Evaluating the genetic status of threatened species is an essential task in conservation genetics.However,the genetic status of threatened species has been mostly evaluated through techniques that fail to estimate gen...Evaluating the genetic status of threatened species is an essential task in conservation genetics.However,the genetic status of threatened species has been mostly evaluated through techniques that fail to estimate genetic diversity at the whole genomic level.Next generation sequencing can meet this demand,but high quality samples such as blood or muscle tissues are required.However,it is difficult to collect such samples from threatened species because sampling work may impact their health.Therefore,it is essential to design a workflow to evaluate the whole genomic status of threatened species using non-destructive sampling.Even though non-destructive sampling has been used in traditional barcoding technique,the barcoding technique cannot evaluate the whole genomic status.Brown Eared Pheasant(Crossoptilon mantchuricum)is an endangered species,with captive populations maintained in Taiyuan Zoo,China,and Europe.However,the genetic diversity,inbreeding pattern,and mutation load of these two populations are unclear.To uncover the genetic status of these two captive populations,we applied 2b-RAD technology to evaluate the genomic status of these populations using feathers as samples.The feathers could be collected by non-destructive sampling.The results indicate that the Taiyuan Zoo population has a lower genetic diversity and higher inbreeding coefficient than the European population.The Taiyuan Zoo population has lethal mutations when homozygous.The current project uses a non-destructive sampling technique to evaluate the whole genomic status of the two captive populations,providing a paradigm for conservation genetics,which will facilitate the development of conservation biology.展开更多
Pancreatic ductal adenocarcinoma(PDAC)is a highly malignant cancer of the digestive system common among humans.However,it is rarely reported in wild animals.In 2018,a giant panda died in the Beijing Zoo.During subsequ...Pancreatic ductal adenocarcinoma(PDAC)is a highly malignant cancer of the digestive system common among humans.However,it is rarely reported in wild animals.In 2018,a giant panda died in the Beijing Zoo.During subsequent histological observation of the pancreas,it was discovered that the glandular epithelial cells had lost the pancreatic acinar structure,tubular areas with obvious structure in the pancreas,and the ductal epithelium was substituted by high columnar mucus cells.Masson staining showed that there were several fibrous tissue proliferative reactions around the ductal adenocarcinoma and immunohistochemical staining revealed that CK7 and CK19 were positively expressed in the pancreatic tissue.Therefore,the pathological diagnosis indicated that the panda had PDAC.In this paper,the panda’s living conditions and pathological diagnosis results are examined,with the aim of providing a reference point for the future diagnosis of wild animal tumors.展开更多
Gibbons are small,arboreal apes that play a critical role in tropical biodiversity and ecosystem ecology.However,nearly all species of gibbons are threatened by habitat loss,illegal trade,hunting,and other human activ...Gibbons are small,arboreal apes that play a critical role in tropical biodiversity and ecosystem ecology.However,nearly all species of gibbons are threatened by habitat loss,illegal trade,hunting,and other human activities.Long-term poor understanding of their genetics and evolution undermines effective conservation efforts.In this study,we analyse comparative population genomic data of four Nomascus species.Our results reveal strong genetic differentiation and gene flow among Nomascus species.Additionally,we identify genomic features that are potentially related to natural selection linked to vocalization,fructose metabolism,motor balance,and body size,consistent with the unique phenotype and adaptability of gibbons.Inbreeding,coupled with population declines due to climate change and historical human activities,leads to reduced genetic diversity and the accumulation of deleterious variations that likely affect cardiovascular disease and the reproductive potential of gibbons and further reduce their fitness,highlighting the urgent need for effective conservation strategies.展开更多
The emergence of multidrug resistance(MDR)in Proteus mirabilis clinical isolates is a growing public health concern and has serious implications for wildlife.What is the role of wildlife has been become one of the hot...The emergence of multidrug resistance(MDR)in Proteus mirabilis clinical isolates is a growing public health concern and has serious implications for wildlife.What is the role of wildlife has been become one of the hot issues in disseminating antimicrobial resistance.Here,54 P.mirabilis isolates from 12 different species were identified.Among them,25 isolates were determined to be MDR by profile of antimicrobial susceptibility;10 MDR P.mirabilis isolates were subjected to comparative genomic analysis by whole genome sequencing.Comprehensive analysis showed that chromosome of P.mirabilis isolates mainly carries multidrug-resistance complex elements harboring resistance to carbapenem genes blaOXA-1,blaNDM-1,and blaTEM-1.Class I integron is the insertion hotspot of IS26;it can be inserted into type I integron at different sites,thus forming a variety of multiple drug resistance decision sites.At the same time,Tn21,Tn7,and SXT/R391 mobile elements cause widespread spread of these drug resistance genes.In conclusion,P.mirabilis isolates from wildlife showed higher resistance to commonly used clinic drugs comparing to those from human.Therefore,wild animals carrying MDR clinical isolates should be paid attention to by the public health.展开更多
Analysis of the intestinal microbiota and physiological parameters in mammalian infancy can reveal health status.In this study,we used a combination of molecular and immunochemical approaches to assess fecal microbiot...Analysis of the intestinal microbiota and physiological parameters in mammalian infancy can reveal health status.In this study,we used a combination of molecular and immunochemical approaches to assess fecal microbiota as well as Cortisol(Cor),Triiodothyronine(T3),and immunoglobulin A(IgA)levels of young forest musk deer(FMD),from birth to one month after weaning(7 days of age–110 days of age).During development as the diet of FMD changes from consuming milk to eating plants,the richness and diversity of intestinal microbiota of young FMD increased significantly.Cor levels remained unchanged throughout early development while significantly increased after weaning,T3 and IgA initially were derived from milk during lactation,significantly decreased after weaning.Correlation network analysis showed that the community of food-oriented microbes were highly structured and that many genera were correlated.Overall,this study provides scientific insights into effective management strategies for the protection of FMD population.展开更多
Potential zoonotic pathogens may be transmitted from wildlife to humans through the illegal wild meat trade,which has become a pressing issue.However,research on the antimicrobial resistance genes(ARGs)of Malayan pang...Potential zoonotic pathogens may be transmitted from wildlife to humans through the illegal wild meat trade,which has become a pressing issue.However,research on the antimicrobial resistance genes(ARGs)of Malayan pangolin(Manis javanica)intestinal bacteria is limited.Here,multidrug-resistant Escherichia coli M172-1(ST354)isolated from Malayan pangolin feces in 2019 was found to be resistant to 13 antibiotics.BGWAS analysis revealed 4 plas-mids,namely,pM172-1.1,pM172-1.2,pM172-1.3,and pM172-1.4,in the isolate.The pM172-1.2,pM172-1.3,and pM172-1.4 plasmids carried ARGs,namely,IncHI2-HI2A,IncX1-X1,and IncX1,respectively.pM172-1.3 and pM172-1.4 contained intact IntI1 integrons(Is26/IntI1/arr2/cmlA5/blaOXA-10/ant(3′′)-IIA/dfrA14/Is26).No-tably,pM172-1.3 resulted from the fusion of 2 pM172-1.4 copies and carried many more ARGs.In addition to pM172-1.3 from the same host,other drug-resistant bacteria(E.coli M159-1(ST48),E.coli S171-1(ST206),and Klebsiella pneumoniae S174-1(ST2354))in the same Malayan pangolin fecal samples also carried 3 plasmids with 100%gene coverage of pM172-1.4 and 99.98%identity.Therefore,ARGs in IncX1 might spread in the intestinalflora of Malayan pangolin and between species via the illegal food chain,posing a potential threat to public health and safety.展开更多
Sheep were domesticated in the Fertile Crescent and then spread globally,where they have been encountering various environmental conditions.The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau ...Sheep were domesticated in the Fertile Crescent and then spread globally,where they have been encountering various environmental conditions.The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years.To explore genomic variants associated with high-altitude adaptation in Tibetan sheep,we analyzed Illumina short-reads of 994 whole genomes representing∼60 sheep breeds/populations at varied altitudes,PacBio High fidelity(HiFi)reads of 13 breeds,and 96 transcriptomes from 12 sheep organs.Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation.Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associatedβ-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds.The haplotype A carried two homologous gene clusters:(1)HBE1,HBE2,HBB-like,and HBBC,and(2)HBE1-like,HBE2-like,HBB-like,and HBB;while the haplotype B lacked the first cluster.The high-altitude sheep showed highly frequent or nearly fixed haplotype A,while the low-altitude sheep dominated by haplotype B.We further demonstrated that sheep with haplotype A had an increased hemoglobin–O_(2)affinity compared with those carrying haplotype B.Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep.Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.展开更多
基金funded by the National Natural Science Foundation of China(Grant No.31872244 to Z.Z.)Priority Academic Program Development of Jiangsu Higher Education Institutions,Beijing Zoo Management Office(No.zx2019016 to J.Z.)the Biodiversity Survey,Monitoring and Assessment Project(2019-2023)of the Ministry of Ecology and Environment,China(No.2019HB2096001006 to Z.Z.)。
文摘Evaluating the genetic status of threatened species is an essential task in conservation genetics.However,the genetic status of threatened species has been mostly evaluated through techniques that fail to estimate genetic diversity at the whole genomic level.Next generation sequencing can meet this demand,but high quality samples such as blood or muscle tissues are required.However,it is difficult to collect such samples from threatened species because sampling work may impact their health.Therefore,it is essential to design a workflow to evaluate the whole genomic status of threatened species using non-destructive sampling.Even though non-destructive sampling has been used in traditional barcoding technique,the barcoding technique cannot evaluate the whole genomic status.Brown Eared Pheasant(Crossoptilon mantchuricum)is an endangered species,with captive populations maintained in Taiyuan Zoo,China,and Europe.However,the genetic diversity,inbreeding pattern,and mutation load of these two populations are unclear.To uncover the genetic status of these two captive populations,we applied 2b-RAD technology to evaluate the genomic status of these populations using feathers as samples.The feathers could be collected by non-destructive sampling.The results indicate that the Taiyuan Zoo population has a lower genetic diversity and higher inbreeding coefficient than the European population.The Taiyuan Zoo population has lethal mutations when homozygous.The current project uses a non-destructive sampling technique to evaluate the whole genomic status of the two captive populations,providing a paradigm for conservation genetics,which will facilitate the development of conservation biology.
基金Technology project of Beijing municipal administration center of parksGrant/Award Number:zx2021019。
文摘Pancreatic ductal adenocarcinoma(PDAC)is a highly malignant cancer of the digestive system common among humans.However,it is rarely reported in wild animals.In 2018,a giant panda died in the Beijing Zoo.During subsequent histological observation of the pancreas,it was discovered that the glandular epithelial cells had lost the pancreatic acinar structure,tubular areas with obvious structure in the pancreas,and the ductal epithelium was substituted by high columnar mucus cells.Masson staining showed that there were several fibrous tissue proliferative reactions around the ductal adenocarcinoma and immunohistochemical staining revealed that CK7 and CK19 were positively expressed in the pancreatic tissue.Therefore,the pathological diagnosis indicated that the panda had PDAC.In this paper,the panda’s living conditions and pathological diagnosis results are examined,with the aim of providing a reference point for the future diagnosis of wild animal tumors.
基金supported by Science and Technology Program from the Forestry Administration of Guangdong Province(2024KJQT0012)the Guangdong Provincial Key R&D Program(2022B1111040001)+2 种基金the National Forestry Administration rare and endangered species field rescue and breeding project(Gui lin hu yu O10)the National Natural Science Foundation of China(32200337)a fellowship from the China Postdoctoral Science Foundation(2022M712003).
文摘Gibbons are small,arboreal apes that play a critical role in tropical biodiversity and ecosystem ecology.However,nearly all species of gibbons are threatened by habitat loss,illegal trade,hunting,and other human activities.Long-term poor understanding of their genetics and evolution undermines effective conservation efforts.In this study,we analyse comparative population genomic data of four Nomascus species.Our results reveal strong genetic differentiation and gene flow among Nomascus species.Additionally,we identify genomic features that are potentially related to natural selection linked to vocalization,fructose metabolism,motor balance,and body size,consistent with the unique phenotype and adaptability of gibbons.Inbreeding,coupled with population declines due to climate change and historical human activities,leads to reduced genetic diversity and the accumulation of deleterious variations that likely affect cardiovascular disease and the reproductive potential of gibbons and further reduce their fitness,highlighting the urgent need for effective conservation strategies.
基金This study was supported by the Introduction of Leading Talents Program of Guangdong Academy of Sciences(No.2016GDASRC-0205)GDAS Special Project of Science and Technology Development(No.2018GDASCX-0107)Earmarked Fund for Hebei Dairy Cattle Innovation Team of Modern Agro-industry Technology Research System(No.HBCT2018120205).
文摘The emergence of multidrug resistance(MDR)in Proteus mirabilis clinical isolates is a growing public health concern and has serious implications for wildlife.What is the role of wildlife has been become one of the hot issues in disseminating antimicrobial resistance.Here,54 P.mirabilis isolates from 12 different species were identified.Among them,25 isolates were determined to be MDR by profile of antimicrobial susceptibility;10 MDR P.mirabilis isolates were subjected to comparative genomic analysis by whole genome sequencing.Comprehensive analysis showed that chromosome of P.mirabilis isolates mainly carries multidrug-resistance complex elements harboring resistance to carbapenem genes blaOXA-1,blaNDM-1,and blaTEM-1.Class I integron is the insertion hotspot of IS26;it can be inserted into type I integron at different sites,thus forming a variety of multiple drug resistance decision sites.At the same time,Tn21,Tn7,and SXT/R391 mobile elements cause widespread spread of these drug resistance genes.In conclusion,P.mirabilis isolates from wildlife showed higher resistance to commonly used clinic drugs comparing to those from human.Therefore,wild animals carrying MDR clinical isolates should be paid attention to by the public health.
基金This work was supported by the National Key R&D program of China(2018YFD0502204)the National Natural Science Foundation of China(31872962).
文摘Analysis of the intestinal microbiota and physiological parameters in mammalian infancy can reveal health status.In this study,we used a combination of molecular and immunochemical approaches to assess fecal microbiota as well as Cortisol(Cor),Triiodothyronine(T3),and immunoglobulin A(IgA)levels of young forest musk deer(FMD),from birth to one month after weaning(7 days of age–110 days of age).During development as the diet of FMD changes from consuming milk to eating plants,the richness and diversity of intestinal microbiota of young FMD increased significantly.Cor levels remained unchanged throughout early development while significantly increased after weaning,T3 and IgA initially were derived from milk during lactation,significantly decreased after weaning.Correlation network analysis showed that the community of food-oriented microbes were highly structured and that many genera were correlated.Overall,this study provides scientific insights into effective management strategies for the protection of FMD population.
基金supported by the Introduction of Leading Talents Program of the Guangdong Academy of Sciences(No.2016GDASRC-0205)the Open project of Beijing Key Laboratory of captive wildlife technology in Beijing Zoo(ZDK202105).
文摘Potential zoonotic pathogens may be transmitted from wildlife to humans through the illegal wild meat trade,which has become a pressing issue.However,research on the antimicrobial resistance genes(ARGs)of Malayan pangolin(Manis javanica)intestinal bacteria is limited.Here,multidrug-resistant Escherichia coli M172-1(ST354)isolated from Malayan pangolin feces in 2019 was found to be resistant to 13 antibiotics.BGWAS analysis revealed 4 plas-mids,namely,pM172-1.1,pM172-1.2,pM172-1.3,and pM172-1.4,in the isolate.The pM172-1.2,pM172-1.3,and pM172-1.4 plasmids carried ARGs,namely,IncHI2-HI2A,IncX1-X1,and IncX1,respectively.pM172-1.3 and pM172-1.4 contained intact IntI1 integrons(Is26/IntI1/arr2/cmlA5/blaOXA-10/ant(3′′)-IIA/dfrA14/Is26).No-tably,pM172-1.3 resulted from the fusion of 2 pM172-1.4 copies and carried many more ARGs.In addition to pM172-1.3 from the same host,other drug-resistant bacteria(E.coli M159-1(ST48),E.coli S171-1(ST206),and Klebsiella pneumoniae S174-1(ST2354))in the same Malayan pangolin fecal samples also carried 3 plasmids with 100%gene coverage of pM172-1.4 and 99.98%identity.Therefore,ARGs in IncX1 might spread in the intestinalflora of Malayan pangolin and between species via the illegal food chain,posing a potential threat to public health and safety.
基金supported by the Tibetan R&D Program,China(Grant No.XZ202101ZD0001N)the China Agriculture Research System(Grant No.CARS-39)the National Natural Science Foundation of China(Grant Nos.31900313,32161143010,and 31972526).
文摘Sheep were domesticated in the Fertile Crescent and then spread globally,where they have been encountering various environmental conditions.The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years.To explore genomic variants associated with high-altitude adaptation in Tibetan sheep,we analyzed Illumina short-reads of 994 whole genomes representing∼60 sheep breeds/populations at varied altitudes,PacBio High fidelity(HiFi)reads of 13 breeds,and 96 transcriptomes from 12 sheep organs.Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation.Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associatedβ-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds.The haplotype A carried two homologous gene clusters:(1)HBE1,HBE2,HBB-like,and HBBC,and(2)HBE1-like,HBE2-like,HBB-like,and HBB;while the haplotype B lacked the first cluster.The high-altitude sheep showed highly frequent or nearly fixed haplotype A,while the low-altitude sheep dominated by haplotype B.We further demonstrated that sheep with haplotype A had an increased hemoglobin–O_(2)affinity compared with those carrying haplotype B.Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep.Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.
