The Permian Basin is a unique ecosystem located in the southwest of the USA.An unanswered question is whether the bacteria in the Permian Basin adapted to the changing paleomarine environment and survived in the remna...The Permian Basin is a unique ecosystem located in the southwest of the USA.An unanswered question is whether the bacteria in the Permian Basin adapted to the changing paleomarine environment and survived in the remnants of Permian groundwater.In our previous study,a novel bacterial strain,Permianibacter aggregans HW001T,was isolated from micro-algae cultures incubated with Permian Basin waters,and was shown to originate from the Permian Ocean.In this study,strain HW001T was shown to be the representative strain of a novel family,classified as‘Permianibacteraceae’.The results of molecular dating suggested that the strain HW001T diverged~447 million years ago(mya),which is the early Permian period(~250 mya).Genome analysis was used to access its potential energy utilization and biosynthesis capacity.A large number of transporters,carbohydrate-active enzymes and protein-degradation related genes have been annotated in the genome of strain HW001T.In addition,a series of important metabolic pathways,such as peptidoglycan biosynthesis,osmotic stress response system and multifunctional quorum sensing were annotated,which may confer the ability to adapt to vari-ous unfavorable environmental conditions.Finally,the evolutionary history of strain HW001T was reconstructed and the horizontal transfer of genes was predicted,indicating that the adaptation of P.aggregans to a changing marine environment depends on the evolution of their metabolic capabilities,especially in signal transmission.In conclusion,the results of this study provide genomic information for revealing the adaptive mechanism of strain HW001T to the changing ancient oceans.展开更多
Global climate change is expected to accelerate biological invasions,necessitating accurate risk forecasting and management strategies.However,current invasion risk assessments often overlook adaptive genomic variatio...Global climate change is expected to accelerate biological invasions,necessitating accurate risk forecasting and management strategies.However,current invasion risk assessments often overlook adaptive genomic variation,which plays a significant role in the persistence and expansion of invasive populations.Here we used Molgula manhattensis,a highly invasive ascidian,as a model to assess its invasion risks along Chinese coasts under climate change.Through population genomics analyses,we identified two genetic clusters,the north and south clusters,based on geographic distributions.To predict invasion risks,we employed the gradient forest and species distribution models to calculate genomic offset and species habitat suitability,respectively.These approaches yielded distinct predictions:the gradient forest model suggested a greater genomic offset to future climatic conditions for the north cluster(i.e.,lower invasion risks),while the species distribution model indicated higher future habitat suitability for the same cluster(i.e,higher invasion risks).By integrating these models,we found that the south cluster exhibited minor genome-niche disruptions in the future,indicating higher invasion risks.Our study highlights the complementary roles of genomic offset and habitat suitability in assessing invasion risks under climate change.Moreover,incorporating adaptive genomic variation into predictive models can significantly enhance future invasion risk predictions and enable effective management strategies for biological invasions in the future.展开更多
The Chinese crested(CC)duck is a unique indigenous waterfowl breed,which has a crest cushion that affects its survival rate.Therefore,the CC duck is an ideal model to investigate the genetic compensation response to m...The Chinese crested(CC)duck is a unique indigenous waterfowl breed,which has a crest cushion that affects its survival rate.Therefore,the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability.In the present study,we first generated a chromosome-level genome of CC ducks.Comparative genomics revealed that genes related to tissue repair,immune function,and tumors were under strong positive selection,indicating that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks.We also assembled a Chinese spot-billed(Csp-b)duck genome,and detected the structural variations(SVs)in the genome assemblies of three ducks(i.e.,CC duck,Csp-b duck,and Peking duck).Functional analysis revealed that several SVs were related to the immune system of CC ducks,further strongly suggesting that genetic compensation in the anti-tumor and immune systems supports the survival of CC ducks.Moreover,we confirmed that the CC duck originated from the mallard ducks.Finally,we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation.Overall,the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.展开更多
Plants produce a large array of specialized metabolites（natural products）that not only are essential for growth and development,but also play important roles in adaptation to the variable stressful environments.Also...Plants produce a large array of specialized metabolites（natural products）that not only are essential for growth and development,but also play important roles in adaptation to the variable stressful environments.Also,many plant metabolites are essential nutrient elements for humans and serve as natural drugs.However,study of the biosynthesis of natural products is still in its infancy,because more than 90%of plant metabolites are unknown and only a small number of genes/ enzymes involved in metabolism are identified in the model plants Arabidopsis and rice.展开更多
基金Funding for this study was provided by the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory(Guang-zhou)(GML2019ZD0606)National Natural Science Foundation of China(92051118)+1 种基金Guangdong Science and Technology Department(2019A1515011139)2020 Li Ka Shing Foundation(LKSF)Cross-Disciplinary Research Grant(2020LKSFG07A).
文摘The Permian Basin is a unique ecosystem located in the southwest of the USA.An unanswered question is whether the bacteria in the Permian Basin adapted to the changing paleomarine environment and survived in the remnants of Permian groundwater.In our previous study,a novel bacterial strain,Permianibacter aggregans HW001T,was isolated from micro-algae cultures incubated with Permian Basin waters,and was shown to originate from the Permian Ocean.In this study,strain HW001T was shown to be the representative strain of a novel family,classified as‘Permianibacteraceae’.The results of molecular dating suggested that the strain HW001T diverged~447 million years ago(mya),which is the early Permian period(~250 mya).Genome analysis was used to access its potential energy utilization and biosynthesis capacity.A large number of transporters,carbohydrate-active enzymes and protein-degradation related genes have been annotated in the genome of strain HW001T.In addition,a series of important metabolic pathways,such as peptidoglycan biosynthesis,osmotic stress response system and multifunctional quorum sensing were annotated,which may confer the ability to adapt to vari-ous unfavorable environmental conditions.Finally,the evolutionary history of strain HW001T was reconstructed and the horizontal transfer of genes was predicted,indicating that the adaptation of P.aggregans to a changing marine environment depends on the evolution of their metabolic capabilities,especially in signal transmission.In conclusion,the results of this study provide genomic information for revealing the adaptive mechanism of strain HW001T to the changing ancient oceans.
基金supported by the National Natural Science Foundation of China(grant numbers 32061143012,42106098,and 42276126).
文摘Global climate change is expected to accelerate biological invasions,necessitating accurate risk forecasting and management strategies.However,current invasion risk assessments often overlook adaptive genomic variation,which plays a significant role in the persistence and expansion of invasive populations.Here we used Molgula manhattensis,a highly invasive ascidian,as a model to assess its invasion risks along Chinese coasts under climate change.Through population genomics analyses,we identified two genetic clusters,the north and south clusters,based on geographic distributions.To predict invasion risks,we employed the gradient forest and species distribution models to calculate genomic offset and species habitat suitability,respectively.These approaches yielded distinct predictions:the gradient forest model suggested a greater genomic offset to future climatic conditions for the north cluster(i.e.,lower invasion risks),while the species distribution model indicated higher future habitat suitability for the same cluster(i.e,higher invasion risks).By integrating these models,we found that the south cluster exhibited minor genome-niche disruptions in the future,indicating higher invasion risks.Our study highlights the complementary roles of genomic offset and habitat suitability in assessing invasion risks under climate change.Moreover,incorporating adaptive genomic variation into predictive models can significantly enhance future invasion risk predictions and enable effective management strategies for biological invasions in the future.
基金supported by the China Agriculture Research System(Grant No.CARS-42)the Jiangsu Agricultural Technology System(Grant No.JATS[2020]435)the Jiangsu Agricultural Science and Technology Innovation Fund(Grant No.CX[18]1004),China.
文摘The Chinese crested(CC)duck is a unique indigenous waterfowl breed,which has a crest cushion that affects its survival rate.Therefore,the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability.In the present study,we first generated a chromosome-level genome of CC ducks.Comparative genomics revealed that genes related to tissue repair,immune function,and tumors were under strong positive selection,indicating that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks.We also assembled a Chinese spot-billed(Csp-b)duck genome,and detected the structural variations(SVs)in the genome assemblies of three ducks(i.e.,CC duck,Csp-b duck,and Peking duck).Functional analysis revealed that several SVs were related to the immune system of CC ducks,further strongly suggesting that genetic compensation in the anti-tumor and immune systems supports the survival of CC ducks.Moreover,we confirmed that the CC duck originated from the mallard ducks.Finally,we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation.Overall,the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.
文摘Plants produce a large array of specialized metabolites（natural products）that not only are essential for growth and development,but also play important roles in adaptation to the variable stressful environments.Also,many plant metabolites are essential nutrient elements for humans and serve as natural drugs.However,study of the biosynthesis of natural products is still in its infancy,because more than 90%of plant metabolites are unknown and only a small number of genes/ enzymes involved in metabolism are identified in the model plants Arabidopsis and rice.
