Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wil...Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wild C.oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress.Here,47 wild C.oleifera from 11 natural distribution sites in China and 4 relative species of C.oleifera were selected for genome sequencing.“Min Temperature of Coldest Month”(BIO6)had the highest comprehensive contribution to wild C.oleifera distribution.The population genetic structure of wild C.oleifera could be divided into two groups:in cold winter(BIO6≤0℃)and warm winter(BIO6>0℃)areas.Wild C.oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N_(e) than those in warm winter areas.155 singlenucleotide polymorphisms(SNPs)were significantly correlated with the key bioclimatic variables(106 SNPs significantly correlated with BIO6).Twenty key SNPs and 15 key copy number variation regions(CNVRs)were found with genotype differentiation>50%between the two groups of wild C.oleifera.Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance,and they were also found within a CNVR suggesting interactions between them.Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress.The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.展开更多
The globin superfamily,central to oxygen(O_(2))cascade dynamics,exemplifies how canalization—evolutionary stabilization of phenotypic traits—enables vertebrates to thrive in extreme environments.In birds,hemoglobins...The globin superfamily,central to oxygen(O_(2))cascade dynamics,exemplifies how canalization—evolutionary stabilization of phenotypic traits—enables vertebrates to thrive in extreme environments.In birds,hemoglobins(Hbs)serve as a paradigm of this process,with structural and functional canalization underpinning their exceptional aerobic capacity and elevational diversification.Despite significant advances of globins in our understanding of avian aerobic adaptation,a comprehensive synthesis of functional diversity,molecular evolution,and structural innovation is essential to fully elucidate their canalized roles in O_(2)homeostasis.Integrating perspectives on globin functional diversity and structural evolution,this review examines how chance(mutation/fixation biases)and contingency(historical genetic/epistatic constraints)shape Hb divergence and parallelism,thereby bridging molecular mechanisms with physiological adaptation in birds.We highlight how avian Hbs,canalized through compensatory substitutions and allosteric regulation,achieves a balance between evolutionary robustness and adaptive plasticity.However,critical gaps remain persist:the roles of understudied globins(e.g.,neuroglobin,globin E)and the mechanisms of genetic assimilation in migratory taxa.We propose an integrative framework that incorporates ecological divergence(elevation,flight endurance),phylogenetic timescales,and systems biology to unravel how canalization directs adaptive compromise.By focusing on birds within the amniotes,this synthesis advances a cohesive model for vertebrate evolution,wherein canalized globins reconcile metabolic precision with ecological innovation.Ultimately,this review refines hypotheses of O_(2)cascade evolution and calls for cross-disciplinary studies to decode the genetic and physiological architecture underlying adaptive canalization in extreme environments.展开更多
Saccharomyces cerevisiae is not naturally capable of efficiently utilizing xylose as a carbon source.When cultured with lignocellulosic hydrolysates containing pretreatment-derived inhibitors,S.cerevisiae suffers from...Saccharomyces cerevisiae is not naturally capable of efficiently utilizing xylose as a carbon source.When cultured with lignocellulosic hydrolysates containing pretreatment-derived inhibitors,S.cerevisiae suffers from much lower sugar uptake,ethanol yield and fermentation efficiency.Thus,considering efficient xylose conversion into ethanol during non-detoxified hydrolysate culture,genetic engineering and adaptive evolution of S.cerevisiae might be a promising joint strategy for improving xylose uptake and ethanol production.In this study,an inhibitor-tolerant strain S.cerevisiae SPSC01-TAF94 was genetically engineered by overexpressing both xylose transport-and metabolism-related genes(N360F,Ru-xyl A,TAL1,TKL1,RKI1 and RPE1),yielding the xylose-utilizing strain TAF94-X,followed by three-stage adaptation in non-detoxified corn stover hydrolysate containing 5 g·L^(-1)acetic acid,0.32 g·L^(-1)furfural,0.17 g·L(-1)HMF and 0.19 g·L^(-1)vanillin as the major inhibitors as well as 20,40 and 60 g·L^(-1)xylose adjusted as the major carbon source,respectively.Finally,an active xylose-utilizing and ethanolproducing strain TAF94-X60 was obtained,which achieved 44.9 g·L^(-1)ethanol with yield of0.41 g·g^(-1),productivity of 0.62 g·L^(-1)·h^(-1)and xylose consumption rate of 0.42 g·L^(-1)·h^(-1)during hydrolysate culture,compared to those of 36.5 g·L^(-1),0.38 g·g^(-1),0.50 g·L^(-1)·h^(-1)and 0.20 g·L^(-1)·h^(-1)obtained with the control strain TAF94-X.The proposed joint strategy effectively utilizes hydrolyzed sugars while eliminating the need for conventional detoxification or water washing processes,thus enhancing the economic feasibility of large-scale lignocellulosic ethanol production.展开更多
Pikas(Lagomorpha:Ochotonidae)are small mouselike lagomorphs.To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet)Plateau(QTP),we collected 226 pikas...Pikas(Lagomorpha:Ochotonidae)are small mouselike lagomorphs.To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet)Plateau(QTP),we collected 226 pikas and measured 20 morphological characteristics and recorded habitat information.We also sequenced the genome of 81specimens,representing 27 putative pika species.The genome-wide tree based on 4?090 coding genes identified five subgenera,i.e.,Alienauroa,Conothoa,Lagotona,Ochotona,and Pika,consistent with morphometric data.Morphologically,Alienauroa and Ochotona had similar traits,including smaller size and earlier divergence time compared to other pikas.Consistently,the habitats of Alienauroa and Ochotona differed from those of the remaining subgenera.Phylogenetic signal analysis detected 83 genes significantly related to morphological characteristics,including several visual and hearingrelated genes.Analysis of shared amino acid substitutions and positively selected genes(PSGs)in Alienauroa and Ochotona identified two genes,i.e.,mitochondrial function-related TSFM(p.Q155E)and low-light visual sensitivity-related PROM1(p.H419Y).Functional experiments demonstrated that TSFM-155E significantly enhanced mitochondrial function compared to TSFM-155Q in other pikas,and PROM1-419Y decreased the modeling of dynamic intracellular chloride efflux upon calcium uptake.Alienauroa and Ochotona individuals mostly inhabit different environments(e.g.,subtropical forests)than other pikas,suggesting that a shift from the larger ancestral type and changes in sensory acuity and energy enhancement may have been required in their new environments.This study increases our understanding of the evolutionary history of pikas.展开更多
Acetic acid and furfural are known as prevalent inhibitors deriving from pretreatment during lignocellulosic ethanol production.They negatively impact cell growth,glucose uptake and ethanol biosynthesis of Saccharomyc...Acetic acid and furfural are known as prevalent inhibitors deriving from pretreatment during lignocellulosic ethanol production.They negatively impact cell growth,glucose uptake and ethanol biosynthesis of Saccharomyces cerevisiae strains.Development of industrial S.cerevisiae strains with high tolerance towards these inhibitors is thus critical for efficient lignocellulosic ethanol production.In this study,the acetic acid or furfural tolerance of different S.cerevisiae strains could be significantly enhanced after adaptive evolution via serial cultivation for 40 generations under stress conditions.The acetic acid-based adaptive strain SPSC01-TA9 produced 30.5 g·L^(-1)ethanol with a yield of 0.46 g·g^(-1)in the presence of 9 g·L^(-1)acetic acid,while the acetic acid/furfural-based adaptive strain SPSC01-TAF94 produced more ethanol of 36.2 g·L^(-1)with increased yield up to 0.49 g·g^(-1)in the presence of both 9 g·L^(-1)acetic acid and 4 g·L^(-1)furfural.Significant improvements were also observed during non-detoxified corn stover hydrolysate culture by SPSC01-TAF94,which achieved ethanol production and yield of 29.1 g·L^(-1)and 0.49 g·g^(-1),respectively,the growth and fermentation efficiency of acetic acid/furfural-based adaptive strain in hydrolysate was 95%higher than those of wildtype strains,indicating the acetic acid-and furfural-based adaptive evolution strategy could be an effective approach for improving lignocellulosic ethanol production.The adapted strains developed in this study with enhanced tolerance against acetic acid and furfural could be potentially contribute to economically feasible and sustainable lignocellulosic biorefinery.展开更多
Next-generation sequencing technology has transformed our ability to assess the taxonomic composition functions of host-associated microbiota and microbiomes. More human microbiome research projects—particularly thos...Next-generation sequencing technology has transformed our ability to assess the taxonomic composition functions of host-associated microbiota and microbiomes. More human microbiome research projects—particularly those that explore genomic mutations within the microbiome—will be launched in the next decade. This review focuses on the coevolution of microbes within a microbiome, which shapes strain-level diversity both within and between host species. We also explore the correlation between microbial genomic mutations and common metabolic diseases, and the adaptive evolution of pathogens and probiotics during invasion and colonization. Finally, we discuss advances in methods and algorithms for annotating and analyzing microbial genomic mutations.展开更多
In the field of phylogenetic analyses, the rbcL gene encoded large subunit Ribulose-1,5-biphosphate carboxylase/oxygenase （Rubisco, EC4.1.1.39）, which plays a crucial role in the process of photosynthesis for most ...In the field of phylogenetic analyses, the rbcL gene encoded large subunit Ribulose-1,5-biphosphate carboxylase/oxygenase （Rubisco, EC4.1.1.39）, which plays a crucial role in the process of photosynthesis for most terrestrial plants, has been considered to be conserved; however, recent controversy regarding rbcL conservation has appeared since it was proposed to be under natural selection within all principal lineages of land plants. In this study, by examining the variation of DNA and protein sequences among 17 species in the family Tamaricaceae, three nonsynonymous mutations were identified to be under positive selection. The favored sites were located in the alph-helix domains of Rubisco, with decreased hydrophobicity and increased entropy, which could facilitate C〇 2 penetration into the active site of Rubisco. We also found that the expression level of rbcL in different genotypes of Reaumuria soongarica shifted in response to various stresses such as drought, temperature, salt, and light. This study not only sheds light on the functional/structural features of Rubisco in the evolution scenarios from 〇 3-like into C4 in Tamaricaceae but also provides useful information on directing genetic performance to enhance photosynthesis efficiency of desert plants for sustaining fragile desert ecosystems; fur-thermore, it promotes the ability to cope with desert aridification and global warming.展开更多
Plants adapt to their local environments through natural or artificial selection of optimal phenotypes.Recent advances in genomics and computational biology,which integrate phenotypic and multi-omics data,have facilit...Plants adapt to their local environments through natural or artificial selection of optimal phenotypes.Recent advances in genomics and computational biology,which integrate phenotypic and multi-omics data,have facilitated the rapid identification of key genes and allelic variations that underlie these adaptive evolutionary processes.Under-standing the underlying molecular mechanisms has significantly enhanced our knowledge of how plants respond to changed habitats,including various biotic and abiotic stresses.In this review,we highlight recent progress in elucidating the ge-netic basis of phenotypic variation in morphological traits and stress responses,as well as the emer-gence of new ecotypes,subspecies,and species during adaptive evolution across varied environ-ments.This occurs through allelic divergences in both coding and non-coding regions in both model and non-model plants.Furthermore,the terrestrial-ization and early diversification of land plants in-volved the acquisition of additional genes,primarily through horizontal gene transfer and whole-genome duplication,which facilitated the development of complex molecular pathways to adapt to increas-ingly diverse environments.Finally,we discuss emerging trends and prospects for exploring and utilizing beneficial alleles for environmental adap-tation,to guide crop breeding efforts in response to global climate change.展开更多
The giant panda(Ailuropoda melanoleuca)is a rare species endemic to China,and also serves as a flagship species for global biodiversity conservation.Elucidating its evolutionary history is of great significance for co...The giant panda(Ailuropoda melanoleuca)is a rare species endemic to China,and also serves as a flagship species for global biodiversity conservation.Elucidating its evolutionary history is of great significance for conservation efforts.However,knowledge about the demographic changes and adaptive evolution of the giant panda remains limited.Paleogenomic research,with its broad temporal and geographic coverage,provides a novel perspective for addressing these questions.Given this,this study discusses three core topics related to the evolution of the giant panda.Firstly,we systematically consolidated the fossil records from the Late Miocene to the Holocene,along with their related studies,illustrating the impact of climatic and anthropogenic factors on the demographic history of the giant panda.In particular,climate change served as the primary driver of population fluctuations during the Pleistocene,leading to two episodes of population expansion and bottleneck.Additionally,human activities played a significant role in population divergence and demographic changes during the Holocene.Secondly,we also elucidated the adaptive process of the giant panda in terms of their highly specialized diet,highlighting long-term adaptation in morphology,genetics,and gut microbiota composition,which have led to its unique adaptive traits.Finally,the potential and significance of the paleogenomic studies in deepening our understanding of the demographic history and adaptive evolution of the giant panda were discussed.Meanwhile,this study demonstrated the potential of paleogenomic approaches for resolving species identification and obtaining individual-level information from fossil specimens,using ancient samples excavated from Baling in Shaanxi and Bamianshan in Hunan as case studies.展开更多
While methodology for determining the mode of evolution in coding sequences has been well established,evaluation of adaptation events in emerging types of phenotype data needs further development.Here,we propose an an...While methodology for determining the mode of evolution in coding sequences has been well established,evaluation of adaptation events in emerging types of phenotype data needs further development.Here,we propose an analysis framework(expression variance decomposition,EVaDe)for comparative single-cell expression data based on phenotypic evolution theory.After decomposing the gene expression variance into separate components,we use two strategies to identify genes exhibiting large between-taxon expression divergence and small within-cell-type expression noise in certain cell types,attributing this pattern to putative adaptive evolution.In a dataset of primate prefrontal cortex,we find that such humanspecific key genes enrich with neurodevelopment-related functions,while most other genes exhibit neutral evolution patterns.Specific neuron types are found to harbor more of these key genes than other cell types,thus likely to have experienced more extensive adaptation.Reassuringly,at the molecular sequence level,the key genes are significantly associated with the rapidly evolving conserved non-coding elements.An additional case analysis comparing the naked mole-rat(NMR)with the mouse suggests that innateimmunity-related genes and cell types have undergone putative expression adaptation in NMR.Overall,the EVaDe framework may effectively probe adaptive evolution mode in single-cell expression data.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
Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution,an important strategy for species survival and persistence.Uncovering the molecular mechanisms of adaptive evolution is ...Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution,an important strategy for species survival and persistence.Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification,phenotypic convergence,and inter-species interaction.As the genome sequences of more and more non-model organisms are becoming available,the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning.In this study,we reviewed the latest research advances in wild animals and plants,focusing on adaptive traits,convergent evolution,and coevolution.Firstly,we focused on the adaptive evolution of morphological,behavioral,and physiological traits.Secondly,we reviewed the phenotypic convergences of life history traits and responding to environmental pressures,and the underlying molecular convergence mechanisms.Thirdly,we summarized the advances of coevolution,including the four main types:mutualism,parasitism,predation and competition.Overall,these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction,demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies.Finally,we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.展开更多
Wild castor grows in the high-altitude tropical desert of the African Plateau,a region known for high ultraviolet radiation,strong light,and extremely dry condition.To investigate the potential genetic basis of adapta...Wild castor grows in the high-altitude tropical desert of the African Plateau,a region known for high ultraviolet radiation,strong light,and extremely dry condition.To investigate the potential genetic basis of adaptation to both highland and tropical deserts,we generated a chromosome-level genome sequence assembly of the wild castor accession WT05,with a genome size of 316 Mb,a scaffold N50 of 31.93 Mb,and a contig N50 of 8.96 Mb,respectively.Compared with cultivated castor and other Euphorbiaceae species,the wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair,photosynthesis,and abiotic stress responses.Genetic variations associated with positive selection were identified in several key genes,such as LIG1,DDB2,and RECG1,involved in nucleotide excision repair.Moreover,a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme environments.The identification of the genes and alleles with selection signatures provides insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert and would facilitate direct improvement of modern castor varieties.展开更多
The adaptation and diversity of animals to the extreme environments of the Qinghai–Tibet Plateau(QTP)are typical materials to study adaptive evolution.The recently discovered Jinchuan yak population has many individu...The adaptation and diversity of animals to the extreme environments of the Qinghai–Tibet Plateau(QTP)are typical materials to study adaptive evolution.The recently discovered Jinchuan yak population has many individuals with multiple ribs.However,little is known about this yak’s origin,evolution,and the genetic mechanisms that formed its unique multirib trait.Here,we report a valuable population genome resource of the Jinchuan yak by resequencing the whole genome of 150 individuals.Population genetic polymorphism and structure analysis reveal that Jinchuan yak can be differentiated as a unique and original yak population among the domestic yak.Combined with geological change,the Jinchuan yak’s evolutionary origin is speculated to be about 6290 years ago,which may be related to the unique geographical environment of the eastern edge of the QTP during this period.Compared with other domestic yaks,this new population has 280 positively selected genes.The genes related to skeletal function hold a considerable and remarkable proportion,suggesting that the specific skeletal characteristics have been enhanced in the adaptive evolution of Jinchuan yak in the extreme plateau environment.The genome-wide association study has revealed that TUBA8 and TUBA4A,the genes that regulate the cytoskeleton,are potential genes associated with the multirib trait.Our findings provide a basis to further understand the generation mechanism of the adaptive evolution of this new population in high-altitude extreme environments and the multivertebrate trait of domestic animals.展开更多
基金funded by the National Natural Science Foundation of China(grant no.32270238 and 31870311).
文摘Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wild C.oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress.Here,47 wild C.oleifera from 11 natural distribution sites in China and 4 relative species of C.oleifera were selected for genome sequencing.“Min Temperature of Coldest Month”(BIO6)had the highest comprehensive contribution to wild C.oleifera distribution.The population genetic structure of wild C.oleifera could be divided into two groups:in cold winter(BIO6≤0℃)and warm winter(BIO6>0℃)areas.Wild C.oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N_(e) than those in warm winter areas.155 singlenucleotide polymorphisms(SNPs)were significantly correlated with the key bioclimatic variables(106 SNPs significantly correlated with BIO6).Twenty key SNPs and 15 key copy number variation regions(CNVRs)were found with genotype differentiation>50%between the two groups of wild C.oleifera.Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance,and they were also found within a CNVR suggesting interactions between them.Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress.The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.
基金supported by the National Natural Science Foundation of China(NSFC 31900313)to X.Z.the Central guide local science and technology development funds(XZ202301YD0007C)to L.Y.+1 种基金NSFC(32471572)National Key Research and Development Program of China(2024YFC2310303)to D.L。
文摘The globin superfamily,central to oxygen(O_(2))cascade dynamics,exemplifies how canalization—evolutionary stabilization of phenotypic traits—enables vertebrates to thrive in extreme environments.In birds,hemoglobins(Hbs)serve as a paradigm of this process,with structural and functional canalization underpinning their exceptional aerobic capacity and elevational diversification.Despite significant advances of globins in our understanding of avian aerobic adaptation,a comprehensive synthesis of functional diversity,molecular evolution,and structural innovation is essential to fully elucidate their canalized roles in O_(2)homeostasis.Integrating perspectives on globin functional diversity and structural evolution,this review examines how chance(mutation/fixation biases)and contingency(historical genetic/epistatic constraints)shape Hb divergence and parallelism,thereby bridging molecular mechanisms with physiological adaptation in birds.We highlight how avian Hbs,canalized through compensatory substitutions and allosteric regulation,achieves a balance between evolutionary robustness and adaptive plasticity.However,critical gaps remain persist:the roles of understudied globins(e.g.,neuroglobin,globin E)and the mechanisms of genetic assimilation in migratory taxa.We propose an integrative framework that incorporates ecological divergence(elevation,flight endurance),phylogenetic timescales,and systems biology to unravel how canalization directs adaptive compromise.By focusing on birds within the amniotes,this synthesis advances a cohesive model for vertebrate evolution,wherein canalized globins reconcile metabolic precision with ecological innovation.Ultimately,this review refines hypotheses of O_(2)cascade evolution and calls for cross-disciplinary studies to decode the genetic and physiological architecture underlying adaptive canalization in extreme environments.
基金supported by the National Key Research and Development Program of China(2021YFC2101303)the National Natural Science Foundation of China(U22A20424 and 22378048)+5 种基金the Major scientific and technological projects of Sinopecthe Dalian Technology Talents Project for Distinguished Young Scholars(2021RJ03)the Fundamental Research Funds for the Central Universities(DUT25LAB104)the Liaoning Revitalization Talents Program(XLYC2202049)the Ningbo Natural Science Foundation(2022J013)the Ningbo Municipal Public Welfare Science and Technology Foundation(2024S004)。
文摘Saccharomyces cerevisiae is not naturally capable of efficiently utilizing xylose as a carbon source.When cultured with lignocellulosic hydrolysates containing pretreatment-derived inhibitors,S.cerevisiae suffers from much lower sugar uptake,ethanol yield and fermentation efficiency.Thus,considering efficient xylose conversion into ethanol during non-detoxified hydrolysate culture,genetic engineering and adaptive evolution of S.cerevisiae might be a promising joint strategy for improving xylose uptake and ethanol production.In this study,an inhibitor-tolerant strain S.cerevisiae SPSC01-TAF94 was genetically engineered by overexpressing both xylose transport-and metabolism-related genes(N360F,Ru-xyl A,TAL1,TKL1,RKI1 and RPE1),yielding the xylose-utilizing strain TAF94-X,followed by three-stage adaptation in non-detoxified corn stover hydrolysate containing 5 g·L^(-1)acetic acid,0.32 g·L^(-1)furfural,0.17 g·L(-1)HMF and 0.19 g·L^(-1)vanillin as the major inhibitors as well as 20,40 and 60 g·L^(-1)xylose adjusted as the major carbon source,respectively.Finally,an active xylose-utilizing and ethanolproducing strain TAF94-X60 was obtained,which achieved 44.9 g·L^(-1)ethanol with yield of0.41 g·g^(-1),productivity of 0.62 g·L^(-1)·h^(-1)and xylose consumption rate of 0.42 g·L^(-1)·h^(-1)during hydrolysate culture,compared to those of 36.5 g·L^(-1),0.38 g·g^(-1),0.50 g·L^(-1)·h^(-1)and 0.20 g·L^(-1)·h^(-1)obtained with the control strain TAF94-X.The proposed joint strategy effectively utilizes hydrolyzed sugars while eliminating the need for conventional detoxification or water washing processes,thus enhancing the economic feasibility of large-scale lignocellulosic ethanol production.
基金supported by the National Natural Science Foundation of China(31470110,31970399)China National GeneBank(CNGB)。
文摘Pikas(Lagomorpha:Ochotonidae)are small mouselike lagomorphs.To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet)Plateau(QTP),we collected 226 pikas and measured 20 morphological characteristics and recorded habitat information.We also sequenced the genome of 81specimens,representing 27 putative pika species.The genome-wide tree based on 4?090 coding genes identified five subgenera,i.e.,Alienauroa,Conothoa,Lagotona,Ochotona,and Pika,consistent with morphometric data.Morphologically,Alienauroa and Ochotona had similar traits,including smaller size and earlier divergence time compared to other pikas.Consistently,the habitats of Alienauroa and Ochotona differed from those of the remaining subgenera.Phylogenetic signal analysis detected 83 genes significantly related to morphological characteristics,including several visual and hearingrelated genes.Analysis of shared amino acid substitutions and positively selected genes(PSGs)in Alienauroa and Ochotona identified two genes,i.e.,mitochondrial function-related TSFM(p.Q155E)and low-light visual sensitivity-related PROM1(p.H419Y).Functional experiments demonstrated that TSFM-155E significantly enhanced mitochondrial function compared to TSFM-155Q in other pikas,and PROM1-419Y decreased the modeling of dynamic intracellular chloride efflux upon calcium uptake.Alienauroa and Ochotona individuals mostly inhabit different environments(e.g.,subtropical forests)than other pikas,suggesting that a shift from the larger ancestral type and changes in sensory acuity and energy enhancement may have been required in their new environments.This study increases our understanding of the evolutionary history of pikas.
基金supported by the National Key Research and Development Program of China(2021YFC2101303)the National Natural Science Foundation of China(U22A20424 and 22378048)+6 种基金the Major Scientific and Technological Projects of Sinopecthe Dalian Technology Talents Project for Distinguished Young Scholars(2021RJ03)the Yunnan Provincial Rural Energy Engineering Key Laboratory(2022KF003)the National Natural Science Foundation of Liaoning Province(2023-MS-110)the Liaoning Revitalization Talents Program(XLYC2202049)the Fundamental Research Funds for the Central Universities(DUT22LK22)the CAS Key Laboratory of Renewable Energy,Guangzhou Institute of Energy Conversion(E229kf0401)。
文摘Acetic acid and furfural are known as prevalent inhibitors deriving from pretreatment during lignocellulosic ethanol production.They negatively impact cell growth,glucose uptake and ethanol biosynthesis of Saccharomyces cerevisiae strains.Development of industrial S.cerevisiae strains with high tolerance towards these inhibitors is thus critical for efficient lignocellulosic ethanol production.In this study,the acetic acid or furfural tolerance of different S.cerevisiae strains could be significantly enhanced after adaptive evolution via serial cultivation for 40 generations under stress conditions.The acetic acid-based adaptive strain SPSC01-TA9 produced 30.5 g·L^(-1)ethanol with a yield of 0.46 g·g^(-1)in the presence of 9 g·L^(-1)acetic acid,while the acetic acid/furfural-based adaptive strain SPSC01-TAF94 produced more ethanol of 36.2 g·L^(-1)with increased yield up to 0.49 g·g^(-1)in the presence of both 9 g·L^(-1)acetic acid and 4 g·L^(-1)furfural.Significant improvements were also observed during non-detoxified corn stover hydrolysate culture by SPSC01-TAF94,which achieved ethanol production and yield of 29.1 g·L^(-1)and 0.49 g·g^(-1),respectively,the growth and fermentation efficiency of acetic acid/furfural-based adaptive strain in hydrolysate was 95%higher than those of wildtype strains,indicating the acetic acid-and furfural-based adaptive evolution strategy could be an effective approach for improving lignocellulosic ethanol production.The adapted strains developed in this study with enhanced tolerance against acetic acid and furfural could be potentially contribute to economically feasible and sustainable lignocellulosic biorefinery.
基金supported by the National Natural Science Foundation of China(31701577).
文摘Next-generation sequencing technology has transformed our ability to assess the taxonomic composition functions of host-associated microbiota and microbiomes. More human microbiome research projects—particularly those that explore genomic mutations within the microbiome—will be launched in the next decade. This review focuses on the coevolution of microbes within a microbiome, which shapes strain-level diversity both within and between host species. We also explore the correlation between microbial genomic mutations and common metabolic diseases, and the adaptive evolution of pathogens and probiotics during invasion and colonization. Finally, we discuss advances in methods and algorithms for annotating and analyzing microbial genomic mutations.
基金supported by the National Natural Science Foundation of China(NSFC,Grant Nos.31370395 and 31500266)the"One Hundred Talents"project of the Chinese Academy of Sciences(Grant No.29Y127E71)
文摘In the field of phylogenetic analyses, the rbcL gene encoded large subunit Ribulose-1,5-biphosphate carboxylase/oxygenase （Rubisco, EC4.1.1.39）, which plays a crucial role in the process of photosynthesis for most terrestrial plants, has been considered to be conserved; however, recent controversy regarding rbcL conservation has appeared since it was proposed to be under natural selection within all principal lineages of land plants. In this study, by examining the variation of DNA and protein sequences among 17 species in the family Tamaricaceae, three nonsynonymous mutations were identified to be under positive selection. The favored sites were located in the alph-helix domains of Rubisco, with decreased hydrophobicity and increased entropy, which could facilitate C〇 2 penetration into the active site of Rubisco. We also found that the expression level of rbcL in different genotypes of Reaumuria soongarica shifted in response to various stresses such as drought, temperature, salt, and light. This study not only sheds light on the functional/structural features of Rubisco in the evolution scenarios from 〇 3-like into C4 in Tamaricaceae but also provides useful information on directing genetic performance to enhance photosynthesis efficiency of desert plants for sustaining fragile desert ecosystems; fur-thermore, it promotes the ability to cope with desert aridification and global warming.
基金supported by the Natural Science Foundation of China(Nos.32030006 and No.32270302)the Natural Science Foundation of Sichuan Province(No.2024NSFSC0340).
文摘Plants adapt to their local environments through natural or artificial selection of optimal phenotypes.Recent advances in genomics and computational biology,which integrate phenotypic and multi-omics data,have facilitated the rapid identification of key genes and allelic variations that underlie these adaptive evolutionary processes.Under-standing the underlying molecular mechanisms has significantly enhanced our knowledge of how plants respond to changed habitats,including various biotic and abiotic stresses.In this review,we highlight recent progress in elucidating the ge-netic basis of phenotypic variation in morphological traits and stress responses,as well as the emer-gence of new ecotypes,subspecies,and species during adaptive evolution across varied environ-ments.This occurs through allelic divergences in both coding and non-coding regions in both model and non-model plants.Furthermore,the terrestrial-ization and early diversification of land plants in-volved the acquisition of additional genes,primarily through horizontal gene transfer and whole-genome duplication,which facilitated the development of complex molecular pathways to adapt to increas-ingly diverse environments.Finally,we discuss emerging trends and prospects for exploring and utilizing beneficial alleles for environmental adap-tation,to guide crop breeding efforts in response to global climate change.
基金supported by the National Natural Science Foundation of China(Grant Nos.32100489,41925009,42262001 and 42102001)。
文摘The giant panda(Ailuropoda melanoleuca)is a rare species endemic to China,and also serves as a flagship species for global biodiversity conservation.Elucidating its evolutionary history is of great significance for conservation efforts.However,knowledge about the demographic changes and adaptive evolution of the giant panda remains limited.Paleogenomic research,with its broad temporal and geographic coverage,provides a novel perspective for addressing these questions.Given this,this study discusses three core topics related to the evolution of the giant panda.Firstly,we systematically consolidated the fossil records from the Late Miocene to the Holocene,along with their related studies,illustrating the impact of climatic and anthropogenic factors on the demographic history of the giant panda.In particular,climate change served as the primary driver of population fluctuations during the Pleistocene,leading to two episodes of population expansion and bottleneck.Additionally,human activities played a significant role in population divergence and demographic changes during the Holocene.Secondly,we also elucidated the adaptive process of the giant panda in terms of their highly specialized diet,highlighting long-term adaptation in morphology,genetics,and gut microbiota composition,which have led to its unique adaptive traits.Finally,the potential and significance of the paleogenomic studies in deepening our understanding of the demographic history and adaptive evolution of the giant panda were discussed.Meanwhile,this study demonstrated the potential of paleogenomic approaches for resolving species identification and obtaining individual-level information from fossil specimens,using ancient samples excavated from Baling in Shaanxi and Bamianshan in Hunan as case studies.
文摘While methodology for determining the mode of evolution in coding sequences has been well established,evaluation of adaptation events in emerging types of phenotype data needs further development.Here,we propose an analysis framework(expression variance decomposition,EVaDe)for comparative single-cell expression data based on phenotypic evolution theory.After decomposing the gene expression variance into separate components,we use two strategies to identify genes exhibiting large between-taxon expression divergence and small within-cell-type expression noise in certain cell types,attributing this pattern to putative adaptive evolution.In a dataset of primate prefrontal cortex,we find that such humanspecific key genes enrich with neurodevelopment-related functions,while most other genes exhibit neutral evolution patterns.Specific neuron types are found to harbor more of these key genes than other cell types,thus likely to have experienced more extensive adaptation.Reassuringly,at the molecular sequence level,the key genes are significantly associated with the rapidly evolving conserved non-coding elements.An additional case analysis comparing the naked mole-rat(NMR)with the mouse suggests that innateimmunity-related genes and cell types have undergone putative expression adaptation in NMR.Overall,the EVaDe framework may effectively probe adaptive evolution mode in single-cell expression data.
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supported by the National Natural Science Foundation of China (31821001)the Strategic Priority Research Program of Chinese Academy of Sciences (XDB31000000)。
文摘Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution,an important strategy for species survival and persistence.Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification,phenotypic convergence,and inter-species interaction.As the genome sequences of more and more non-model organisms are becoming available,the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning.In this study,we reviewed the latest research advances in wild animals and plants,focusing on adaptive traits,convergent evolution,and coevolution.Firstly,we focused on the adaptive evolution of morphological,behavioral,and physiological traits.Secondly,we reviewed the phenotypic convergences of life history traits and responding to environmental pressures,and the underlying molecular convergence mechanisms.Thirdly,we summarized the advances of coevolution,including the four main types:mutualism,parasitism,predation and competition.Overall,these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction,demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies.Finally,we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.
基金supported by the National Key R&D Program of China(Grant No.2018YFA0901800)the National Natural Science Foundation of China(Grant No.32072101)+1 种基金the Guangdong Basic and Applied Basic Research Foundation,China(Grant No.2019A1515111150)the Shenzhen Science and Technology Program,China(Grant No.KQTD20180411143628272)。
文摘Wild castor grows in the high-altitude tropical desert of the African Plateau,a region known for high ultraviolet radiation,strong light,and extremely dry condition.To investigate the potential genetic basis of adaptation to both highland and tropical deserts,we generated a chromosome-level genome sequence assembly of the wild castor accession WT05,with a genome size of 316 Mb,a scaffold N50 of 31.93 Mb,and a contig N50 of 8.96 Mb,respectively.Compared with cultivated castor and other Euphorbiaceae species,the wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair,photosynthesis,and abiotic stress responses.Genetic variations associated with positive selection were identified in several key genes,such as LIG1,DDB2,and RECG1,involved in nucleotide excision repair.Moreover,a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme environments.The identification of the genes and alleles with selection signatures provides insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert and would facilitate direct improvement of modern castor varieties.
基金supported by the National Natural Science Foundation of China(Grant No.31872361)“the Fundamental Research Funds for the Central Universities”,Southwest Minzu University(2018NQN02)Sichuan provincial central government guiding local science and technology development in 2020(20ZYZYTS0020).
文摘The adaptation and diversity of animals to the extreme environments of the Qinghai–Tibet Plateau(QTP)are typical materials to study adaptive evolution.The recently discovered Jinchuan yak population has many individuals with multiple ribs.However,little is known about this yak’s origin,evolution,and the genetic mechanisms that formed its unique multirib trait.Here,we report a valuable population genome resource of the Jinchuan yak by resequencing the whole genome of 150 individuals.Population genetic polymorphism and structure analysis reveal that Jinchuan yak can be differentiated as a unique and original yak population among the domestic yak.Combined with geological change,the Jinchuan yak’s evolutionary origin is speculated to be about 6290 years ago,which may be related to the unique geographical environment of the eastern edge of the QTP during this period.Compared with other domestic yaks,this new population has 280 positively selected genes.The genes related to skeletal function hold a considerable and remarkable proportion,suggesting that the specific skeletal characteristics have been enhanced in the adaptive evolution of Jinchuan yak in the extreme plateau environment.The genome-wide association study has revealed that TUBA8 and TUBA4A,the genes that regulate the cytoskeleton,are potential genes associated with the multirib trait.Our findings provide a basis to further understand the generation mechanism of the adaptive evolution of this new population in high-altitude extreme environments and the multivertebrate trait of domestic animals.
