Chekiang,the smallest province of China,is situated in the eastern part of the country,Facing east to the sea,it lies between the latitudes 27°-31°N,and the longitudes118-123°E.With the exception of the...Chekiang,the smallest province of China,is situated in the eastern part of the country,Facing east to the sea,it lies between the latitudes 27°-31°N,and the longitudes118-123°E.With the exception of the local plains along Chientang Kiang and Tai Hu Basin which are comparatively,flat and low,Chekiang is a rather hilly region,average height about 500 meters,while some valleys and basins are as low as 50 meters or even less.展开更多
Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demon...Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau.Here,we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred.We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys(including 24 from the Tibetan Plateau).Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs.In Tibetan donkeys,however,another gene,i.e.,EGLN1,was likely involved in their adaptation to high altitude.In addition,admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys.Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau,as well as the existence of a closely related species already adapted to hypoxia,Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.展开更多
The kiang(Equus kiang)can only be observed in the Qinghai–Tibet Plateau(QTP).The kiang displayed excellent athletic performance in the high-altitude environment,which attracted wide interest in the investigation of t...The kiang(Equus kiang)can only be observed in the Qinghai–Tibet Plateau(QTP).The kiang displayed excellent athletic performance in the high-altitude environment,which attracted wide interest in the investigation of the potential adaptive mechanisms to the extreme environment.Here,we assembled a chromosome-level genome of the kiang based on Hi-C sequencing technology.A total of 324.14 Gb clean data were generated,and the chromosomelevel genome with 26 chromosomes(25+X)and scaffold N50 of 101.77 Mb was obtained for the kiang.The genomic synteny analysis revealed large-scale chromosomal rearrangement during the evolution process of Equus species.Phylogenetic and divergence analyses revealed that the kiang was the sister branch to the ass and diverged from a common ancestor at approximately 13.5 Mya.The expanded gene families were mainly related to the hypoxia response,metabolism,and immunity.The kiang suffered a significant loss of olfaction-related genes,which might indicate decreased olfactory sensibility.Positively selected genes(PSGs)detected in the kiang were mainly associated with hypoxia response.Especially,there were two species-specific missense amino acid mutations in the PSG STAT3 annotated in the hypoxia-inducible factor 1 signal pathway,which may play an important role in the high-altitude adaptation of the kiang.Moreover,structure variations in the kiang genome were also identified,which possibly contributed to the high-altitude adaptation of the kiang.Comparative analysis revealed a lot of speciesspecific insertions and deletions in the kiang genome,such as PIK3CB and AKT with 3258 and 189 bp insertions in the intron region,respectively,possibly affecting the expression and regulation of hypoxia-related downstream pathways.This study provided valuable genomic resources,and our findings help a better understanding of the underlying adaptive strategies to the high-altitude environment in the kiang.展开更多
文摘Chekiang,the smallest province of China,is situated in the eastern part of the country,Facing east to the sea,it lies between the latitudes 27°-31°N,and the longitudes118-123°E.With the exception of the local plains along Chientang Kiang and Tai Hu Basin which are comparatively,flat and low,Chekiang is a rather hilly region,average height about 500 meters,while some valleys and basins are as low as 50 meters or even less.
基金supported by the National Natural Science Foundation of China(31621062)Strategic Priority Research Program of the Chinese Academy of Sciences(XDA2004010302)+4 种基金Second Tibetan Plateau Scientific Expedition and Research(STEP)Program(2019QZKK05010703)supported by the National Natural Science Foundation of China(91731304,31822048)Strategic Priority Research Program of the Chinese Academy of Sciences(XDB13020600)Qinghai Department of Science and Technology Major ProjectState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan,Yunnan University(2018KF001)supported by the Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(Large Research Infrastructure Funding)
文摘Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau.Here,we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred.We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys(including 24 from the Tibetan Plateau).Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs.In Tibetan donkeys,however,another gene,i.e.,EGLN1,was likely involved in their adaptation to high altitude.In addition,admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys.Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau,as well as the existence of a closely related species already adapted to hypoxia,Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.
基金supported by the Second Tibetan Plateau Scientific Expedition and Research Program(No.2019QZKK0501)the National Natural Science Foundation of China(No.32270454).
文摘The kiang(Equus kiang)can only be observed in the Qinghai–Tibet Plateau(QTP).The kiang displayed excellent athletic performance in the high-altitude environment,which attracted wide interest in the investigation of the potential adaptive mechanisms to the extreme environment.Here,we assembled a chromosome-level genome of the kiang based on Hi-C sequencing technology.A total of 324.14 Gb clean data were generated,and the chromosomelevel genome with 26 chromosomes(25+X)and scaffold N50 of 101.77 Mb was obtained for the kiang.The genomic synteny analysis revealed large-scale chromosomal rearrangement during the evolution process of Equus species.Phylogenetic and divergence analyses revealed that the kiang was the sister branch to the ass and diverged from a common ancestor at approximately 13.5 Mya.The expanded gene families were mainly related to the hypoxia response,metabolism,and immunity.The kiang suffered a significant loss of olfaction-related genes,which might indicate decreased olfactory sensibility.Positively selected genes(PSGs)detected in the kiang were mainly associated with hypoxia response.Especially,there were two species-specific missense amino acid mutations in the PSG STAT3 annotated in the hypoxia-inducible factor 1 signal pathway,which may play an important role in the high-altitude adaptation of the kiang.Moreover,structure variations in the kiang genome were also identified,which possibly contributed to the high-altitude adaptation of the kiang.Comparative analysis revealed a lot of speciesspecific insertions and deletions in the kiang genome,such as PIK3CB and AKT with 3258 and 189 bp insertions in the intron region,respectively,possibly affecting the expression and regulation of hypoxia-related downstream pathways.This study provided valuable genomic resources,and our findings help a better understanding of the underlying adaptive strategies to the high-altitude environment in the kiang.
