Maca （Lepidium meyenii Walp, 2n = 8x = 64）, belonging to the Brassicaceae family, is an economic plant cultivated in the central Andes sierra in Peru （4000-4500 m）. Considering that the rapid uplift of the central...Maca （Lepidium meyenii Walp, 2n = 8x = 64）, belonging to the Brassicaceae family, is an economic plant cultivated in the central Andes sierra in Peru （4000-4500 m）. Considering that the rapid uplift of the central Andes occurred 5-10 million years ago （Ma）, an evolutionary question arises regarding how plants such as maca acquire high-altitude adaptation within a short geological period. Here, we report the high-quality genome assembly of maca, in which two closely spaced maca-specific whole-genome duplications （WGDs; ~6.7 Ma） were identified. Comparative genomic analysis between maca and closely related Brassicaceae species revealed expansions of maca genes and gene families involved in abiotic stress response, hormone signaling pathway, and secondary metabolite biosynthesis via WGDs. The retention and subsequent functional divergence of many duplicated genes may account for the morphological and physiological changes （i.e., small leaf shape and self-fertility） in maca in a high-altitude environment. In addition, some duplicated maca genes were identified with functions in morphological adaptation （i.e., LEAF CURLING RESPONSIVENESS） and abiotic stress response （i.e., GL YClNE-RICH RNA-BINDING PROTEINS and DNA-DAMAGE-REPAIR/TOLERATION2） under positive selection. Collectively, the maca genome provides use- ful information to understand the important roles of WGDs in the high-altitude adaptation of plants in the Andes.展开更多
The timing and mechanisms of the human occupation of the demanding high-altitude Tibetan Plateau environment are of great interest.Here,we report on our reinvestigations and dating of the Nwya Devu site,located nearly...The timing and mechanisms of the human occupation of the demanding high-altitude Tibetan Plateau environment are of great interest.Here,we report on our reinvestigations and dating of the Nwya Devu site,located nearly 4600 meters above sea level on the central Tibetan Plateau.A new microblade techno-complex was identified on a lower lake shore at this site,distinct from the previously reported blade tool assemblage.These two lithic assemblages were dated to 45.6±2.6 and10.3±0.5 ka using optically stimulated luminescence and accelerator mass spectrometry^(14)C methods.They represent,respectively,the earliest known Paleolithic and microlithic sites on the interior Tibetan Plateau,indicating multiple occupation episodes of hunter-gatherers during the past 45 ka.Our studies reveal that relatively stable depositional conditions and a paleoenvironment characterized by a comparatively warm climate facilitated these multiple occupations at Nwya Devu.The contemporaneous occurrence of the Upper Paleolithic blade technology on the Tibetan Plateau and most of Eurasia between 50 and 40 ka indicates rapid,large-scale dispersals of humans that profoundly affected human demography on a large scale.Combining new archaeological evidence and previously reported genetic data,we conclude that the Tibetan Plateau provided a relatively stable habitat for Upper Paleolithic hunter-gatherers,which may have contributed to the complex and multiple-origin gene pool of present-day Tibetans.展开更多
During the past 3000 years,cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia,ultraviolet(UV)radiation,and extreme cold.The genetic mechanism underlying thi...During the past 3000 years,cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia,ultraviolet(UV)radiation,and extreme cold.The genetic mechanism underlying this rapid adaptation is not yet well understood.Here,we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations,including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 m.Our genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine ancestries.We found that recently selected genes in Tibetan cattle were related to body size(HMGA2 and NCAPG)and energy expenditure(DUOXA2).We identified signals of sympatric introgression from yak into Tibetan cattle at different altitudes,covering 0.64%–3.26%of their genomes,which included introgressed genes responsible for hypoxia response(EGLN1),cold adaptation(LRP11),DNA damage repair(LATS1),and UV radiation resistance(GNPAT).We observed that introgressed yak alleles were associated with noncoding variants,including those in present EGLN1.In Tibetan cattle,three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1,suggesting that these genomic variants enhance hypoxia tolerance.Taken together,our results indicated complex adaptation processes in Tibetan cattle,where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments.展开更多
DNA methylation plays a crucial role in environmental adaptations.Here,using whole-genome bisulfite sequencing,we generated comprehensive genome-wide DNA methylation profiles for the high-altitude Yunnan snub-nosed mo...DNA methylation plays a crucial role in environmental adaptations.Here,using whole-genome bisulfite sequencing,we generated comprehensive genome-wide DNA methylation profiles for the high-altitude Yunnan snub-nosed monkey(Rhinopithecus bieti)and the closely related golden snub-nosed monkey(R.roxellana).Our findings indicated a slight increase in overall DNA methylation levels in golden snub-nosed monkeys compared to Yunnan snub-nosed monkeys,suggesting a higher prevalence of hypermethylated genomic regions in the former.Comparative genomic methylation analysis demonstrated that genes associated with differentially methylated regions were involved in membrane fusion,vesicular formation and trafficking,hemoglobin function,cell cycle regulation,and neuronal differentiation.These results suggest that the high-altitude-related epigenetic modifications are extensive,involving a complete adaptation process from the inhibition of single Ca^(2+)channel proteins to multiple proteins collaboratively enhancing vesicular function or inhibiting cell differentiation and proliferation.Functional assays demonstrated that overexpression or down-regulation of candidate genes,such as SNX10,TIMELESS,and CACYBP,influenced cell viability under stress conditions.Overall,this research suggests that comparing DNA methylation across closely related species can identify novel candidate genomic regions and genes associated with local adaptations,thereby deepening our understanding of the mechanisms underlying environmental adaptations.展开更多
位于平流层的高空平台向上连接卫星、向下连接低空无人机,能够有效支撑空天地一体化信息网络,提供灵活的应急通信。然而,针对高空平台至无人机的下行链路,传统算法采用固定速率,降低链路的平均传输速率,增加了链路的中断概率。为此,提...位于平流层的高空平台向上连接卫星、向下连接低空无人机,能够有效支撑空天地一体化信息网络,提供灵活的应急通信。然而,针对高空平台至无人机的下行链路,传统算法采用固定速率,降低链路的平均传输速率,增加了链路的中断概率。为此,提出基于速率匹配的自由空间光通信(free space optical,FSO)和射频(radio frequency,RF)链路的动态切换算法(rate adaptation-based free space optical and RF dynamic switching,RADS)。RADS算法优先使用FSO链路,若FSO链路的瞬时信噪比低于阈值,就切入RF链路。同时,根据所接收信号的信噪比,采用满足最低误码率要求的传输模式,进而满足速率要求。仿真结果表明,相比于传统的固定速率算法,提出的RADS算法降低了链路中断概率,提升了速率。展开更多
Chinese snub-nosed monkeys (genus Rhinopithecus, subfamily Colobinae), including R. bieti, R. brelichi and R. roxellana, are well-known as the non-human primates with the highest known altitudinal distribution. They r...Chinese snub-nosed monkeys (genus Rhinopithecus, subfamily Colobinae), including R. bieti, R. brelichi and R. roxellana, are well-known as the non-human primates with the highest known altitudinal distribution. They represent an interesting model organism of adaptation to the extreme environmental stresses. However, no study at the molecular level has yet been reported for the high-altitude adaptation in Chinese snub-nosed monkeys. Leptin, as an adipocyte-derived hormone, is believed to play an important role in energy homeostasis in adaptation to high altitude environments. In the present study, we sequenced and compared leptin sequences of the Chinese snub-nosed monkeys (R. bieti and R. roxellana) with their lowland close relative R. avunculus and other Colobines. Unexpectedly, no amino acid changes were observed in the 7 Colobinae species examined, including the 2 Chinese snub-nosed monkeys, indicating no difference in the evolutionary pattern of the Leptin gene between high-altitude monkeys and their lowland counterparts. In contrast to a previous finding of adaptive evolution of Leptin gene in plateau pikas, our study suggests that this gene may not have an important role in high-altitude adaptation of Chinese snub-nosed monkeys. Other nuclear genes associated with energy metabolism, or mitochondrial genes, are most likely to be involved the molecular mechanism underlying adaptation of these monkeys to cold and hypoxia associated with the highland environment.展开更多
Persistent uplift means the Qinghai-Tibet Plateau(QTP)is an ideal natural laboratory to investigate genome evolution and adaptation within highland environments.However,how paleogeographic and paleoclimatic events inf...Persistent uplift means the Qinghai-Tibet Plateau(QTP)is an ideal natural laboratory to investigate genome evolution and adaptation within highland environments.However,how paleogeographic and paleoclimatic events influence the genome and population of endemic fish species remains unclear.Glyptosternon maculatum is an ancient endemic fish found on the QTP and the only critically endangered species in the Sisoridae family.Here,we found that major transposons in the G.maculatum genome showed episodic bursts,consistent with contemporaneous geological and climatic events during the QTP formation.Notably,histone genes showed significant expansion in the G.maculatum genome,which may be mediated by long interspersed nuclear elements(LINE)repetitive element duplications.Population analysis showed that ancestral G.maculatum populations experienced two significant depressions 2.6 million years ago(Mya)and 10000 years ago,exhibiting excellent synchronization with Quaternary glaciation and the Younger Dryas,respectively.Thus,we propose that paleogeography and paleoclimate were dominating driving forces for population dynamics in endemic fish on the QTP.Tectonic movements and temperature fluctuation likely destroyed the habitat and disrupted the drainage connectivity among populations.These factors may have caused severe bottlenecks and limited migration among ancestral G.maculatum populations,resulting in the low genetic diversity and endangered status of the species today.展开更多
DNA methylation(DNAm)is one of the major epigenetic mechanisms in humans and is important in diverse cellular processes.The variation of DNAm in the human population is related to both genetic and environmental factor...DNA methylation(DNAm)is one of the major epigenetic mechanisms in humans and is important in diverse cellular processes.The variation of DNAm in the human population is related to both genetic and environmental factors.However,the DNAm profiles have not been investigated in the Chinese population of diverse ethnicities.Here,we performed double-strand bisulfite sequencing(DSBS)for 32 Chinese individuals representing four major ethnic groups including Han Chinese,Tibetan,Zhuang,and Mongolian.We identified a total of 604,649 SNPs and quantified DNAm at more than 14 million Cp Gs in the population.We found global DNAm-based epigenetic structure is different from the genetic structure of the population,and ethnic difference only partially explains the variation of DNAm.Surprisingly,non-ethnic-specific DNAm variations showed stronger correlation with the global genetic divergence than these ethnic-specific DNAm.Differentially methylated regions(DMRs)among these ethnic groups were found around genes in diverse biological processes.Especially,these DMR-genes between Tibetan and nonTibetans were enriched around high-altitude genes including EPAS1 and EGLN1,suggesting DNAm alteration plays an important role in high-altitude adaptation.Our results provide the first batch of epigenetic maps for Chinese populations and the first evidence of the association of epigenetic changes with Tibetans'high-altitude adaptation.展开更多
文摘Maca （Lepidium meyenii Walp, 2n = 8x = 64）, belonging to the Brassicaceae family, is an economic plant cultivated in the central Andes sierra in Peru （4000-4500 m）. Considering that the rapid uplift of the central Andes occurred 5-10 million years ago （Ma）, an evolutionary question arises regarding how plants such as maca acquire high-altitude adaptation within a short geological period. Here, we report the high-quality genome assembly of maca, in which two closely spaced maca-specific whole-genome duplications （WGDs; ~6.7 Ma） were identified. Comparative genomic analysis between maca and closely related Brassicaceae species revealed expansions of maca genes and gene families involved in abiotic stress response, hormone signaling pathway, and secondary metabolite biosynthesis via WGDs. The retention and subsequent functional divergence of many duplicated genes may account for the morphological and physiological changes （i.e., small leaf shape and self-fertility） in maca in a high-altitude environment. In addition, some duplicated maca genes were identified with functions in morphological adaptation （i.e., LEAF CURLING RESPONSIVENESS） and abiotic stress response （i.e., GL YClNE-RICH RNA-BINDING PROTEINS and DNA-DAMAGE-REPAIR/TOLERATION2） under positive selection. Collectively, the maca genome provides use- ful information to understand the important roles of WGDs in the high-altitude adaptation of plants in the Andes.
基金supported by the National Natural Science Foundation of China(Grant Nos.41888101,41977380 and 42072033)the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant Nos.XDB26000000 and XDA2004010102)+3 种基金the Second Tibetan Plateau Scientific Expedition and Research(Grant No.2019QZKK0601)the National Social Science Foundation of China(Grant No.21@WTK001)supported by the Chinese Academy of Sciences President’s International Fellowship Initiative Award(Grant No.2018VCA0016)the Je Tsongkhapa Endowment for Central and Inner Asian Archaeology at the University of Arizona。
文摘The timing and mechanisms of the human occupation of the demanding high-altitude Tibetan Plateau environment are of great interest.Here,we report on our reinvestigations and dating of the Nwya Devu site,located nearly 4600 meters above sea level on the central Tibetan Plateau.A new microblade techno-complex was identified on a lower lake shore at this site,distinct from the previously reported blade tool assemblage.These two lithic assemblages were dated to 45.6±2.6 and10.3±0.5 ka using optically stimulated luminescence and accelerator mass spectrometry^(14)C methods.They represent,respectively,the earliest known Paleolithic and microlithic sites on the interior Tibetan Plateau,indicating multiple occupation episodes of hunter-gatherers during the past 45 ka.Our studies reveal that relatively stable depositional conditions and a paleoenvironment characterized by a comparatively warm climate facilitated these multiple occupations at Nwya Devu.The contemporaneous occurrence of the Upper Paleolithic blade technology on the Tibetan Plateau and most of Eurasia between 50 and 40 ka indicates rapid,large-scale dispersals of humans that profoundly affected human demography on a large scale.Combining new archaeological evidence and previously reported genetic data,we conclude that the Tibetan Plateau provided a relatively stable habitat for Upper Paleolithic hunter-gatherers,which may have contributed to the complex and multiple-origin gene pool of present-day Tibetans.
基金supported by the National Key R&D Program of China(2021YFD1200400 and 2021YFF1001000)the National Natural Science Foundation of China(32102523,32372854,31861143014,32260823,and 32172706)+5 种基金the Key Research and Development Program of Xizang Autonomous Region of China(XZ202301ZY0008N)the Yunnan Expert Workstations(202305AF150156),the China Agriculture Research System of MOF and MARA(CARS-37)the Postdoctoral Fellowship Program of CPSF(GZC20232149)the Program of Yunling Scholar and Yunling Cattle Special Program of Yunnan Joint Laboratory of Seeds and Seeding Industry(202205AR070001)the Construction of Yunling Cattle Technology Innovation Center and Industrialization of Achievements(2019ZG007)Finally,we thank the High-Performance Computing(HPC)Center of Northwest A&F University(NWAFU)and Hefei Advanced Computing Center for providing computing resources.
文摘During the past 3000 years,cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia,ultraviolet(UV)radiation,and extreme cold.The genetic mechanism underlying this rapid adaptation is not yet well understood.Here,we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations,including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 m.Our genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine ancestries.We found that recently selected genes in Tibetan cattle were related to body size(HMGA2 and NCAPG)and energy expenditure(DUOXA2).We identified signals of sympatric introgression from yak into Tibetan cattle at different altitudes,covering 0.64%–3.26%of their genomes,which included introgressed genes responsible for hypoxia response(EGLN1),cold adaptation(LRP11),DNA damage repair(LATS1),and UV radiation resistance(GNPAT).We observed that introgressed yak alleles were associated with noncoding variants,including those in present EGLN1.In Tibetan cattle,three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1,suggesting that these genomic variants enhance hypoxia tolerance.Taken together,our results indicated complex adaptation processes in Tibetan cattle,where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments.
文摘有关动物适应异质性海拔环境的研究,已在表型、解剖学、生理学、基因组学和转录组学等方面广泛开展,但是很少关注小RNA(micro RNAs或miRNAs)的生态适应性功能.草原毛虫是青藏高原高寒草地的重要害虫,并对不同海拔环境产生了良好的适应性.为此,本研究以两种栖息于青藏高原不同海拔环境的黄斑草原毛虫和门源草原毛虫为研究对象,基于Illumina Hi Seq技术对这两种草原毛虫的miRNA转录组进行了高通量测序.结果表明,两种草原毛虫中共鉴定到109个成熟miRNAs,其中47个为保守miRNAs.在所有miRNAs种,共有9个miRNAs的表达水平在两种草原毛虫间存在显著差异性.对这9个差异性表达的miRNAs采用实时荧光定量PCR进行验证,发现8个基因的表达水平与高通量测序结果完全一致.功能分析表明,差异性表达的miRNAs共预测到93个靶基因.这些靶基因主要富集到脂、核酸和维生素等代谢或衰老相关的GO条目,并与代谢、抗寒和低氧等KEGG通路相关(如AMPK信号通路、Wnt信号通路和m TOR信号通路).这些研究表明,miRNAs在草原毛虫对异质性海拔环境的适应性进化过程中具有重要作用.该研究加深了对青藏高原特有昆虫适应高海拔环境的遗传基础的理解.
基金supported by the National Natural Science Foundation of China(32330015,31821001)Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000)。
文摘DNA methylation plays a crucial role in environmental adaptations.Here,using whole-genome bisulfite sequencing,we generated comprehensive genome-wide DNA methylation profiles for the high-altitude Yunnan snub-nosed monkey(Rhinopithecus bieti)and the closely related golden snub-nosed monkey(R.roxellana).Our findings indicated a slight increase in overall DNA methylation levels in golden snub-nosed monkeys compared to Yunnan snub-nosed monkeys,suggesting a higher prevalence of hypermethylated genomic regions in the former.Comparative genomic methylation analysis demonstrated that genes associated with differentially methylated regions were involved in membrane fusion,vesicular formation and trafficking,hemoglobin function,cell cycle regulation,and neuronal differentiation.These results suggest that the high-altitude-related epigenetic modifications are extensive,involving a complete adaptation process from the inhibition of single Ca^(2+)channel proteins to multiple proteins collaboratively enhancing vesicular function or inhibiting cell differentiation and proliferation.Functional assays demonstrated that overexpression or down-regulation of candidate genes,such as SNX10,TIMELESS,and CACYBP,influenced cell viability under stress conditions.Overall,this research suggests that comparing DNA methylation across closely related species can identify novel candidate genomic regions and genes associated with local adaptations,thereby deepening our understanding of the mechanisms underlying environmental adaptations.
文摘位于平流层的高空平台向上连接卫星、向下连接低空无人机,能够有效支撑空天地一体化信息网络,提供灵活的应急通信。然而,针对高空平台至无人机的下行链路,传统算法采用固定速率,降低链路的平均传输速率,增加了链路的中断概率。为此,提出基于速率匹配的自由空间光通信(free space optical,FSO)和射频(radio frequency,RF)链路的动态切换算法(rate adaptation-based free space optical and RF dynamic switching,RADS)。RADS算法优先使用FSO链路,若FSO链路的瞬时信噪比低于阈值,就切入RF链路。同时,根据所接收信号的信噪比,采用满足最低误码率要求的传输模式,进而满足速率要求。仿真结果表明,相比于传统的固定速率算法,提出的RADS算法降低了链路中断概率,提升了速率。
基金supported by the National Basic Research Program of China (2007CB411600)National Natural Science Foundation of China (U0836603)
文摘Chinese snub-nosed monkeys (genus Rhinopithecus, subfamily Colobinae), including R. bieti, R. brelichi and R. roxellana, are well-known as the non-human primates with the highest known altitudinal distribution. They represent an interesting model organism of adaptation to the extreme environmental stresses. However, no study at the molecular level has yet been reported for the high-altitude adaptation in Chinese snub-nosed monkeys. Leptin, as an adipocyte-derived hormone, is believed to play an important role in energy homeostasis in adaptation to high altitude environments. In the present study, we sequenced and compared leptin sequences of the Chinese snub-nosed monkeys (R. bieti and R. roxellana) with their lowland close relative R. avunculus and other Colobines. Unexpectedly, no amino acid changes were observed in the 7 Colobinae species examined, including the 2 Chinese snub-nosed monkeys, indicating no difference in the evolutionary pattern of the Leptin gene between high-altitude monkeys and their lowland counterparts. In contrast to a previous finding of adaptive evolution of Leptin gene in plateau pikas, our study suggests that this gene may not have an important role in high-altitude adaptation of Chinese snub-nosed monkeys. Other nuclear genes associated with energy metabolism, or mitochondrial genes, are most likely to be involved the molecular mechanism underlying adaptation of these monkeys to cold and hypoxia associated with the highland environment.
基金supported by the Key Research and Development Projects in Tibet:Preservation of Characteristic Biological Germplasm Resources and Utilization of Gene Technology in Tibet(XZ202001ZY0016N)National Natural Science Foundation of China(32072980)Special Finance of Tibet Autonomous Region(XZNKY-2019-C-053)。
文摘Persistent uplift means the Qinghai-Tibet Plateau(QTP)is an ideal natural laboratory to investigate genome evolution and adaptation within highland environments.However,how paleogeographic and paleoclimatic events influence the genome and population of endemic fish species remains unclear.Glyptosternon maculatum is an ancient endemic fish found on the QTP and the only critically endangered species in the Sisoridae family.Here,we found that major transposons in the G.maculatum genome showed episodic bursts,consistent with contemporaneous geological and climatic events during the QTP formation.Notably,histone genes showed significant expansion in the G.maculatum genome,which may be mediated by long interspersed nuclear elements(LINE)repetitive element duplications.Population analysis showed that ancestral G.maculatum populations experienced two significant depressions 2.6 million years ago(Mya)and 10000 years ago,exhibiting excellent synchronization with Quaternary glaciation and the Younger Dryas,respectively.Thus,we propose that paleogeography and paleoclimate were dominating driving forces for population dynamics in endemic fish on the QTP.Tectonic movements and temperature fluctuation likely destroyed the habitat and disrupted the drainage connectivity among populations.These factors may have caused severe bottlenecks and limited migration among ancestral G.maculatum populations,resulting in the low genetic diversity and endangered status of the species today.
基金the National Key Research and Development Program of China(2016YFC0900402)the Basic Science Center Program(32288101)+1 种基金the National Natural Science Foundation of China(32030020 and 31961130380)the Shanghai Municipal Science and Technology Major Project(2017SHZDZX01)。
文摘DNA methylation(DNAm)is one of the major epigenetic mechanisms in humans and is important in diverse cellular processes.The variation of DNAm in the human population is related to both genetic and environmental factors.However,the DNAm profiles have not been investigated in the Chinese population of diverse ethnicities.Here,we performed double-strand bisulfite sequencing(DSBS)for 32 Chinese individuals representing four major ethnic groups including Han Chinese,Tibetan,Zhuang,and Mongolian.We identified a total of 604,649 SNPs and quantified DNAm at more than 14 million Cp Gs in the population.We found global DNAm-based epigenetic structure is different from the genetic structure of the population,and ethnic difference only partially explains the variation of DNAm.Surprisingly,non-ethnic-specific DNAm variations showed stronger correlation with the global genetic divergence than these ethnic-specific DNAm.Differentially methylated regions(DMRs)among these ethnic groups were found around genes in diverse biological processes.Especially,these DMR-genes between Tibetan and nonTibetans were enriched around high-altitude genes including EPAS1 and EGLN1,suggesting DNAm alteration plays an important role in high-altitude adaptation.Our results provide the first batch of epigenetic maps for Chinese populations and the first evidence of the association of epigenetic changes with Tibetans'high-altitude adaptation.
