Tree peony belongs to one of the Saxifragales families,Paeoniaceae.It is one of the most famous ornamental plants,and is also a promising woody oil plant.Although two Paeoniaceae genomes have been released,their assem...Tree peony belongs to one of the Saxifragales families,Paeoniaceae.It is one of the most famous ornamental plants,and is also a promising woody oil plant.Although two Paeoniaceae genomes have been released,their assembly qualities are still to be improved.Additionally,more genomes from wild peonies are needed to accelerate genomic-assisted breeding.Here we assemble a high-quality and chromosome-scale 10.3-Gb genome of a wild Tibetan tree peony,Paeonia ludlowii,which features substantial sequence divergence,including around 75%specific sequences and gene-level differentials compared with other peony genomes.Our phylogenetic analyses suggest that Saxifragales and Vitales are sister taxa and,together with rosids,they are the sister taxon to asterids.The P.ludlowii genome is characterized by frequent chromosome reductions,centromere rearrangements,broadly distributed heterochromatin,and recent continuous bursts of transposable element(TE)movement in peony,although it lacks recent whole-genome duplication.These recent TE bursts appeared during the uplift and glacial period of the Qinghai-Tibet Plateau,perhaps contributing to adaptation to rapid climate changes.Further integrated analyses with methylome data revealed that genome expansion in peony might be dynamically affected by complex interactions among TE proliferation,TE removal,and DNA methylation silencing.Such interactions also impact numerous recently duplicated genes,particularly those related to oil biosynthesis and flower traits.This genome resource will not only provide the genomic basis for tree peony breeding but also shed light on the study of the evolution of huge genome structures as well as their protein-coding genes.展开更多
The ice phenology of alpine lakes on the Tibetan Plateau(TP)is a rapid and direct responder to climate changes,and the variations in lake ice exhibit high temporal frequency characteristics.MODIS and passive microwave...The ice phenology of alpine lakes on the Tibetan Plateau(TP)is a rapid and direct responder to climate changes,and the variations in lake ice exhibit high temporal frequency characteristics.MODIS and passive microwave data are widely used to monitor lake ice changes with high temporal resolution.However,the low spatial resolutions make it difficult to effectively quantify the freeze-melt dynamics of lakes.This work used Sentinel-1 synthetic aperture radar(SAR)data to derive high-resolution ice maps(about 6 days),then with the aid of Sentinel-2 optical images to quantify freeze-melt processes in three typical lakes on the TP(e.g.Selin Co,Ayakekumu Lake,and Nam Co).The results showed that three lakes had an average annual ice period of 125-157 days and a complete ice cover period of 72-115 days,from 2018 to 2022.They exhibit different ice phenology patterns.Nam Co is characterized by repeated episodes of freezing,melting,and refreezing,resulting in a prolonged freeze-up period.Meanwhile,the break-up period of Nam Co lasts for a longer duration(about 19 days),and the break-up exhibits a smooth process.Similarly,Ayakekumu Lake showed more significant inter-annual fluctuations in the freeze-up period,with deviations of up to 28 days observed among different years.Compared to the other two lakes,Selin Co experienced a relatively short freeze-up and break-up period.In short,Sentinel-1 SAR data can effectively monitor the weekly and seasonal variations in lake ice on the TP.Particularly,this data facilitates quantification of the freeze-melt dynamics.展开更多
"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic s..."Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.展开更多
基金This project was supported by grants from the National Natural Science Foundation of China(No.32270685)the Tibet Economic Forest Seedling Cultivation Project(202375)the local Science and Technology innovation projects of the central government(XZ202301YD0037C).We thank the high-performance computing platform at the National Key Laboratory of Crop Genetic Improvement at Huazhong Agricultural University.
文摘Tree peony belongs to one of the Saxifragales families,Paeoniaceae.It is one of the most famous ornamental plants,and is also a promising woody oil plant.Although two Paeoniaceae genomes have been released,their assembly qualities are still to be improved.Additionally,more genomes from wild peonies are needed to accelerate genomic-assisted breeding.Here we assemble a high-quality and chromosome-scale 10.3-Gb genome of a wild Tibetan tree peony,Paeonia ludlowii,which features substantial sequence divergence,including around 75%specific sequences and gene-level differentials compared with other peony genomes.Our phylogenetic analyses suggest that Saxifragales and Vitales are sister taxa and,together with rosids,they are the sister taxon to asterids.The P.ludlowii genome is characterized by frequent chromosome reductions,centromere rearrangements,broadly distributed heterochromatin,and recent continuous bursts of transposable element(TE)movement in peony,although it lacks recent whole-genome duplication.These recent TE bursts appeared during the uplift and glacial period of the Qinghai-Tibet Plateau,perhaps contributing to adaptation to rapid climate changes.Further integrated analyses with methylome data revealed that genome expansion in peony might be dynamically affected by complex interactions among TE proliferation,TE removal,and DNA methylation silencing.Such interactions also impact numerous recently duplicated genes,particularly those related to oil biosynthesis and flower traits.This genome resource will not only provide the genomic basis for tree peony breeding but also shed light on the study of the evolution of huge genome structures as well as their protein-coding genes.
基金supported financially by the National Nature Science Foundation of China(No.41901129)the University Natural Sciences Research Project of Anhui Educational committee(KJ2020JD06)DUAN Zheng acknowledges the support from the Joint China-Sweden Mobility Grant funded by NSFC and STINT(CH2019-8250).
文摘The ice phenology of alpine lakes on the Tibetan Plateau(TP)is a rapid and direct responder to climate changes,and the variations in lake ice exhibit high temporal frequency characteristics.MODIS and passive microwave data are widely used to monitor lake ice changes with high temporal resolution.However,the low spatial resolutions make it difficult to effectively quantify the freeze-melt dynamics of lakes.This work used Sentinel-1 synthetic aperture radar(SAR)data to derive high-resolution ice maps(about 6 days),then with the aid of Sentinel-2 optical images to quantify freeze-melt processes in three typical lakes on the TP(e.g.Selin Co,Ayakekumu Lake,and Nam Co).The results showed that three lakes had an average annual ice period of 125-157 days and a complete ice cover period of 72-115 days,from 2018 to 2022.They exhibit different ice phenology patterns.Nam Co is characterized by repeated episodes of freezing,melting,and refreezing,resulting in a prolonged freeze-up period.Meanwhile,the break-up period of Nam Co lasts for a longer duration(about 19 days),and the break-up exhibits a smooth process.Similarly,Ayakekumu Lake showed more significant inter-annual fluctuations in the freeze-up period,with deviations of up to 28 days observed among different years.Compared to the other two lakes,Selin Co experienced a relatively short freeze-up and break-up period.In short,Sentinel-1 SAR data can effectively monitor the weekly and seasonal variations in lake ice on the TP.Particularly,this data facilitates quantification of the freeze-melt dynamics.
基金supported by the National Natural Science Foundation of China(NSFC,31970564,32000397,32171982)the Fundamental Research Funds for the Central Universities(2662023PY004)。
文摘"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.
