Understanding how species diverge and adapt is fundamental to unraveling biodiversity.While environmental impacts on species evolution are well-documented,the roles of intrinsic life-history traits remain underexplore...Understanding how species diverge and adapt is fundamental to unraveling biodiversity.While environmental impacts on species evolution are well-documented,the roles of intrinsic life-history traits remain underexplored.The Qinghai-Xizang Plateau,with its harsh conditions and unique biodiversity,offers a natural laboratory for such investigations.Here,we examine two sympatric small mammals—the solitary,low-dispersal plateau zokor(Eospalax baileyi)and the social,high-dispersal plateau pika(Ochotona curzoniae)—to elucidate how life-history traits shape population structures and adaptive strategies.Through whole-genome sequencing and cardiac-blood phenotype analyses,we reveal striking differences in their evolutionary trajectories.Despite enduring similar environmental pressures,plateau zokor populations exhibit pronounced genetic subdivisions,high inbreeding,and distinct local adaptations.In contrast,plateau pika populations display genetic panmixia,widespread diversity,and adaptive uniformity.Demographic inference highlights that plateau zokors experienced severe population bottlenecks and restricted gene flow during glacial periods,underscoring the impact of dispersal capacity on evolutionary outcomes.Our findings demonstrate that intrinsic biological traits,particularly dispersal ability,fundamentally influence genetic architecture,population connectivity,and local adaptation.This study not only provides empirical evidence of how life-history traits shape evolutionary dynamics but also offers a framework for integrating intrinsic and extrinsic factors in understanding biodiversity formation.展开更多
The mound-making behavior of plateau zokors is one of the most important factors in remodeling meadow microtopography and causing soil erosion in the Yellow River source area of western China,but little is known about...The mound-making behavior of plateau zokors is one of the most important factors in remodeling meadow microtopography and causing soil erosion in the Yellow River source area of western China,but little is known about the effects of microtopography on particle size characteristics(PSC)of eroded sediments from the bare slopes of zokor mounds during different rainfall events.In this study,we analyzed the relationship of microtopographic features derived from laser point cloud data and PSC of eroded sediments at six simulated rainfall intensities(all lasting 60 min).The effects of microtopography on PSC of eroded sediments were studied via partial least squares regression(PLSR)and structural equation modeling(SEM).The results showed that:(1)15-20 minutes from the beginning of rainfall was the sensitive period of soil loss from the slopes,and the function relationship between the rate of sediment and runoff and rainfall intensity can better predict the development trend of soil erosion;(2)Intense erosion occurred mainly in the upper half of the zokor mound,while deposition was mainly limited to its lower half.It is suggested that diminished plateau zokor activity intensity can effectively prevent and control soil erosion;(3)The PSC of eroded sediment is dominated by silt,followed by sand,with clay being the least abundant,and the eroded sediments with a particle size of 10-20μm were sensitive and highly susceptible to rainfall erosion.This finding facilitates the understanding of the formation process of surface geomorphology and the mechanism of soil erosion;(4)The PLSR model indicates that microtopography has an extensive influence on eroded sediments during hydraulic erosion,and the SEM analysis results further confirm that the fractal dimension was the best parameter to represent the PSC of eroded sediments,whereas surface cutting degree was the dominant factor controlling the PSC of eroded sediments.These findings are crucial for predicting soil erosion in the Yellow River source area and provide a new perspective for understanding soil erosion mechanisms in alpine meadow ecosystems.展开更多
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 farmlands.Six species in Eospala...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 farmlands.Six species in Eospalax were described a century ago but their taxonomy and phylogeny remain controversial.In this study,we performed high-depth whole-genome sequencing of 47 zokor samples,comprising all six previously described species.Genomic analyses revealed a reliable and robust phylogeny of Eospalax and supported the validity of the six named species.According 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 Mountains.The most recent divergences occurred between E.baileyi and E.smithii and between E.rufescens and E.rothschildi 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 zokors.Morphological and molecular analyses strongly suggested that the specimens represent a new species,formally described here as Eospalax muliensis sp.nov.The 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.Interestingly,Eospalax muliensis sp.nov.possesses more supposedly plesiomorphic characters,suggesting a possible origin of the genus in the Hengduan Mountains.展开更多
Mounds constructed by plateau zokors,which is widely distributed in alpine meadows significantly modified plant community structure.However,the variations of plant community structure under the disturbance of plateau ...Mounds constructed by plateau zokors,which is widely distributed in alpine meadows significantly modified plant community structure.However,the variations of plant community structure under the disturbance of plateau zokor-made mound are less concerned.Therefore,we investigated the responses of plant community on zokor-made mound of different years(1 a and 3-4 a),and compared with undisturbed sites(no mound)in an alpine meadow in the eastern Qinghai-Tibetan Plateau(QTP),China.Species richness,coverage and Simpson diversity index were all significantly reduced by the presence of zokor-made mound,but plant heights were significantly increased,particularly in grasses and sedges.Several perennial forage species showed an increased importance value and niche breadth,including Koeleria macrantha,Elymus nutans and Poa pratensis.The effect of zokor-made mound on niche overlap showed that more intense interspecific competition produced a greater utilization of environmental resources.And this interspecific niche overlap was strengthened as succession progressed.The bare mound created by zokor burrowing activities provided a colonizing opportunity for non-dominant forage species,resulting in abundant plant species and plant diversity during the succession period.We concluded that presence of zokor-made mound was conducive to regeneration and vitality of plant community in alpine meadows,thus improving their resilience to anthropogenic stress.展开更多
Plateau zokor(Eospalax baileyi)is a subterranean rodent and seasonal breeder.During the non-breeding season,the testicles regress,leading to the arrest of spermatogenesis and loss of fertility.The identification of th...Plateau zokor(Eospalax baileyi)is a subterranean rodent and seasonal breeder.During the non-breeding season,the testicles regress,leading to the arrest of spermatogenesis and loss of fertility.The identification of the specific germ cell type at which spermatogenesis is arrested,as well as potential regulatory factors during the non-breeding season,is important for understanding seasonal spermatogenesis in subterranean species.This study analyzed genes in spermatocytes of plateau zokor by referring to single-cell RNA results in mice.We discovered that spermatogenesis is arrested at the spermatocyte during the non-breeding season,which was corroborated via immunofluorescence staining results.The analysis of gene expression during different stages of meiotic prophase I has revealed that germ cell development may be arrested,starting from zygonema,during the non-breeding season.Meanwhile,we discovered that the apoptosis genes were up-regulated,leading to apoptosis in spermatocytes.To confirm that the germ cell differentiation was blocked during the non-breeding season due to a decrease in the androgen level,we used androgen receptor antagonist(flutamide)to intervene in the breeding season and found that the inner diameter of the seminiferous tubules was significantly reduced,spermatogenesis was arrested,and spermatocytes underwent apoptosis.This study revealed that spermatocytes are the terminal of germ cell differentiation in plateau zokor during the non-breeding season and that the arrest of differentiation is attributed to a decline in androgen levels.Our results complement the theoretical basis of seasonal reproduction in plateau zokor.展开更多
The Gansu zokor(Eospalax cansus),a subterranean rodent endemic to the Loess Plateau of China,exhibits remarkable adaptability to hypoxic environments.While gut microbiota are known to regulate lipid metabolism through...The Gansu zokor(Eospalax cansus),a subterranean rodent endemic to the Loess Plateau of China,exhibits remarkable adaptability to hypoxic environments.While gut microbiota are known to regulate lipid metabolism through bile acid(BA)pathways,this phenomenon has not been investigated in subterranean rodents exposed to hypoxia.This study employed 16SrRNA sequencing,targeted analysis of BA metabolites in colonic contents,and assessments of BA and lipid metabolites alongside molecular analyses in the liver and ileum under conditions of acute and chronic hypoxia in Gansu zokors.The results revealed that hypoxia altered the composition of gut microbiota and BA pools in Gansu zokors.Hypoxia-induced changes increased the abundance of gut microbiota associated with BA metabolism,thereby modulating lipid metabolism via farnesoid X receptor(FXR)signaling in the distal ileum and liver cells.Under acute hypoxia,FXR upregulated lipid synthesis and suppressed fatty acidβ-oxidation by downregulating the carnitine palmitoyl-transferase1A(CPT1A)expression.Conversely,during chronic hypoxia,particularly under long-term exposure,FXR reduced lipid synthesis and enhanced fatty acidβ-oxidation by upregulating acyl-CoA oxidase(ACOX1)expression.In both hypoxic conditions,FXR facilitated lipoprotein metabolism.In summary,this study elucidates that gut microbiota-mediated BA metabolic pathways contribute to the Gansu zokor’s ability to maintain lipid metabolic homeostasis and adaptation to hypoxia.展开更多
To help resolve the systematic position of Myospalacine(zokors)and to clarify the phylogenetic relationships among zokor species,complete mitochondrial 12S rRNA and cytochrome b gene sequences were determined for seve...To help resolve the systematic position of Myospalacine(zokors)and to clarify the phylogenetic relationships among zokor species,complete mitochondrial 12S rRNA and cytochrome b gene sequences were determined for seven zokor species from China.Phylogenetic relationships among all extant zokors,except the Siberian zokor(Myospalax myospalax)and Smith’s zokor(Eospalax smithi),were reconstructed with the Chinese bamboo rat(Rhizomys sinensis)as an outgroup.Our results support the generic status of Eospalax and also support the validity of the specific status of Eospalax cansus,Eospalax baileyi and Eospalax rufescens.展开更多
Background:Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau.This extreme living env ironment makes it a great model to study animal adaptation to hypoxia,low temperature,and...Background:Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau.This extreme living env ironment makes it a great model to study animal adaptation to hypoxia,low temperature,and high carbon dioxide concentration.Methods:We provide an integrated resource,ZokorDB,for tissue specific regulatory network annotation for zokor.ZokorDB is based on a high-quality draft genome of a plateau zokor at 3,300 m and its transcriptional profiles in brain,heart,liver,kidney,and lung.The conserved non-coding elements of zokor are annotated by their nearest genes and upstream transcriptional factor motif binding sites.Results:ZokorDB provides a general draft gene regulatory network(GRN),Le?potential transcription factor(TF)binds to non-coding regulatory elements and regulates the expression of target genes(TG).Furthermore,we refined the GRN by incorporating matched RNA-seq and DNase-seq data from mouse ENCODE project and reconstructed five tissue-specific regulatory networks.Conclusions:A web-based,open-access database is developed for easily searching,visualizing,and downloading the annotation and data.The pipeline of non-coding region annotation for zokor will be useful for other non-model species.ZokorDB is free available at the website(bigd.big.ac.cn/zokordb/).展开更多
All organisms respond to variation in their environments and manage environmental stress through metabolic adjustments.The plateau zokor(Myospalax baileyi) is an endemic and keystone subterranean rodent species that i...All organisms respond to variation in their environments and manage environmental stress through metabolic adjustments.The plateau zokor(Myospalax baileyi) is an endemic and keystone subterranean rodent species that inhabits the Qinghai-Tibet Plateau between 2800 and 4200 m above sea level.It is a hypoxic-tolerant mammal with a high ratio of oxygen utilization that enables it to cope with its harsh surroundings.To explore the molecular mechanism of altitude acclimatization of the plateau zokor,we cloned the zokor erythropoietin(Epo) gene and used real-time PCR to compare Epo mRNA levels in zokors inhabiting 16 different altitudes.The full-length zokor Epo open reading frame was 579 bp that encoded a precursor peptide of 192 amino acids with a signal peptide of 26 residues.The Epo gene of the plateau zokor was 81%-95% homologous to that of human,mouse,rat,root vole and the Golan Heights blind mole rat,with the highest homology(95%) to species of the genus Spalax.Epo mRNA was detected mainly in the zokor kidney and spleen among 8 selected tissues.The level of Epo mRNA increased in the liver and kidney with increases in altitude.The increase in the kidney was 5 times that in the liver.Remarkably,expression of Epo mRNA in the kidney of zokors living at the highest altitude(4268 m) was 12-fold higher than that of zokors living at the lowest(2492 m) altitude.These findings provide essential information for understanding the possible role of Epo in adaptation to hypoxia in the plateau zokor.展开更多
基金supported by the Second Tibetan Plateau Scientific Expedition and Research(STEP)Program(2019QZKK05010900 and 2019QZKK05010405)the National Natural Science Foundation of China(32100339 and 32200350)+3 种基金Yunnan Revitalization Talent Support Program Top team(202405AS350022)supported by the Youth Innovation Promotion Association,Chinese Academy of Sciencessupported by Yunnan Fundamental Research Projects(202201AU070208)supported by Yunnan Revitalization Talent Support Program Yunling Scholar Project(XML)。
文摘Understanding how species diverge and adapt is fundamental to unraveling biodiversity.While environmental impacts on species evolution are well-documented,the roles of intrinsic life-history traits remain underexplored.The Qinghai-Xizang Plateau,with its harsh conditions and unique biodiversity,offers a natural laboratory for such investigations.Here,we examine two sympatric small mammals—the solitary,low-dispersal plateau zokor(Eospalax baileyi)and the social,high-dispersal plateau pika(Ochotona curzoniae)—to elucidate how life-history traits shape population structures and adaptive strategies.Through whole-genome sequencing and cardiac-blood phenotype analyses,we reveal striking differences in their evolutionary trajectories.Despite enduring similar environmental pressures,plateau zokor populations exhibit pronounced genetic subdivisions,high inbreeding,and distinct local adaptations.In contrast,plateau pika populations display genetic panmixia,widespread diversity,and adaptive uniformity.Demographic inference highlights that plateau zokors experienced severe population bottlenecks and restricted gene flow during glacial periods,underscoring the impact of dispersal capacity on evolutionary outcomes.Our findings demonstrate that intrinsic biological traits,particularly dispersal ability,fundamentally influence genetic architecture,population connectivity,and local adaptation.This study not only provides empirical evidence of how life-history traits shape evolutionary dynamics but also offers a framework for integrating intrinsic and extrinsic factors in understanding biodiversity formation.
基金financially supported by the Qinghai University Graduate Student Research and Practice Innovation Project(2025-GPKY-12)Basic Research Project of Qinghai Provincial Science and Technology Department(2021-ZJ-701)+1 种基金National Natural Science Foundation of China(U23A20159,42161068)the 111 Project of China(D18013)。
文摘The mound-making behavior of plateau zokors is one of the most important factors in remodeling meadow microtopography and causing soil erosion in the Yellow River source area of western China,but little is known about the effects of microtopography on particle size characteristics(PSC)of eroded sediments from the bare slopes of zokor mounds during different rainfall events.In this study,we analyzed the relationship of microtopographic features derived from laser point cloud data and PSC of eroded sediments at six simulated rainfall intensities(all lasting 60 min).The effects of microtopography on PSC of eroded sediments were studied via partial least squares regression(PLSR)and structural equation modeling(SEM).The results showed that:(1)15-20 minutes from the beginning of rainfall was the sensitive period of soil loss from the slopes,and the function relationship between the rate of sediment and runoff and rainfall intensity can better predict the development trend of soil erosion;(2)Intense erosion occurred mainly in the upper half of the zokor mound,while deposition was mainly limited to its lower half.It is suggested that diminished plateau zokor activity intensity can effectively prevent and control soil erosion;(3)The PSC of eroded sediment is dominated by silt,followed by sand,with clay being the least abundant,and the eroded sediments with a particle size of 10-20μm were sensitive and highly susceptible to rainfall erosion.This finding facilitates the understanding of the formation process of surface geomorphology and the mechanism of soil erosion;(4)The PLSR model indicates that microtopography has an extensive influence on eroded sediments during hydraulic erosion,and the SEM analysis results further confirm that the fractal dimension was the best parameter to represent the PSC of eroded sediments,whereas surface cutting degree was the dominant factor controlling the PSC of eroded sediments.These findings are crucial for predicting soil erosion in the Yellow River source area and provide a new perspective for understanding soil erosion mechanisms in alpine meadow ecosystems.
基金supported by the Second Tibetan Plateau Scientific Expedition and Research(STEP)Program(2019QZKK05010218,2019QZKK05010110)National Natural Science Foundation of China(32100339,31871277)+2 种基金supported by the Yunling Scholar ProjectTen-Thousand Talents Plan of Yunnan Provincesupported by the Youth Innovation Promotion Association,Chinese Academy of Sciences。
文摘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 farmlands.Six species in Eospalax were described a century ago but their taxonomy and phylogeny remain controversial.In this study,we performed high-depth whole-genome sequencing of 47 zokor samples,comprising all six previously described species.Genomic analyses revealed a reliable and robust phylogeny of Eospalax and supported the validity of the six named species.According 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 Mountains.The most recent divergences occurred between E.baileyi and E.smithii and between E.rufescens and E.rothschildi 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 zokors.Morphological and molecular analyses strongly suggested that the specimens represent a new species,formally described here as Eospalax muliensis sp.nov.The 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.Interestingly,Eospalax muliensis sp.nov.possesses more supposedly plesiomorphic characters,suggesting a possible origin of the genus in the Hengduan Mountains.
基金This study was funded by the Lushan Plant Special Project of Lushan Botanical Garden,Chinese Academy of Sciences(2019ZWZX01).
文摘Mounds constructed by plateau zokors,which is widely distributed in alpine meadows significantly modified plant community structure.However,the variations of plant community structure under the disturbance of plateau zokor-made mound are less concerned.Therefore,we investigated the responses of plant community on zokor-made mound of different years(1 a and 3-4 a),and compared with undisturbed sites(no mound)in an alpine meadow in the eastern Qinghai-Tibetan Plateau(QTP),China.Species richness,coverage and Simpson diversity index were all significantly reduced by the presence of zokor-made mound,but plant heights were significantly increased,particularly in grasses and sedges.Several perennial forage species showed an increased importance value and niche breadth,including Koeleria macrantha,Elymus nutans and Poa pratensis.The effect of zokor-made mound on niche overlap showed that more intense interspecific competition produced a greater utilization of environmental resources.And this interspecific niche overlap was strengthened as succession progressed.The bare mound created by zokor burrowing activities provided a colonizing opportunity for non-dominant forage species,resulting in abundant plant species and plant diversity during the succession period.We concluded that presence of zokor-made mound was conducive to regeneration and vitality of plant community in alpine meadows,thus improving their resilience to anthropogenic stress.
基金supported by an Open Project of the Key Laboratory of Grassland Ecosystem(Gansu Agricultural University),Ministry of Education(KLGE202204)the“Innovation Star”project of Gansu Province’s outstanding graduate students(2023CXZX-621)+1 种基金the National Natural Science Foundation of China(32272566 and 31760706)the Industrial Support Program Project(2022CYZC-47)of Gansu Provincial Education Department.
文摘Plateau zokor(Eospalax baileyi)is a subterranean rodent and seasonal breeder.During the non-breeding season,the testicles regress,leading to the arrest of spermatogenesis and loss of fertility.The identification of the specific germ cell type at which spermatogenesis is arrested,as well as potential regulatory factors during the non-breeding season,is important for understanding seasonal spermatogenesis in subterranean species.This study analyzed genes in spermatocytes of plateau zokor by referring to single-cell RNA results in mice.We discovered that spermatogenesis is arrested at the spermatocyte during the non-breeding season,which was corroborated via immunofluorescence staining results.The analysis of gene expression during different stages of meiotic prophase I has revealed that germ cell development may be arrested,starting from zygonema,during the non-breeding season.Meanwhile,we discovered that the apoptosis genes were up-regulated,leading to apoptosis in spermatocytes.To confirm that the germ cell differentiation was blocked during the non-breeding season due to a decrease in the androgen level,we used androgen receptor antagonist(flutamide)to intervene in the breeding season and found that the inner diameter of the seminiferous tubules was significantly reduced,spermatogenesis was arrested,and spermatocytes underwent apoptosis.This study revealed that spermatocytes are the terminal of germ cell differentiation in plateau zokor during the non-breeding season and that the arrest of differentiation is attributed to a decline in androgen levels.Our results complement the theoretical basis of seasonal reproduction in plateau zokor.
基金supported by the Natural Science Basic Research Program of Shaanxi(Program No.2024JC-ZDXM-14).
文摘The Gansu zokor(Eospalax cansus),a subterranean rodent endemic to the Loess Plateau of China,exhibits remarkable adaptability to hypoxic environments.While gut microbiota are known to regulate lipid metabolism through bile acid(BA)pathways,this phenomenon has not been investigated in subterranean rodents exposed to hypoxia.This study employed 16SrRNA sequencing,targeted analysis of BA metabolites in colonic contents,and assessments of BA and lipid metabolites alongside molecular analyses in the liver and ileum under conditions of acute and chronic hypoxia in Gansu zokors.The results revealed that hypoxia altered the composition of gut microbiota and BA pools in Gansu zokors.Hypoxia-induced changes increased the abundance of gut microbiota associated with BA metabolism,thereby modulating lipid metabolism via farnesoid X receptor(FXR)signaling in the distal ileum and liver cells.Under acute hypoxia,FXR upregulated lipid synthesis and suppressed fatty acidβ-oxidation by downregulating the carnitine palmitoyl-transferase1A(CPT1A)expression.Conversely,during chronic hypoxia,particularly under long-term exposure,FXR reduced lipid synthesis and enhanced fatty acidβ-oxidation by upregulating acyl-CoA oxidase(ACOX1)expression.In both hypoxic conditions,FXR facilitated lipoprotein metabolism.In summary,this study elucidates that gut microbiota-mediated BA metabolic pathways contribute to the Gansu zokor’s ability to maintain lipid metabolic homeostasis and adaptation to hypoxia.
基金funded by the National Natural Science Foundation of China(No:30770256)the Key Projects(SZD 0420)of Sichuan Province.
文摘To help resolve the systematic position of Myospalacine(zokors)and to clarify the phylogenetic relationships among zokor species,complete mitochondrial 12S rRNA and cytochrome b gene sequences were determined for seven zokor species from China.Phylogenetic relationships among all extant zokors,except the Siberian zokor(Myospalax myospalax)and Smith’s zokor(Eospalax smithi),were reconstructed with the Chinese bamboo rat(Rhizomys sinensis)as an outgroup.Our results support the generic status of Eospalax and also support the validity of the specific status of Eospalax cansus,Eospalax baileyi and Eospalax rufescens.
基金ZokorDB is supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDB13000000)The authors are also supported by the National Natural Science Foundation of China(NSFC)(Nos.11871463,11871462,61671444 and 61621003)+1 种基金We thank all the lab members for discussions on data collection,genome alignment,annotation,GRN reconstructionWe thank Dr.Yilei Wu and his group for help on database design and management.
文摘Background:Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau.This extreme living env ironment makes it a great model to study animal adaptation to hypoxia,low temperature,and high carbon dioxide concentration.Methods:We provide an integrated resource,ZokorDB,for tissue specific regulatory network annotation for zokor.ZokorDB is based on a high-quality draft genome of a plateau zokor at 3,300 m and its transcriptional profiles in brain,heart,liver,kidney,and lung.The conserved non-coding elements of zokor are annotated by their nearest genes and upstream transcriptional factor motif binding sites.Results:ZokorDB provides a general draft gene regulatory network(GRN),Le?potential transcription factor(TF)binds to non-coding regulatory elements and regulates the expression of target genes(TG).Furthermore,we refined the GRN by incorporating matched RNA-seq and DNase-seq data from mouse ENCODE project and reconstructed five tissue-specific regulatory networks.Conclusions:A web-based,open-access database is developed for easily searching,visualizing,and downloading the annotation and data.The pipeline of non-coding region annotation for zokor will be useful for other non-model species.ZokorDB is free available at the website(bigd.big.ac.cn/zokordb/).
基金supported by Key Innovation Research Program,Chinese Academy of Sciences (KSCX2-EW-N-05)the National Basic Research Program of China (2012CB722506)the Key Projects in the Nationa Science & Technology Pillar Program (2009BAI83B01)
文摘All organisms respond to variation in their environments and manage environmental stress through metabolic adjustments.The plateau zokor(Myospalax baileyi) is an endemic and keystone subterranean rodent species that inhabits the Qinghai-Tibet Plateau between 2800 and 4200 m above sea level.It is a hypoxic-tolerant mammal with a high ratio of oxygen utilization that enables it to cope with its harsh surroundings.To explore the molecular mechanism of altitude acclimatization of the plateau zokor,we cloned the zokor erythropoietin(Epo) gene and used real-time PCR to compare Epo mRNA levels in zokors inhabiting 16 different altitudes.The full-length zokor Epo open reading frame was 579 bp that encoded a precursor peptide of 192 amino acids with a signal peptide of 26 residues.The Epo gene of the plateau zokor was 81%-95% homologous to that of human,mouse,rat,root vole and the Golan Heights blind mole rat,with the highest homology(95%) to species of the genus Spalax.Epo mRNA was detected mainly in the zokor kidney and spleen among 8 selected tissues.The level of Epo mRNA increased in the liver and kidney with increases in altitude.The increase in the kidney was 5 times that in the liver.Remarkably,expression of Epo mRNA in the kidney of zokors living at the highest altitude(4268 m) was 12-fold higher than that of zokors living at the lowest(2492 m) altitude.These findings provide essential information for understanding the possible role of Epo in adaptation to hypoxia in the plateau zokor.
