Microbial communities such as those residing in the human gut are highly diverse and complex,and many with important implications for health and diseases.The effects and functions of these microbial communities are de...Microbial communities such as those residing in the human gut are highly diverse and complex,and many with important implications for health and diseases.The effects and functions of these microbial communities are determined not only by their species compositions and diversities but also by the dynamic intra-and inter-cellular states at the transcriptional level.Powerful and scalable technologies capable of acquiring single-microbe-resolution RNA sequencing information in order to achieve a comprehensive understanding of complex microbial communities together with their hosts are therefore utterly needed.Here we report the development and utilization of a droplet-based smRNA-seq(single-microbe RNA sequencing)method capable of identifying large species varieties in human samples,which we name smRandom-seq2.Together with a triple-module computational pipeline designed for the bacteria and bacteriophage sequencing data by smRandom-seq2 in four human gut samples,we established a single-cell level bacterial transcriptional landscape of human gut microbiome,which included 29,742 single microbes and 329 unique species.Distinct adaptive response states among species in Prevotella and Roseburia genera and intrinsic adaptive strategy heterogeneity in Phascolarctobacterium succinatutens were uncovered.Additionally,we identified hundreds of novel host-phage transcriptional activity associations in the human gut microbiome.Our results indicated that smRandom-seq2 is a high-throughput and high-resolution smRNA-seq technique that is highly adaptable to complex microbial communities in real-world situations and promises new perspectives in the understanding of human microbiomes.展开更多
Machine learning(ML)is one of the key technologies for next-generation breeding,and“big data”is the cornerstone for development of ML algorithms that are applicable to crop breeding practices.Currently,there is a sh...Machine learning(ML)is one of the key technologies for next-generation breeding,and“big data”is the cornerstone for development of ML algorithms that are applicable to crop breeding practices.Currently,there is a shortage of databases containing phenotype data and corresponding genomic data,i.e.,genome-to-phenotype(G2P)paired data,that can be used in the development of ML algorithms for breeding.To fill this gap,we constructed a user-friendly database named the BreedingAIDB(http://ibi.zju.edu.cn/BreedingAIDB)to provide breeders and ML experts with easily accessible G2P paired data for crops,as well as ML tools.展开更多
Rye(Secale cereale)is an important crop with multiple uses and a valuable genetic resource for wheat breeding.However,due to its complex genome and outcrossing nature,the origin of cultivated rye remains elusive.The g...Rye(Secale cereale)is an important crop with multiple uses and a valuable genetic resource for wheat breeding.However,due to its complex genome and outcrossing nature,the origin of cultivated rye remains elusive.The geneticist N.I.Vavilov proposed that cultivated rye had been domesticated from weedy rye,rather than directly from wild species like other crops.Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds.To this end,in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild,weedy,and cultivated rye,and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans.We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits,including shattering,grain yield,and disease resistance.Furthermore,we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye.Taken together,our findings unravel the domestication history of cultivated rye,suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale,and provide an important resource for future rye and wheat breeding.展开更多
基金supported by the National Natural Science Foundation of China(No.32200073 and 32250710678,Y.W.)Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang(No.2021R01012,Y.W.)+1 种基金“Pioneer”R&D programs of Zhejiang Province(No.2024C03005,Y.W.)Key R&D Program of Zhejiang(No.2024SSYS0022,Y.W.).
文摘Microbial communities such as those residing in the human gut are highly diverse and complex,and many with important implications for health and diseases.The effects and functions of these microbial communities are determined not only by their species compositions and diversities but also by the dynamic intra-and inter-cellular states at the transcriptional level.Powerful and scalable technologies capable of acquiring single-microbe-resolution RNA sequencing information in order to achieve a comprehensive understanding of complex microbial communities together with their hosts are therefore utterly needed.Here we report the development and utilization of a droplet-based smRNA-seq(single-microbe RNA sequencing)method capable of identifying large species varieties in human samples,which we name smRandom-seq2.Together with a triple-module computational pipeline designed for the bacteria and bacteriophage sequencing data by smRandom-seq2 in four human gut samples,we established a single-cell level bacterial transcriptional landscape of human gut microbiome,which included 29,742 single microbes and 329 unique species.Distinct adaptive response states among species in Prevotella and Roseburia genera and intrinsic adaptive strategy heterogeneity in Phascolarctobacterium succinatutens were uncovered.Additionally,we identified hundreds of novel host-phage transcriptional activity associations in the human gut microbiome.Our results indicated that smRandom-seq2 is a high-throughput and high-resolution smRNA-seq technique that is highly adaptable to complex microbial communities in real-world situations and promises new perspectives in the understanding of human microbiomes.
基金supported by the STI2030-Major Projects(2023ZD04076)the Hainan Province Science and Technology Special Fund(ZDYF2022XDNY271).
文摘Machine learning(ML)is one of the key technologies for next-generation breeding,and“big data”is the cornerstone for development of ML algorithms that are applicable to crop breeding practices.Currently,there is a shortage of databases containing phenotype data and corresponding genomic data,i.e.,genome-to-phenotype(G2P)paired data,that can be used in the development of ML algorithms for breeding.To fill this gap,we constructed a user-friendly database named the BreedingAIDB(http://ibi.zju.edu.cn/BreedingAIDB)to provide breeders and ML experts with easily accessible G2P paired data for crops,as well as ML tools.
基金This work was supported by the National Natural Science Foundation(grant 9143511)Department of Science and Technology of Zhejiang Province(grant 2020C02002)+1 种基金the Zhejiang Natural Science Foundation(grant LZ17C130001)the Jiangsu Collaborative Innovation Center for Modern Crop Production,and the 111 Project(grant B17039)to L.F.
文摘Rye(Secale cereale)is an important crop with multiple uses and a valuable genetic resource for wheat breeding.However,due to its complex genome and outcrossing nature,the origin of cultivated rye remains elusive.The geneticist N.I.Vavilov proposed that cultivated rye had been domesticated from weedy rye,rather than directly from wild species like other crops.Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds.To this end,in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild,weedy,and cultivated rye,and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans.We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits,including shattering,grain yield,and disease resistance.Furthermore,we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye.Taken together,our findings unravel the domestication history of cultivated rye,suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale,and provide an important resource for future rye and wheat breeding.
