Med Beijing 100094 Peoples R China Chinese Acad Sci Ctr Excellence Anim Evolut & Genet Kunming 650223 Yunnan Peoples R China

Mammalian chemosignals-or scent marks-are characterized by astounding chemical diversity, reflecting both complex biochemical pathways that produce them and rich information exchange with conspecifics. The microbiome of scent glands was thought to play prominent role in the chemical signal synthesis, with diverse microbiota metabolizing glandular products to produce odorants that may be used as chemosignals. Here, we use gas chromatography-mass spectrometry and metagenomic shotgun sequencing to explore this phenomenon in the anogenital gland secretions (AGS) of the giant panda (Ailuropoda melanoleuca). We find that this gland contains a diverse community of fermentative bacteria with enzymes that support metabolic pathways (e.g., lipid degradation) for the productions of volatile odorants specialized for chemical communication. We found quantitative and qualitative differences in the microbiota between AGS and digestive tract, a finding which was mirrored by differences among chemical compounds that could be used for olfactory communication. Volatile chemical compounds were more diverse and abundant in AGS than fecal samples, and our evidence suggests that metabolic pathways have been specialized for the synthesis of chemosignals for communication. The panda's microbiome is rich with genes coding for enzymes that participate in the fermentation pathways producing chemical compounds commonly deployed in mammalian chemosignals. These findings illuminate the poorly understood phenomena involved in the role of symbiotic bacteria in the production of chemosignals.

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Genomic Signatures of Coevolution between Nonmodel Mammals and Parasitic Roundworms

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MOLECULAR BIOLOGY AND EVOLUTION 2021年第2期38卷 531-544页

作者： Hu, Yibo Yu, Lijun Fan, Huizhong Huang, Guangping Wu, Qi Nie, Yonggang Liu, Shuai Yan, Li wei, fuwen Chinese Acad Sci Inst Zool CAS Key Lab Anim Ecol & Conservat Biol Beijing Peoples R China Univ Chinese Acad Sci Beijing Peoples R China Chinese Acad Sci Ctr Excellence Anim Evolut & Genet Kunming Yunnan Peoples R China

Antagonistic coevolution between host and parasite drives species evolution. However, most of the studies only focus on parasitism adaptation and do not explore the coevolution mechanisms from the perspective of both host and parasite. Here, through the de novo sequencing and assembly of the genomes of giant panda roundworm, red panda roundworm, and lion roundworm parasitic on tiger, we investigated the genomic mechanisms of coevolution between nonmodel mammals and their parasitic roundworms and those of roundworm parasitism in general. The genome-wide phylogeny revealed that these parasitic roundworms have not phylogenetically coevolved with their hosts. The CTSZ and prolyl 4-hydroxylase subunit beta (P4HB) immunoregulatory proteins played a central role in protein interaction between mammals and parasitic roundworms. The gene tree comparison identified that seven pairs of interactive proteins had consistent phylogenetic topology, suggesting their coevolution during host-parasite interaction. These coevolutionary proteins were particularly relevant to immune response. In addition, we found that the roundworms of both pandas exhibited higher proportions of metallopeptidase genes, and some positively selected genes were highly related to their larvae's fast development. Our findings provide novel insights into the genetic mechanisms of coevolution between nonmodel mammals and parasites and offer the valuable genomic resources for scientific ascariasis prevention in both pandas.

关键词： coevolution comparative genomics parasitism pandas

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