Osmanthus fragrans is a well-known ornamental plant that has been domesticated in China for 2500 years.More than 160 cultivars have been found during this long period of domestication,and they have subsequently been d...Osmanthus fragrans is a well-known ornamental plant that has been domesticated in China for 2500 years.More than 160 cultivars have been found during this long period of domestication,and they have subsequently been divided into four cultivar groups,including the Yingui,Jingui,Dangui,and Sijigui groups.These groups provide a set of materials to study genetic evolution and variability.Here,we constructed a reference genome of O.fragrans‘Liuyejingui’in the Jingui group and investigated its floral color traits and domestication history by resequencing a total of 122 samples,including 119 O.fragrans accessions and three other Osmanthus species,at an average sequencing depth of 15×.The population structure analysis showed that these 119 accessions formed an apparent regional cluster.The results of linkage disequilibrium(LD)decay analysis suggested that varieties with orange/red flower color in the Dangui group had undergone more artificial directional selection;these varieties had the highest LD values among the four groups,followed by the Sijigui,Jingui,and Yingui groups.Through a genome-wide association study,we further identified significant quantitative trait loci and genomic regions containing several genes,such as ethylene-responsive transcription factor 2 and Arabidopsis pseudoresponse regulator 2,that are positively associated with petal color.Moreover,we found a frameshift mutation with a 34-bp deletion in the first coding region of the carotenoid cleavage dioxygenase 4 gene.This frameshift mutation existed in at least one site on both alleles in all varieties of the Dangui group.The results from this study shed light on the genetic basis of domestication in woody plants,such as O.fragrans.展开更多
Hemerocallis citrina Borani(huang hua cai in Chinese)is an important horticultural crop whose flower buds are widely consumed as a delicious vegetable in Asia.Here we assembled a high-quality reference genome of H.cit...Hemerocallis citrina Borani(huang hua cai in Chinese)is an important horticultural crop whose flower buds are widely consumed as a delicious vegetable in Asia.Here we assembled a high-quality reference genome of H.citrina using single-molecule sequencing and Hi-C technologies.The genome assembly was 3.77 Gb and consisted of 3183 contigs with a contig N50 of 2.09 Mb,which were further clustered into 11 pseudochromosomes.A larger portion(3.25 Gb or 86.20%)was annotated as a repetitive content and 54,295 protein-coding genes were annotated in the genome.Genome evolution analysis showed that H.citrina experienced a recent whole-genome duplication(WGD)event at~15.73 million years ago(Mya),which was the main factor leading to many multiple copies of orthologous genes.We used this reference genome to predict 20 genes involved in the rutin biosynthesis pathway.Moreover,our metabolomics data revealed neither colchicine nor its precursors in H.citrina,challenging the long-standing belief that this alkaloid causes poisoning by the plant.The results of our disruptive research are further substantiated by our genomic finding that H.citrina does not contain any genes involved in colchicine biosynthesis.The high-quality genome lays a solid foundation for genetic research and molecular breeding of H.citrina.展开更多
In recent years,the field of shotgun metagenomics has witnessed remarkable advancements,primarily driven by the development and refinement of next-generation sequencing technologies,particularly long-read sequencing p...In recent years,the field of shotgun metagenomics has witnessed remarkable advancements,primarily driven by the development and refinement of next-generation sequencing technologies,particularly long-read sequencing platforms such as Nanopore and PacBio.These platforms have significantly improved the ability to analyze microbial communities directly from environmental samples,providing valuable information on their composition,function,and dynamics without the need for pure cultivation.These technologies enhance metagenomic data assembly,annotation,and analysis by addressing longer reads,higher error rates,and complex data.In this review,we provide a comprehensive overview of the historical development of long-read metagenomics,highlighting significant landmarks and advancements.We also explore the diverse applications of long-read metagenomics,emphasizing its impact across various fields.Additionally,we summarize the essential computational tools and resources,including software,databases,and packages,developed to enhance the efficiency and accuracy of metagenomic analysis.Finally,we provide a practical guide for the installation and use of notable software available on GitHub(https://github.com/zhangtianyuan666/LongMetagenome).Overall,this review assists the metagenomics community in exploring microbial life in unprecedented depth by providing a roadmap for successful resource utilization and emphasizing possibilities for innovation.展开更多
基金supported by research grants provided by the National Natural Science Foundation of China(31600569 and 31700617)the Natural Science Foundation of Hubei Province(2017CFB235)+1 种基金the Nuclear Technology Innovation team project of Hubei University of Science and Technology(H2019002)the Science and Technology Project of Xianning(2020NYYF02)。
文摘Osmanthus fragrans is a well-known ornamental plant that has been domesticated in China for 2500 years.More than 160 cultivars have been found during this long period of domestication,and they have subsequently been divided into four cultivar groups,including the Yingui,Jingui,Dangui,and Sijigui groups.These groups provide a set of materials to study genetic evolution and variability.Here,we constructed a reference genome of O.fragrans‘Liuyejingui’in the Jingui group and investigated its floral color traits and domestication history by resequencing a total of 122 samples,including 119 O.fragrans accessions and three other Osmanthus species,at an average sequencing depth of 15×.The population structure analysis showed that these 119 accessions formed an apparent regional cluster.The results of linkage disequilibrium(LD)decay analysis suggested that varieties with orange/red flower color in the Dangui group had undergone more artificial directional selection;these varieties had the highest LD values among the four groups,followed by the Sijigui,Jingui,and Yingui groups.Through a genome-wide association study,we further identified significant quantitative trait loci and genomic regions containing several genes,such as ethylene-responsive transcription factor 2 and Arabidopsis pseudoresponse regulator 2,that are positively associated with petal color.Moreover,we found a frameshift mutation with a 34-bp deletion in the first coding region of the carotenoid cleavage dioxygenase 4 gene.This frameshift mutation existed in at least one site on both alleles in all varieties of the Dangui group.The results from this study shed light on the genetic basis of domestication in woody plants,such as O.fragrans.
基金the“National Key R&D Program of China(2017YFD0501500),”“Hunan Provincial Key Research and Development Project(2020NK2031)”“The Special Funds for Development of Local Science and Technology from Central Government(2019XF5067).”。
文摘Hemerocallis citrina Borani(huang hua cai in Chinese)is an important horticultural crop whose flower buds are widely consumed as a delicious vegetable in Asia.Here we assembled a high-quality reference genome of H.citrina using single-molecule sequencing and Hi-C technologies.The genome assembly was 3.77 Gb and consisted of 3183 contigs with a contig N50 of 2.09 Mb,which were further clustered into 11 pseudochromosomes.A larger portion(3.25 Gb or 86.20%)was annotated as a repetitive content and 54,295 protein-coding genes were annotated in the genome.Genome evolution analysis showed that H.citrina experienced a recent whole-genome duplication(WGD)event at~15.73 million years ago(Mya),which was the main factor leading to many multiple copies of orthologous genes.We used this reference genome to predict 20 genes involved in the rutin biosynthesis pathway.Moreover,our metabolomics data revealed neither colchicine nor its precursors in H.citrina,challenging the long-standing belief that this alkaloid causes poisoning by the plant.The results of our disruptive research are further substantiated by our genomic finding that H.citrina does not contain any genes involved in colchicine biosynthesis.The high-quality genome lays a solid foundation for genetic research and molecular breeding of H.citrina.
基金supported by the National Natural Science Foundation of China(Grant Nos.32470055 and U23A20148)the Basic Research Center for Crop Biosafety Sciences(Grant No.CAAS-BRC-CB-2025-01)the Agricultural Science and Technology Innovation Program(Grant No.CAAS-ZDRW202308),China.
文摘In recent years,the field of shotgun metagenomics has witnessed remarkable advancements,primarily driven by the development and refinement of next-generation sequencing technologies,particularly long-read sequencing platforms such as Nanopore and PacBio.These platforms have significantly improved the ability to analyze microbial communities directly from environmental samples,providing valuable information on their composition,function,and dynamics without the need for pure cultivation.These technologies enhance metagenomic data assembly,annotation,and analysis by addressing longer reads,higher error rates,and complex data.In this review,we provide a comprehensive overview of the historical development of long-read metagenomics,highlighting significant landmarks and advancements.We also explore the diverse applications of long-read metagenomics,emphasizing its impact across various fields.Additionally,we summarize the essential computational tools and resources,including software,databases,and packages,developed to enhance the efficiency and accuracy of metagenomic analysis.Finally,we provide a practical guide for the installation and use of notable software available on GitHub(https://github.com/zhangtianyuan666/LongMetagenome).Overall,this review assists the metagenomics community in exploring microbial life in unprecedented depth by providing a roadmap for successful resource utilization and emphasizing possibilities for innovation.
