Endothelial PAS domain protein 1 gene (EPAS1) is a key transcription factor that activates the expression of oxygen-regu- lated genes. In this study, in order to better understand the effects of EPAS1 gene on hemato...Endothelial PAS domain protein 1 gene (EPAS1) is a key transcription factor that activates the expression of oxygen-regu- lated genes. In this study, in order to better understand the effects of EPAS1 gene on hematologic parameters in yak, we firstly quantified the tissue expression patterns for EPASl mRNA of yak, identified polymorphism in this gene and evaluated its association with hematologic parameters. Expression of EPAS1 mRNA was detected in all eight tissues (heart, liver, lung, spleen, pancreas, kidney, muscles and ovary). The expressions of EPAS1 in lung and pancreas were extremely higher than other tissues examined. Three novel single nucleotide polymorphisms (SNPs) (g.83052 C〉T, g.83065 G〉A and g.83067 C〉A) within the EPAS1 were identified and genotyped in Pali (PL), Gannan (GN) and Tianzhu White (TZW) yak breeds. Significant higher frequencies of the AA and GA genotypes and A allele of the g.83065 G〉A were observed in the PL and GN breeds than that in the TZW breed (P〈0.01). Association analysis of the PL breed indicated that the g.83065 G〉A polymorphism was significantly associated with hemoglobin (HGB) concentration in yaks (P〈0.05). Individuals with genotype AA had significantly higher HGB concentration (P〈0.05) than those with genotype GA and GG. All these results will help our further understanding of biological functional of yak EPAS1 gene in responding to hypoxia and also indicate EPAS1 might contribute to the hypoxia adaptation of the yak.展开更多
Background: Vascular endothelial growth factor A (VEGFA) can induce endothelial cell proliferation, promote cell migration, and inhibit apoptosis. These processes play key roles in physiological blood vessel format...Background: Vascular endothelial growth factor A (VEGFA) can induce endothelial cell proliferation, promote cell migration, and inhibit apoptosis. These processes play key roles in physiological blood vessel formation and pathological angiogenesis. Methods: In this study, we examined VEGFA gene expression in the heart, liver, and kidney of Tibetan pigs (-I-P), Yorkshire pigs that migrated to high altitudes (YH), and Yorkshire pigs that lived at low altitudes (YL). We used PCR and Sanger sequencing to screen for single nucleotide polymorphisms (SNPs) in 5'-flanking DNA and exons of the VEGFA gene. Quantitative real-time PCR and western blots were used to measure expression levels and PCR products were sequenced. Results: Results showed that the VEGFA mRNA and protein expression in heart, liver and kidney of TP was higher than that in YH and YL. In addition, the mRNA sequence of the pig VEGFA gene was conserved among pig breeds, and only five SNPs were found in the 5'-flanking region of the VEGFA gene, the allele frequency distributions of the 5 SNPs were not significantly different between the TP, Yorkshire (YL), and Diannan small-ear (DN) pig populations. Conclusion: In conclusion, the Tibetan pig showed high tissues, which suggests that the VEGFA gene may play a levels of VEGFA gene expression in several hypoxic major functional role in hypoxic adaptation.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
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
The yeast HAL1 gene was introduced into Arabidopsis thaliana by Agrobacterium tumefaciens-mediated transformation with vacuum infiltration under the control of CaMV 35S promoter. Thirty-three individual kanamycin resi...The yeast HAL1 gene was introduced into Arabidopsis thaliana by Agrobacterium tumefaciens-mediated transformation with vacuum infiltration under the control of CaMV 35S promoter. Thirty-three individual kanamycin resistant plants were obtained from 75,000 seeds. Southern blotting analysis indicated that HAL1 gene had been integrated into all of the transgenic plants’ genomes. The copy number of HAL1 gene in transgenic plants was mostly 1 to 3 by Southern analysis. Phenotypes of transgenic plants have no differences with wild type plants. several samples of transformants were self-pollinated, and progenies from transformed and non-transformed plants (controls) were evaluated for salt tolerance and gene expression. Measurement of concentrations of intracellular K+ and Na+ showed that transgenic lines were able to retain less Na+ than that of the control under salt stress. Results from different tests indicated the expression of HAL1 gene promotes a higher level of salt tolerance in vivo in the transgenic Arabidopsis plants.展开更多
Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology.The use of genomic data has greatly advanced our understandings on this ...Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology.The use of genomic data has greatly advanced our understandings on this issue,as well as other aspects of evolutionary biology,including molecular adaptation,speciation,and even conservation of endangered species.Despite the well-recognized advantages,usages of genomic data are still limited to non-mammal vertebrate groups,partly due to the difficulties in assembling large or highly heterozygous genomes.Although this is particularly the case for amphibians,nonetheless,several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape,giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms.At the same time,these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians.In this review,we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data,and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era,as well as directions for future research.展开更多
Pseudoalteromonas sp. SM9913 is a phychrotmphic bacterium isolated from the deep-sea sediment. The genes encoding chaperones DnaJ and DnaK of P. sp. SM9913 were cloned by normal PCR and TAIL - PCR (GenBank accession ...Pseudoalteromonas sp. SM9913 is a phychrotmphic bacterium isolated from the deep-sea sediment. The genes encoding chaperones DnaJ and DnaK of P. sp. SM9913 were cloned by normal PCR and TAIL - PCR (GenBank accession Nos DQ640312, DQ504163 ). The chaperones DnaJ and DnaK from the strain SM9913 contain such conserved domains as those of many other bacteria, and show some cold-adapted characteristics in their structures when compared with those from psychro-, meso-and themophilic bacteria. It is indicated that chaperones DnaJ and DnaK of P. sp. SM9913 may be adapted to low temperature in deep-sea and function well in assisting folding, assembling and translocation of proteins at low temperature. This research lays a foundation for the further study on the cold-adapted mechanism of chaperones DnaJ and DnaK of cold-adapted microorganisms.展开更多
Aerobic anoxygenic phototrophic bacteria(AAPB)are photoheterotrophic prokaryotes able to use both light and dissolved organic matter as energy sources.Roseicitreum antarcticum ZS2-28^(T)was isolated from intertidal se...Aerobic anoxygenic phototrophic bacteria(AAPB)are photoheterotrophic prokaryotes able to use both light and dissolved organic matter as energy sources.Roseicitreum antarcticum ZS2-28^(T)was isolated from intertidal sediment in the Larsemann Hills,Princess Elizabeth Land,Antarctica,and was able to produce bacteriochlorophyll a.It is the type strain of the sole species within the genus Roseicitreum.The complete genome sequence of the bacterium was determined using Illumina HiSeq X and PacBio RSII systems.The genome of R.antarcticum ZS2-28^(T)was 4253095 bp and consisted of one chromosome and four plasmids.A number of genes related to the bacteriochlorophyll a production,photosynthetic reaction,cold adaptation,salt adaptation,ultra-violet resistance and DNA damage repairing were found in the genome.In addition to genomic islands and typeⅣsecretion systems,genes related to gene transfer agents were detected in the genome of R.antarcticum ZS2-28^(T),suggesting that this bacterium can adapt to its environment by acquiring exogenous nucleic acids.The annotated complete genome sequence provides genetic insights into the environmental adaptation and ecological function of R.antarcticum ZS2-28^(T)in Antarctic coastal area.展开更多
The Tibetan Partridge(Perdix hodgsoniae)is an endemic species distributed in high-altitude areas of 3600–5600 m on the Qinghai–Tibet Plateau.To explore how the species is adapted to the high elevation environment,we...The Tibetan Partridge(Perdix hodgsoniae)is an endemic species distributed in high-altitude areas of 3600–5600 m on the Qinghai–Tibet Plateau.To explore how the species is adapted to the high elevation environment,we as-sembled a draft genome based on both the Illumina and PacBio sequencing platforms with its population genetics and genomics analysis.In total,134.74 Gb short reads and 30.81 Gb long reads raw data were generated.The 1.05-Gb assembled genome had a contig N50 of 4.56 Mb,with 91.94%complete BUSCOs.The 17457 genes were annotated,and 11.35%of the genome was composed of repeat sequences.The phylogenetic tree showed that P.hodgsoniae was located at the basal position of the clade,including Golden Pheasant(Chrysolophus pictus),Common Pheasant(Phasianus colchicus),and Mikado Pheasant(Syrmaticus mikado).We found that 1014,2595,and 2732 of the 6641 one-to-one orthologous genes were under positive selection in P.hodgsoniae,detected using PAML,BUSTED,and aBSREL programs,respectively,of which 965 genes were common under positive selec-tion with 3 different programs.Several positively selected genes and immunity pathways relevant to high-altitude adaptation were detected.Gene family evolution showed that 99 gene families experienced significant expansion events,while 6 gene families were under contraction.The total number of olfactory receptor genes was relatively low in P.hodgsoniae.Genomic data provide an important resource for a further study on the evolutionary history of P.hodgsoniae,which provides a new insight into its high-altitude adaptation mechanisms.展开更多
Yellow maize contains high levels of β-carotene(βC), making it an important crop for combating vitamin A deficiency through biofortification. In this study, nine maize inbred lines were selected at random from 31 pr...Yellow maize contains high levels of β-carotene(βC), making it an important crop for combating vitamin A deficiency through biofortification. In this study, nine maize inbred lines were selected at random from 31 provitamin A(PVA) maize inbred lines and crossed in a partial diallel mating design to develop 36 crosses. The crosses were evaluated in the field in two locations(Samaru and Kerawa) and their seed carotenoid content were determined by high-performance liquid chromatography. The modes of gene action, heritability, and correlations between agronomic traits and carotenoid content were estimated. Additive genetic variances(σ~2a) were lower than non-additive genetic variances(σ~2d) for all the carotenoids, plant height(PH), and grain yield(GY), suggesting a preponderance of non-additive gene action. Broad-sense heritability(H^2) was high(H^2> 60%) for zeaxanthin,days to anthesis, and PH, moderate(30% < H^2< 60%) for lutein and GY, and low(H^2< 30%)for alpha carotene, beta cryptoxanthin, βC, and PVA. Genetic advance as a percentage of mean, considered with H^2, also suggests a preponderance of non-additive gene action for PVA carotenoids. Hybrid variety development is thus an appropriate approach to improving grain yield and PVA. GY showed no significant genotypic correlations with carotenoid content, suggesting that these traits can be improved concurrently. Thus, there is ample scope for improvement of PVA and GY in the sample of tropical-adapted maize.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
野生大豆(Glycine soja Sieb.&Zucc.)是栽培大豆(Glycine max [L.] Merr.)的近缘祖先种。在大豆驯化的过程中,栽培大豆丢失了大量的基因或等位变异,导致栽培大豆的遗传多样性降低,这严重限制了栽培大豆品种选育和改良的有效性与丰...野生大豆(Glycine soja Sieb.&Zucc.)是栽培大豆(Glycine max [L.] Merr.)的近缘祖先种。在大豆驯化的过程中,栽培大豆丢失了大量的基因或等位变异,导致栽培大豆的遗传多样性降低,这严重限制了栽培大豆品种选育和改良的有效性与丰富性。我国野生大豆种质资源丰富,蕴藏着许多高蛋白含量、抗病虫、耐干旱、耐盐碱等方面的潜力基因,挖掘潜力基因并利用分子设计育种技术应用到现代的栽培大豆品种中,能够有效地拓宽栽培大豆的遗传多样性。本文综述了野生大豆的分布规律和形态特征、近年来在野生大豆中发掘的重要功能基因或位点,包括百粒重、开花期和成熟期、蛋白质和油分含量、抗病、抗虫、耐盐碱、耐干旱等重要农艺性状基因,并讨论这些重要基因或位点在未来栽培大豆育种中的应用潜力,以期为育种家培育和改良大豆新品种提供一种新的育种思路和策略。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
基金supported by the Special Fund for Agro-scientific Research in the Public Interest,China (201003061)the Key Technologies R&D Program of China during the 12thFive-Year Plan period (2012BAD13B05)+1 种基金the Great Project of Science and Technology of Gansu Province in China (1102NKDA027)the National Natural Science Foundation of China (31101702)
文摘Endothelial PAS domain protein 1 gene (EPAS1) is a key transcription factor that activates the expression of oxygen-regu- lated genes. In this study, in order to better understand the effects of EPAS1 gene on hematologic parameters in yak, we firstly quantified the tissue expression patterns for EPASl mRNA of yak, identified polymorphism in this gene and evaluated its association with hematologic parameters. Expression of EPAS1 mRNA was detected in all eight tissues (heart, liver, lung, spleen, pancreas, kidney, muscles and ovary). The expressions of EPAS1 in lung and pancreas were extremely higher than other tissues examined. Three novel single nucleotide polymorphisms (SNPs) (g.83052 C〉T, g.83065 G〉A and g.83067 C〉A) within the EPAS1 were identified and genotyped in Pali (PL), Gannan (GN) and Tianzhu White (TZW) yak breeds. Significant higher frequencies of the AA and GA genotypes and A allele of the g.83065 G〉A were observed in the PL and GN breeds than that in the TZW breed (P〈0.01). Association analysis of the PL breed indicated that the g.83065 G〉A polymorphism was significantly associated with hemoglobin (HGB) concentration in yaks (P〈0.05). Individuals with genotype AA had significantly higher HGB concentration (P〈0.05) than those with genotype GA and GG. All these results will help our further understanding of biological functional of yak EPAS1 gene in responding to hypoxia and also indicate EPAS1 might contribute to the hypoxia adaptation of the yak.
基金supported by the National Major Special Project on New Varieties Cultivation for Transgenic Organisms (2016ZX08009-003-006)the National Key Technology R&D Program (2012BAD03B03)the Program for Changjiang Scholar and Innovation Research Team in University (IRT1191)
文摘Background: Vascular endothelial growth factor A (VEGFA) can induce endothelial cell proliferation, promote cell migration, and inhibit apoptosis. These processes play key roles in physiological blood vessel formation and pathological angiogenesis. Methods: In this study, we examined VEGFA gene expression in the heart, liver, and kidney of Tibetan pigs (-I-P), Yorkshire pigs that migrated to high altitudes (YH), and Yorkshire pigs that lived at low altitudes (YL). We used PCR and Sanger sequencing to screen for single nucleotide polymorphisms (SNPs) in 5'-flanking DNA and exons of the VEGFA gene. Quantitative real-time PCR and western blots were used to measure expression levels and PCR products were sequenced. Results: Results showed that the VEGFA mRNA and protein expression in heart, liver and kidney of TP was higher than that in YH and YL. In addition, the mRNA sequence of the pig VEGFA gene was conserved among pig breeds, and only five SNPs were found in the 5'-flanking region of the VEGFA gene, the allele frequency distributions of the 5 SNPs were not significantly different between the TP, Yorkshire (YL), and Diannan small-ear (DN) pig populations. Conclusion: In conclusion, the Tibetan pig showed high tissues, which suggests that the VEGFA gene may play a levels of VEGFA gene expression in several hypoxic major functional role in hypoxic adaptation.
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.
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a grant from State 863 National High Technology Research Development Project of China, No. 819-0803.
文摘The yeast HAL1 gene was introduced into Arabidopsis thaliana by Agrobacterium tumefaciens-mediated transformation with vacuum infiltration under the control of CaMV 35S promoter. Thirty-three individual kanamycin resistant plants were obtained from 75,000 seeds. Southern blotting analysis indicated that HAL1 gene had been integrated into all of the transgenic plants’ genomes. The copy number of HAL1 gene in transgenic plants was mostly 1 to 3 by Southern analysis. Phenotypes of transgenic plants have no differences with wild type plants. several samples of transformants were self-pollinated, and progenies from transformed and non-transformed plants (controls) were evaluated for salt tolerance and gene expression. Measurement of concentrations of intracellular K+ and Na+ showed that transgenic lines were able to retain less Na+ than that of the control under salt stress. Results from different tests indicated the expression of HAL1 gene promotes a higher level of salt tolerance in vivo in the transgenic Arabidopsis plants.
基金This study was supported by the National Natural Science Foundation of China(31671326,31871275)the Highlevel Talent Introduction Program of Yunnan University to Y.B.S。
文摘Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology.The use of genomic data has greatly advanced our understandings on this issue,as well as other aspects of evolutionary biology,including molecular adaptation,speciation,and even conservation of endangered species.Despite the well-recognized advantages,usages of genomic data are still limited to non-mammal vertebrate groups,partly due to the difficulties in assembling large or highly heterozygous genomes.Although this is particularly the case for amphibians,nonetheless,several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape,giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms.At the same time,these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians.In this review,we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data,and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era,as well as directions for future research.
基金The work was supported by the Hi-Tech Research and Development Program of China under contract Nos 2006AA09Z414 and 2007AA091903;the China Ocean Mineral Resources R & D Association under contract No. DYXM - 115 - 02 - 2 - 6;the National Natural Science Foundation of China under contract No. Z2004D02;the Natural Science Foundation of Shandong Province of China under contract No. Z2004D02;the Foundation for Young Excellent Scientists in Shandong Province of China under contract No. 2006BS02002;the Program for New Century Excellent Talents in University under contract No. NCET - 06 - 0578.
文摘Pseudoalteromonas sp. SM9913 is a phychrotmphic bacterium isolated from the deep-sea sediment. The genes encoding chaperones DnaJ and DnaK of P. sp. SM9913 were cloned by normal PCR and TAIL - PCR (GenBank accession Nos DQ640312, DQ504163 ). The chaperones DnaJ and DnaK from the strain SM9913 contain such conserved domains as those of many other bacteria, and show some cold-adapted characteristics in their structures when compared with those from psychro-, meso-and themophilic bacteria. It is indicated that chaperones DnaJ and DnaK of P. sp. SM9913 may be adapted to low temperature in deep-sea and function well in assisting folding, assembling and translocation of proteins at low temperature. This research lays a foundation for the further study on the cold-adapted mechanism of chaperones DnaJ and DnaK of cold-adapted microorganisms.
基金the National Key R&D Program of China(Grant no.2018YFC1406903)the National Natural Science Foundation of China(Grant nos.91851201 and 41476171).
文摘Aerobic anoxygenic phototrophic bacteria(AAPB)are photoheterotrophic prokaryotes able to use both light and dissolved organic matter as energy sources.Roseicitreum antarcticum ZS2-28^(T)was isolated from intertidal sediment in the Larsemann Hills,Princess Elizabeth Land,Antarctica,and was able to produce bacteriochlorophyll a.It is the type strain of the sole species within the genus Roseicitreum.The complete genome sequence of the bacterium was determined using Illumina HiSeq X and PacBio RSII systems.The genome of R.antarcticum ZS2-28^(T)was 4253095 bp and consisted of one chromosome and four plasmids.A number of genes related to the bacteriochlorophyll a production,photosynthetic reaction,cold adaptation,salt adaptation,ultra-violet resistance and DNA damage repairing were found in the genome.In addition to genomic islands and typeⅣsecretion systems,genes related to gene transfer agents were detected in the genome of R.antarcticum ZS2-28^(T),suggesting that this bacterium can adapt to its environment by acquiring exogenous nucleic acids.The annotated complete genome sequence provides genetic insights into the environmental adaptation and ecological function of R.antarcticum ZS2-28^(T)in Antarctic coastal area.
基金The National Center for Biotechnology Information(NCBI)BioProject and BioSample accession numbers of Perdix hodgsoniae are PRJNA760267 and SAMN21212221,respectivelyThe raw reads have been deposited in the NCBI SRA database with the accession numbers SRR15900414(Illumina),SRR15900412,and SRR15900413(PacBio).
文摘The Tibetan Partridge(Perdix hodgsoniae)is an endemic species distributed in high-altitude areas of 3600–5600 m on the Qinghai–Tibet Plateau.To explore how the species is adapted to the high elevation environment,we as-sembled a draft genome based on both the Illumina and PacBio sequencing platforms with its population genetics and genomics analysis.In total,134.74 Gb short reads and 30.81 Gb long reads raw data were generated.The 1.05-Gb assembled genome had a contig N50 of 4.56 Mb,with 91.94%complete BUSCOs.The 17457 genes were annotated,and 11.35%of the genome was composed of repeat sequences.The phylogenetic tree showed that P.hodgsoniae was located at the basal position of the clade,including Golden Pheasant(Chrysolophus pictus),Common Pheasant(Phasianus colchicus),and Mikado Pheasant(Syrmaticus mikado).We found that 1014,2595,and 2732 of the 6641 one-to-one orthologous genes were under positive selection in P.hodgsoniae,detected using PAML,BUSTED,and aBSREL programs,respectively,of which 965 genes were common under positive selec-tion with 3 different programs.Several positively selected genes and immunity pathways relevant to high-altitude adaptation were detected.Gene family evolution showed that 99 gene families experienced significant expansion events,while 6 gene families were under contraction.The total number of olfactory receptor genes was relatively low in P.hodgsoniae.Genomic data provide an important resource for a further study on the evolutionary history of P.hodgsoniae,which provides a new insight into its high-altitude adaptation mechanisms.
基金the Institutefor Agricultural Research, Ahmadu Bello University (IAR/ABU) Samaru, Nigeria, for the funding support provided for this study
文摘Yellow maize contains high levels of β-carotene(βC), making it an important crop for combating vitamin A deficiency through biofortification. In this study, nine maize inbred lines were selected at random from 31 provitamin A(PVA) maize inbred lines and crossed in a partial diallel mating design to develop 36 crosses. The crosses were evaluated in the field in two locations(Samaru and Kerawa) and their seed carotenoid content were determined by high-performance liquid chromatography. The modes of gene action, heritability, and correlations between agronomic traits and carotenoid content were estimated. Additive genetic variances(σ~2a) were lower than non-additive genetic variances(σ~2d) for all the carotenoids, plant height(PH), and grain yield(GY), suggesting a preponderance of non-additive gene action. Broad-sense heritability(H^2) was high(H^2> 60%) for zeaxanthin,days to anthesis, and PH, moderate(30% < H^2< 60%) for lutein and GY, and low(H^2< 30%)for alpha carotene, beta cryptoxanthin, βC, and PVA. Genetic advance as a percentage of mean, considered with H^2, also suggests a preponderance of non-additive gene action for PVA carotenoids. Hybrid variety development is thus an appropriate approach to improving grain yield and PVA. GY showed no significant genotypic correlations with carotenoid content, suggesting that these traits can be improved concurrently. Thus, there is ample scope for improvement of PVA and GY in the sample of tropical-adapted maize.
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.
文摘野生大豆(Glycine soja Sieb.&Zucc.)是栽培大豆(Glycine max [L.] Merr.)的近缘祖先种。在大豆驯化的过程中,栽培大豆丢失了大量的基因或等位变异,导致栽培大豆的遗传多样性降低,这严重限制了栽培大豆品种选育和改良的有效性与丰富性。我国野生大豆种质资源丰富,蕴藏着许多高蛋白含量、抗病虫、耐干旱、耐盐碱等方面的潜力基因,挖掘潜力基因并利用分子设计育种技术应用到现代的栽培大豆品种中,能够有效地拓宽栽培大豆的遗传多样性。本文综述了野生大豆的分布规律和形态特征、近年来在野生大豆中发掘的重要功能基因或位点,包括百粒重、开花期和成熟期、蛋白质和油分含量、抗病、抗虫、耐盐碱、耐干旱等重要农艺性状基因,并讨论这些重要基因或位点在未来栽培大豆育种中的应用潜力,以期为育种家培育和改良大豆新品种提供一种新的育种思路和策略。
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.