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
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(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.
