IR64 is an elite Xian/indica variety developed by International Rice Research Institute(IRRl)in 1985,which has been the most widely grown variety and core breeding parent in South/Southeast Asia(Mackill and Khush,2018...IR64 is an elite Xian/indica variety developed by International Rice Research Institute(IRRl)in 1985,which has been the most widely grown variety and core breeding parent in South/Southeast Asia(Mackill and Khush,2018).IR64 has been utilized to develop stress-tolerant(such as drought-adapted and submergenceresistant)near-isogenic lines,underscoring its great potential in agricultural genomics(Tanaka et al.,2020).展开更多
Structural variations(SVs≥50 bp)are a critical but underexplored source of genetic diversity in cattle,shaping traits vital for productivity,adaptability,and health.Advances in long-read sequencing,pangenome graph co...Structural variations(SVs≥50 bp)are a critical but underexplored source of genetic diversity in cattle,shaping traits vital for productivity,adaptability,and health.Advances in long-read sequencing,pangenome graph construction,and near-complete genome assemblies now allow accurate SV detection and genotyping.These innovations overcome the limitations of single-reference genomes,enabling the discovery of complex SVs,including nested and overlapping variants,and providing access to previously inaccessible genomic regions such as centromeres and telomeres.This review highlights the current landscape of cattle SV research,with emphasis on integrating longread sequencing and pangenome frameworks to uncover breed-specific and population-level variation.While many SVs are linked to economically important traits such as feed efficiency and disease resistance,their broader regulatory impacts remain an active area of investigation.Emerging functional genomics approaches,including transcriptomics,epigenomics,and genome editing,will clarify how SVs influence gene regulation and phenotype.Looking forward,the integration of SV catalogs with multi-omics data,imputation resources,and artificial intelligence-driven models will be essential for translating discoveries into breeding and conservation applications.Integrating structural variants into breeding pipelines promises to revolutionize livestock genomics,enabling precision selection and sustainable agriculture despite challenges in cost,data sharing,and functional validation.展开更多
Previous investigations into gut microbiota dysbiosis in patients with Parkinson’s disease have relied on 16S rRNA amplicon sequencing and assembly-free metagenomic approaches.However,there is an urgent need to study...Previous investigations into gut microbiota dysbiosis in patients with Parkinson’s disease have relied on 16S rRNA amplicon sequencing and assembly-free metagenomic approaches.However,there is an urgent need to study the function of the gut microbiome at the genome level using metagenome-assembled genomes.Here,we conducted single-sample metagenomic binning analysis using shotgun metagenomic sequencing data and retrieved 2837 metagenome-assembled genomes to explore the gut microbiota profile at the genome level.Reconstructing microbial genomes from metagenomic sequences greatly enriched the diversity and number of microbial genomes,especially those of uncultivable strains.By integrating the analysis of metagenome-assembled genomes with clinical parameters,we observed higherα-diversity indexes and a very different composition of microbial communities in patients with Parkinson’s disease.We also identified microbial species and metagenome-assembled genomes that were significantly associated with clinical characteristics,including disease severity,medication,motor complications,and non-motor symptoms.The genes of Parkinson’s disease severity-associated metagenome-assembled genomes were distributed across multiple pathways,such as carbon metabolism,phosphonate metabolism,carbohydrate metabolism,amino acid metabolism,fatty acid metabolism,bile acid metabolism,metabolism of cofactors and vitamins,neuroprotective molecules,immunogenic components,toxic metabolites,translation,and bacterial secretion.Our work provides a comprehensive resource for investigating the gut microbiota-Parkinson’s disease relationship at the genome level,which may enhance our comprehension of the underlying mechanisms of this disease.展开更多
Non-O1/non-O139 Vibrio(V.)cholerae(NOVC)has emerged as a potential pathogen in patients with compromised health conditions[1].We report the whole genome sequencing(WGS)of a rare NOVC sepsis isolate(GenBank Accession:G...Non-O1/non-O139 Vibrio(V.)cholerae(NOVC)has emerged as a potential pathogen in patients with compromised health conditions[1].We report the whole genome sequencing(WGS)of a rare NOVC sepsis isolate(GenBank Accession:GCF_051906115.1)from an 89-year-old male admitted to the Intensive Care Unit(ICU)with septic shock(lactate 6.61 mmol/L)digestive illness.展开更多
Emerging and powerful genome editing tools,particularly CRISPR/Cas9,are facilitating functional genomics research and accelerating crop improvement(Jiang et al.2021;Cao et al.2023;Chen C et al.2023;Liu et al.2023a).Ho...Emerging and powerful genome editing tools,particularly CRISPR/Cas9,are facilitating functional genomics research and accelerating crop improvement(Jiang et al.2021;Cao et al.2023;Chen C et al.2023;Liu et al.2023a).However,the detection and screening of transgenic lines remain major bottlenecks,being time-consuming,labor-intensive,and inefficient during transformation and subsequent mutation identification.A simple and efficient visual marker system plays a critical role in addressing these challenges.Recent studies demonstrated that the GmW1 and RUBY reporter systems were used to obtain visual transgenic soybean(Glycine max) plants(Chen L et al.2023;Chen et al.2024).展开更多
The genus Clematis(Ranunculaceae)comprises over 300 species with remarkable morphological and ecological diversity worldwide.Despite its horticultural,medicinal,and ecological importance,a well-resolved phylogeny and ...The genus Clematis(Ranunculaceae)comprises over 300 species with remarkable morphological and ecological diversity worldwide.Despite its horticultural,medicinal,and ecological importance,a well-resolved phylogeny and coherent infrageneric classification are still lacking.Here,we reconstruct a robust phylogeny for Clematis using a phylogenomic approach and revise its infrageneric taxonomy.We incorporated 198 samples representing 151 species,two subspecies,and 12 varieties,covering all subgenera and most sections worldwide,obtained from both fresh and herbarium material.Nuclear single nucleotide polymorphisms(SNPs)and complete plastid genomes were assembled for phylogenetic analyses.We also prepared a nuclear ribosomal ITS(nrITS)dataset comprising 171 species,two subspecies,and 12 varieties(217 samples)to include as many species as possible for phylogenetic inference.Phylogenies based on plastid genomes and nrITS exhibited limited resolution and modest support,highlighting challenges in resolving certain relationships.Nuclear SNP analyses yielded a robust phylogenetic tree with 22 well-supported clades corresponding to 22 sections,with most previously recognized subgenera and sections not recovered as monophyletic.Ancestral state reconstruction of 12 key morphological characters revealed multiple independent origins of character states.This study presents the first comprehensive sectional classification for Clematis based on robust phylogenomic evidence,redefines morphological characteristics for each section,and resolves long-standing taxonomic ambiguities.Our results establish a framework for future studies on the evolution,ecology,and horticultural potential of this globally significant genus.展开更多
The Leafminers,representing a diverse group of insects from various genera within the Agromyzidae family,pose a significant threat to spinach(Spinacia oleracea L.)production.This study aimed to identify single nucleot...The Leafminers,representing a diverse group of insects from various genera within the Agromyzidae family,pose a significant threat to spinach(Spinacia oleracea L.)production.This study aimed to identify single nucleotide polymorphism(SNP)markers associated with leafminer resistance through a genome-wide association study(GWAS)and to evaluate the prediction accuracy(PA)for selecting resistant spinach using genomic prediction(GP).Using a dataset of 84301 SNPs obtained from whole-genome resequencing,seven GWAS models,including BLINK,FarmCPU,MLM,and MLMM in GAPIT 3,as well as MLM,GLM,and SMR in TASSEL 5,were employed to perform GWAS on a panel of 286 USDA spinach germplasm accessions.Three SNP markers,namely 1_115279256_C_T,3_157082529_C_T,and 4_168510908_T_G on chromosomes 1,3,and 4,respectively,were identified as associated with leafminer resistance.In the 30 kb flanking regions of these markers,four candidate genes(SOV1g031330,SOV1g031340,SOV4g047270,and SOV4g047280),encoding LOB domain-containing protein,KH domain-containing protein,were discovered.Nodulin-like domain-containing protein,and SAM domain-containing protein,were discovered.The PA for leafminer resistance selection was estimated using ten different SNP sets,including two GWAS-derived marker sets(three and 51 SNPs)and eight random marker sets(ranging from 51 to 10 K SNPs)analyzed by seven GP models.The findings emphasized the superior performance of GWAS-derived SNP sets,reaching a PA of up to 0.79 using the cBLUP model.Notably,this research marks the pioneering application of GP in the context of insect resistance,providing a significant advancement in the understanding and management of leafminer resistance in spinach cultivation.展开更多
Iris domestica,a perennial herb of the Iridaceae family,is widely recognized for its rich isoflavone content and broad therapeutic properties.To elucidate the biosynthetic pathway of these medicinally significant comp...Iris domestica,a perennial herb of the Iridaceae family,is widely recognized for its rich isoflavone content and broad therapeutic properties.To elucidate the biosynthetic pathway of these medicinally significant compounds,we constructed a haplotype-resolved genome assembly of this species.Transcriptomic and metabolomic analyses revealed tissue-specific accumulation of isoflavone,particularly in rhizomes and roots.Functional characterization identified two candidate isoflavone synthase genes,among which IdIFS was confirmed to promote the biosynthesis of key compounds tectorigenin and irisflorentin.The high-quality genome assembly presented here provides a foundational resource for further research into the evolution,secondary metabolite,and environmental adaptation of I.domestica.展开更多
The genetic basis of early-stage salt tolerance in alfalfa(Medicago sativa L.),a key factor limiting its productivity,remains poorly understood.To dissect this complex trait,we integrate genome-wide association studie...The genetic basis of early-stage salt tolerance in alfalfa(Medicago sativa L.),a key factor limiting its productivity,remains poorly understood.To dissect this complex trait,we integrate genome-wide association studies(GWAS)and transcriptomics from 176 accessions within a machine learning based genomic prediction framework.Analysis reveals weak genetic correlations among four salt-tolerance traits and a gradual decline in performance under increasing salt stress.GWAS identify 60 significant associated SNPs,with the highest number detected under 100 mM salt stress.Salt tolerance exhibits an additive effect from favorable haplotypes,which are most abundant in Chinese accessions.GWAS-associated genes are related to key regulators of hormone signaling and osmotic adjustment,while transcriptome analysis indicates a global repression of stress-responsive transcription factors.Integrating these multi-omics datasets allows us to identify 14 candidate genes,including MsHSD1(seed dormancy)and MsMTATP6(energy metabolism).Crucially,incorporating these markers into genomic prediction models improve cross-population predictive accuracy to an average of 54.4%.This study provides insights into the genetic architecture of salt tolerance in alfalfa and offers valuable markers to facilitate molecular breeding.展开更多
Inoculation of starter culture is a viable method to improve the quality of fermented foods,but its effect on the flavor metabolite profiles and the underlying mechanisms are still unclear.This study aimed to elucidat...Inoculation of starter culture is a viable method to improve the quality of fermented foods,but its effect on the flavor metabolite profiles and the underlying mechanisms are still unclear.This study aimed to elucidate the effects of starters(Lactiplantibacillus plantarum(LP)and Staphylococcus simulans(SS)individually or in combination(LS))on the flavor metabolite profiles of fermented sausages via metabolomics and genomics.L.plantarum markedly modified the composition of bacterial communities and made Lactobacillus spp.dominant in sausages(98.29%and 85.03%in LP and LS groups,respectively).Additionally,inoculation with a single starter,L.plantarum,and a mixed starter yielded similar non-volatile flavor metabolites,which were mainly characterized at the amino acid and peptide levels(relative intensities of 349.65 and 348.62 for the LP and LS groups,respectively).Meanwhile,the mixed starter group had the most volatile flavor metabolites(relative intensity of 34728.67),some of which were contributed by L.plantarum,such as ethyl acetate(relative intensities of 583.33 and 588.33 for the LP and LS groups,respectively)and benzaldehyde(relative intensities of 786.67 and 909.00 for the LP and LS groups,respectively),and several of which were generated by S.simulans,such as ethyl propionate(relative intensities of 214.67 and 136.67 for the SS and LS groups,respectively)and benzyl alcohol(relative intensities of 720.00 and 656.00 for the SS and LS groups,respectively).Furthermore,L.plantarum was found to possess more genes encoding peptidases(48)and carbohydrate-active enzymes(124),while S.simulans had more genes related to lipid hydrolysis(12).In conclusion,differences in the properties and combinations of indigenous strains play a crucial role in the generation of flavor metabolites in sausages.展开更多
Radish(Raphanus sativus L.)is an important cruciferous root vegetable,with bolting regulated by multiple genes.However,the genetic mechanisms underlying bolting regulation remain unclear.Here,the genome of the cultiva...Radish(Raphanus sativus L.)is an important cruciferous root vegetable,with bolting regulated by multiple genes.However,the genetic mechanisms underlying bolting regulation remain unclear.Here,the genome of the cultivar C60213 is assembled into a high-quality,gap-free telomere-to-telomere structure,spanning nine chromosomes and totaling 472.71 Mb,using a combination of Oxford Nanopore,PacBio,and Hi-C sequencing technologies.It identifies 49,768 protein-coding genes,97.38%of which are functionally annotated.Repetitive sequences constitute 59.72%of the genome,primarily comprising long terminal repeats.A high-density genetic linkage map is constructed using an F2 population derived from a cross between early-and late-bolting radishes,identifying seven major quantitative trait loci associated with bolting and flowering.RNA-seq and quantitative real-time PCR analysis reveal that the RsMIPS3 gene is found to be associated with bolting,with its expression decreasing during this process.Notably,RsMIPS3 overexpression in Arabidopsis delays bolting,confirming its role in regulating bolting time.These findings advance radish genome research and provide a valuable target for breeding late-bolting varieties.展开更多
The Chamidae are widely distributed in the tropical to temperate seas,with>70 known species.Currently,their classification relies mainly on traditional morphological methods and identification primarily on small fr...The Chamidae are widely distributed in the tropical to temperate seas,with>70 known species.Currently,their classification relies mainly on traditional morphological methods and identification primarily on small fragment genes,such as COI.The intrafamily phylogenetic relationships are ambiguous,lacking support from reliable molecular data.In this study,the mitochondrial genomes of eight species of Chamidae were sequenced for the first time and then annotated.Their structures and compositional characteristics were analyzed.The mitochondrial gene order in this family differed significantly.Concurrently,the evolutionary position and phylogenetic relationship among Chamidae species were explored,and the Veneroida phylogenetic tree was recreated.Maximum Likelihood and Bayesian Inference analyses supported the monophyly of Chamidae.Additionally,the divergence time within Chamidae was estimated based on mitochondrial DNA sequences,with the most ancient divergence estimated to occur during the early Cretaceous period,128 MYA.This phylogeny is significant for understanding the diversity and taxonomic status of Chamidae.展开更多
Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a...Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data.To dissect this classic cyto-nuclear conflict,we developed the‘PhyloForensics’framework,a novel diagnostic approach to systematically identify sources of phylogenetic instability.This framework revealed that signal heterogeneity(topological entropy variance)and information content(the proportion of informative sites)are the primary drivers of gene-tree conflict.Empirically validating this,we show that removing a small subset of“loudly conflicted”genes resolves deep-level incongruence,yielding a single,highly-supported topology previously obscured by noise.Finally,complementing this sequence-based resolution,we demonstrate that mitogenome architecture provides powerful phylogenetic signals,revealing predictable,mitogenome-wide evolutionary patterns,such as a significant negative correlation between branch length and both GC content and RNA editing sites.By integrating a validated conflict-resolution framework with architectural genomics,our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories.展开更多
Soybean(Glycine max L.)is a globally vital crop for oil production and food security.High-quality genomic resources are instrumental for both functional genomics and breeding.Here,we report a near-complete,high-qualit...Soybean(Glycine max L.)is a globally vital crop for oil production and food security.High-quality genomic resources are instrumental for both functional genomics and breeding.Here,we report a near-complete,high-quality genome assembly of the elite cultivar Tianlong 1(TL1),featuring fully resolved telomeres and centromeres,as well as a gap-free assembly of 14 of its 20 chromosomes.On the basis of the genome assembly,we generate an ethyl methanesulfonate(EMS)-mutagenized population comprising 2555 M7 plants.Whole-genome resequencing of 288 EMS mutants uncovers 1,163,869 high-confidence single-nucleotide polymorphisms(SNPs)and 542,709 insertions/deletions(InDels),achieving 91.89%coverage of predicted protein-coding genes.Phenotypic screening demonstrates robust genotype–phenotype associations,with two nonsynonymous mutants displaying pronounced defects in seed and leaf development.Collectively,the chromosome-scale TL1 genome assembly and the extensively characterized mutant population establish valuable resources for functional genomics and precision breeding in soybean and related legume species.展开更多
Finger millet(Eleusine coracana Gaertn.),a nutritionally rich and drought-resilient C4 cereal,possesses exceptional grain storage longevity(up to 50 years).Here,we report a high-quality genome assembly of the allotetr...Finger millet(Eleusine coracana Gaertn.),a nutritionally rich and drought-resilient C4 cereal,possesses exceptional grain storage longevity(up to 50 years).Here,we report a high-quality genome assembly of the allotetraploid cultivar C142,revealing extensive structural rearrangements between its two subgenomes(subA and subB),which are associated with asymmetric gene expression and subgenome dominance favoring subA.SubB diverged from subA and E.indica approximately 6.8 million years ago.Subsequently,two whole-genome duplication events shaped the current genome architecture,contributing to gene redundancy and adaptive potential.Notably,expansion of stress-related gene families,such as aldo-keto reductases,suggests a role in oxidative stress response and drought adaptation.Using genome-wide association studies,we identify several candidate genes associated with key agronomic traits.Among them,EcMDHAR,encoding monodehydroascorbate reductase,plays a critical role in enhancing drought tolerance.Different EcMDHAR haplotypes exhibit distinct expression profiles,supporting their functional relevance in drought adaptation.This genomic resource not only advances our understanding of polyploid genome evolution in millets,but also provides a foundation for genome-assisted improvement of drought resistance and nutritional quality in finger millet.展开更多
Trentepohliales is a completely terrestrial order within Ulvophyceae(the core Chlorophyta),and its closely related lineages are mainly marine macroalgae(green seaweeds).Despite the considerable interest in their biote...Trentepohliales is a completely terrestrial order within Ulvophyceae(the core Chlorophyta),and its closely related lineages are mainly marine macroalgae(green seaweeds).Despite the considerable interest in their biotechnological potential,little is known about their adaptations to challenging terrestrial habitats.Here,we assemble the high-quality reference genome of Trentepohlia odorata.This alga shows duplications of key genes associated with lipid metabolism and carotenoid synthesis,potentially facilitating intracellular accumulation of lipid droplets and carotenoids.We further reveal positive selection and expansion of gene families involved in vesicle trafficking and cell division regulation in T.odorata compared with other algae(cleavage furrow-mediated cell division)in Ulvophyceae,providing a genetic foundation for the evolution of phragmoplast-mediated cell division.The combined C_(4)-like and biophysical CO_(2)-concentrating mechanisms(CCMs)of T.odorata enable adaptation to fluctuating CO_(2) environments,and support efficient photosynthesis under CO_(2)-limited conditions.Adaptive strategies of T.odorata to terrestrial stressors,such as drought,intense light,and UV-B radiation,include horizontally acquired genes involved in cell wall synthesis and remodeling,homeostasis of aldehydes,and expanded genes associated with reactive oxygen species(ROS),DNA repair,and photoprotection.Our study provides a valuable genomic resource for studying aerial algae and improves understanding of plant terrestrialization.展开更多
Early prevention and control of coal spontaneous combustion have emerged as a critical research area in coal mine safety.Due to their sustainability and environmental friendliness,microorganisms have gained attention....Early prevention and control of coal spontaneous combustion have emerged as a critical research area in coal mine safety.Due to their sustainability and environmental friendliness,microorganisms have gained attention.A filamentous fungus was collected in the coal mine and identified as Absidia spinosa.Results indicated that the mycelium effectively covered and repaired many coal pores.The oxygen consumption ratio of A.spinosa was higher in coal-containing environments than in coal-free conditions.The fungus significantly impacted aliphatic functional groups,disrupting bridging bonds and side chains connected to aromatic structures and reducing the relative content of C—O bonds.Additionally,A.spinosa increases the ignition temperature by 25.34℃.The total heat release was decreased by approximately 32.58%,and the activation energies were increased.The genome of Absidia spinosa revealed genes related to oxygen consumption,small molecule degradation,and secretion of metabolic products,such as those annotated under GO ID:0140657,etc.The pathways involved in the degradation of small organic molecules(e.g.,ko00626,etc.),carbon fixation,and nitrogen cycling,all linked to coal decomposition.Through oxygen consumption and the alteration of coal-active structures,A.spinosa effectively inhibits CSC,providing an experimental basis for exploring eco-friendly biological control methods in the goaf.展开更多
Natural hybridization is known to play a vital role in speciation;however,the mechanisms underlying the early stages of natural hybridization remain unclear.Where two plant species come into contact,two driving forces...Natural hybridization is known to play a vital role in speciation;however,the mechanisms underlying the early stages of natural hybridization remain unclear.Where two plant species come into contact,two driving forces may balance the dynamic consequences of hybridization:fusion by hybridization-mediated gene flow,and separation by reproductive isolation(RI)(Ma et al.,2010a,b;Chang et al.,2022).展开更多
The demand for extended electric vehicle(EV)range necessitates advanced lightweighting strategies.This study introduces a materials genome approach,augmented by machine learning(ML),for optimizing lightweight composit...The demand for extended electric vehicle(EV)range necessitates advanced lightweighting strategies.This study introduces a materials genome approach,augmented by machine learning(ML),for optimizing lightweight composite designs for EVs.A comprehensive materials genome database was developed,encompassing composites based on carbon,glass,and natural fibers.This database systematically records critical parameters such as mechanical properties,density,cost,and environmental impact.Machine learning models,including Random Forest,Support Vector Machines,and Artificial Neural Networks,were employed to construct a predictive system for material performance.Subsequent material composition optimization was performed using amulti-objective genetic algorithm.Experimental validation demonstrated that an optimized carbon fiber/bio-based resin composite achieved a 45%weight reduction compared to conventional steel,while maintaining equivalent structural strength.The predictive accuracy of the models reached 94.2%.A cost-benefit analysis indicated that despite a 15%increase in material cost,the overall vehicle energy consumption decreased by 12%,leading to an 18%total cost saving over a five-year operational lifecycle,under a representative mid-size battery electric vehicle(BEV)operational scenario.展开更多
基金supported by the Natural Science Foundation of Anhui Province(2408085MC058 and 2308085QC91)National Natural Science Foundation of China(32301783and U21A20214)+5 种基金Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS CSIAF-202303)Nanfan special project,CAAS(YYLH2309,YBXM2322,YYLH2401)Scientific Innovation 2030 Project(2022ZD0401703)CAAS Innovative Team Award,Science and Technology of Innovative research program of Anhui Province(202423m1005002)National Key Research and Development Program of China(2023YFD1200900)the Natural Science Foundation General Program of Hebei Province(C2024204242).
文摘IR64 is an elite Xian/indica variety developed by International Rice Research Institute(IRRl)in 1985,which has been the most widely grown variety and core breeding parent in South/Southeast Asia(Mackill and Khush,2018).IR64 has been utilized to develop stress-tolerant(such as drought-adapted and submergenceresistant)near-isogenic lines,underscoring its great potential in agricultural genomics(Tanaka et al.,2020).
基金supported in part by AFRI grant numbers 2019-7015-29321 and 2021-67015-33409 from the USDA National Institute of Food and Agriculture(NIFA)the SCINet project of the USDA ARS project number 0500-00093-001-00-D。
文摘Structural variations(SVs≥50 bp)are a critical but underexplored source of genetic diversity in cattle,shaping traits vital for productivity,adaptability,and health.Advances in long-read sequencing,pangenome graph construction,and near-complete genome assemblies now allow accurate SV detection and genotyping.These innovations overcome the limitations of single-reference genomes,enabling the discovery of complex SVs,including nested and overlapping variants,and providing access to previously inaccessible genomic regions such as centromeres and telomeres.This review highlights the current landscape of cattle SV research,with emphasis on integrating longread sequencing and pangenome frameworks to uncover breed-specific and population-level variation.While many SVs are linked to economically important traits such as feed efficiency and disease resistance,their broader regulatory impacts remain an active area of investigation.Emerging functional genomics approaches,including transcriptomics,epigenomics,and genome editing,will clarify how SVs influence gene regulation and phenotype.Looking forward,the integration of SV catalogs with multi-omics data,imputation resources,and artificial intelligence-driven models will be essential for translating discoveries into breeding and conservation applications.Integrating structural variants into breeding pipelines promises to revolutionize livestock genomics,enabling precision selection and sustainable agriculture despite challenges in cost,data sharing,and functional validation.
基金supported by the National Key R&D Program of China,No.2022YFE0210100(to XY)the Shanghai Rising-Star Program,No.22QA1405700(to XY)the National Natural Science Foundation of China,Nos.82301418(to YZ),82171246(to QX),and 82371251(to QX).
文摘Previous investigations into gut microbiota dysbiosis in patients with Parkinson’s disease have relied on 16S rRNA amplicon sequencing and assembly-free metagenomic approaches.However,there is an urgent need to study the function of the gut microbiome at the genome level using metagenome-assembled genomes.Here,we conducted single-sample metagenomic binning analysis using shotgun metagenomic sequencing data and retrieved 2837 metagenome-assembled genomes to explore the gut microbiota profile at the genome level.Reconstructing microbial genomes from metagenomic sequences greatly enriched the diversity and number of microbial genomes,especially those of uncultivable strains.By integrating the analysis of metagenome-assembled genomes with clinical parameters,we observed higherα-diversity indexes and a very different composition of microbial communities in patients with Parkinson’s disease.We also identified microbial species and metagenome-assembled genomes that were significantly associated with clinical characteristics,including disease severity,medication,motor complications,and non-motor symptoms.The genes of Parkinson’s disease severity-associated metagenome-assembled genomes were distributed across multiple pathways,such as carbon metabolism,phosphonate metabolism,carbohydrate metabolism,amino acid metabolism,fatty acid metabolism,bile acid metabolism,metabolism of cofactors and vitamins,neuroprotective molecules,immunogenic components,toxic metabolites,translation,and bacterial secretion.Our work provides a comprehensive resource for investigating the gut microbiota-Parkinson’s disease relationship at the genome level,which may enhance our comprehension of the underlying mechanisms of this disease.
文摘Non-O1/non-O139 Vibrio(V.)cholerae(NOVC)has emerged as a potential pathogen in patients with compromised health conditions[1].We report the whole genome sequencing(WGS)of a rare NOVC sepsis isolate(GenBank Accession:GCF_051906115.1)from an 89-year-old male admitted to the Intensive Care Unit(ICU)with septic shock(lactate 6.61 mmol/L)digestive illness.
基金supported by the Jilin Science and Technology Development Program,China (20240602032RC)the Jilin Agricultural Science and Technology Innovation Project,China (CXGC2024ZD001)+1 种基金the Jilin Agricultural Science and Technology Innovation Project,China (CXGC2024ZY012)the Jilin Province Development and Reform Commission-Project for Improving the Independent Innovation Capacity of Major Grain Crops,China (2024C002)。
文摘Emerging and powerful genome editing tools,particularly CRISPR/Cas9,are facilitating functional genomics research and accelerating crop improvement(Jiang et al.2021;Cao et al.2023;Chen C et al.2023;Liu et al.2023a).However,the detection and screening of transgenic lines remain major bottlenecks,being time-consuming,labor-intensive,and inefficient during transformation and subsequent mutation identification.A simple and efficient visual marker system plays a critical role in addressing these challenges.Recent studies demonstrated that the GmW1 and RUBY reporter systems were used to obtain visual transgenic soybean(Glycine max) plants(Chen L et al.2023;Chen et al.2024).
基金funded by the National Natural Science Foundation of China(grant no.31670207).
文摘The genus Clematis(Ranunculaceae)comprises over 300 species with remarkable morphological and ecological diversity worldwide.Despite its horticultural,medicinal,and ecological importance,a well-resolved phylogeny and coherent infrageneric classification are still lacking.Here,we reconstruct a robust phylogeny for Clematis using a phylogenomic approach and revise its infrageneric taxonomy.We incorporated 198 samples representing 151 species,two subspecies,and 12 varieties,covering all subgenera and most sections worldwide,obtained from both fresh and herbarium material.Nuclear single nucleotide polymorphisms(SNPs)and complete plastid genomes were assembled for phylogenetic analyses.We also prepared a nuclear ribosomal ITS(nrITS)dataset comprising 171 species,two subspecies,and 12 varieties(217 samples)to include as many species as possible for phylogenetic inference.Phylogenies based on plastid genomes and nrITS exhibited limited resolution and modest support,highlighting challenges in resolving certain relationships.Nuclear SNP analyses yielded a robust phylogenetic tree with 22 well-supported clades corresponding to 22 sections,with most previously recognized subgenera and sections not recovered as monophyletic.Ancestral state reconstruction of 12 key morphological characters revealed multiple independent origins of character states.This study presents the first comprehensive sectional classification for Clematis based on robust phylogenomic evidence,redefines morphological characteristics for each section,and resolves long-standing taxonomic ambiguities.Our results establish a framework for future studies on the evolution,ecology,and horticultural potential of this globally significant genus.
基金supported by USDA-SCRI(Grant Nos.2017-51181-26830 and 2023-51181-41321)USDA-AMS SCMP(Grant No.16SCCMAR0001)+1 种基金Arkansas Department of Agriculture SCBGP(Grant No.AM22SCBGPAR1130-00)USDA NIFA Hatch project ARK0VG2018 and ARK02440.
文摘The Leafminers,representing a diverse group of insects from various genera within the Agromyzidae family,pose a significant threat to spinach(Spinacia oleracea L.)production.This study aimed to identify single nucleotide polymorphism(SNP)markers associated with leafminer resistance through a genome-wide association study(GWAS)and to evaluate the prediction accuracy(PA)for selecting resistant spinach using genomic prediction(GP).Using a dataset of 84301 SNPs obtained from whole-genome resequencing,seven GWAS models,including BLINK,FarmCPU,MLM,and MLMM in GAPIT 3,as well as MLM,GLM,and SMR in TASSEL 5,were employed to perform GWAS on a panel of 286 USDA spinach germplasm accessions.Three SNP markers,namely 1_115279256_C_T,3_157082529_C_T,and 4_168510908_T_G on chromosomes 1,3,and 4,respectively,were identified as associated with leafminer resistance.In the 30 kb flanking regions of these markers,four candidate genes(SOV1g031330,SOV1g031340,SOV4g047270,and SOV4g047280),encoding LOB domain-containing protein,KH domain-containing protein,were discovered.Nodulin-like domain-containing protein,and SAM domain-containing protein,were discovered.The PA for leafminer resistance selection was estimated using ten different SNP sets,including two GWAS-derived marker sets(three and 51 SNPs)and eight random marker sets(ranging from 51 to 10 K SNPs)analyzed by seven GP models.The findings emphasized the superior performance of GWAS-derived SNP sets,reaching a PA of up to 0.79 using the cBLUP model.Notably,this research marks the pioneering application of GP in the context of insect resistance,providing a significant advancement in the understanding and management of leafminer resistance in spinach cultivation.
文摘Iris domestica,a perennial herb of the Iridaceae family,is widely recognized for its rich isoflavone content and broad therapeutic properties.To elucidate the biosynthetic pathway of these medicinally significant compounds,we constructed a haplotype-resolved genome assembly of this species.Transcriptomic and metabolomic analyses revealed tissue-specific accumulation of isoflavone,particularly in rhizomes and roots.Functional characterization identified two candidate isoflavone synthase genes,among which IdIFS was confirmed to promote the biosynthesis of key compounds tectorigenin and irisflorentin.The high-quality genome assembly presented here provides a foundational resource for further research into the evolution,secondary metabolite,and environmental adaptation of I.domestica.
基金supported by the National Key Research and Development Program of China(2022YFF1003203)Biological Breeding-National Science and Technology Major Project(2022ZDo4011)+2 种基金the Central Public-interest Scientific Institution Basal Research Fund(Y2025YC44)the Central Public-interest Scientific Institution Basal Research Fund(2025-YWF-ZYSQ-04)the China Postdoctoral Science Foundation(2023M733832).
文摘The genetic basis of early-stage salt tolerance in alfalfa(Medicago sativa L.),a key factor limiting its productivity,remains poorly understood.To dissect this complex trait,we integrate genome-wide association studies(GWAS)and transcriptomics from 176 accessions within a machine learning based genomic prediction framework.Analysis reveals weak genetic correlations among four salt-tolerance traits and a gradual decline in performance under increasing salt stress.GWAS identify 60 significant associated SNPs,with the highest number detected under 100 mM salt stress.Salt tolerance exhibits an additive effect from favorable haplotypes,which are most abundant in Chinese accessions.GWAS-associated genes are related to key regulators of hormone signaling and osmotic adjustment,while transcriptome analysis indicates a global repression of stress-responsive transcription factors.Integrating these multi-omics datasets allows us to identify 14 candidate genes,including MsHSD1(seed dormancy)and MsMTATP6(energy metabolism).Crucially,incorporating these markers into genomic prediction models improve cross-population predictive accuracy to an average of 54.4%.This study provides insights into the genetic architecture of salt tolerance in alfalfa and offers valuable markers to facilitate molecular breeding.
基金supported by the Priority Academic Program Development of Jiangsu Higher Education Institution(PAPD).
文摘Inoculation of starter culture is a viable method to improve the quality of fermented foods,but its effect on the flavor metabolite profiles and the underlying mechanisms are still unclear.This study aimed to elucidate the effects of starters(Lactiplantibacillus plantarum(LP)and Staphylococcus simulans(SS)individually or in combination(LS))on the flavor metabolite profiles of fermented sausages via metabolomics and genomics.L.plantarum markedly modified the composition of bacterial communities and made Lactobacillus spp.dominant in sausages(98.29%and 85.03%in LP and LS groups,respectively).Additionally,inoculation with a single starter,L.plantarum,and a mixed starter yielded similar non-volatile flavor metabolites,which were mainly characterized at the amino acid and peptide levels(relative intensities of 349.65 and 348.62 for the LP and LS groups,respectively).Meanwhile,the mixed starter group had the most volatile flavor metabolites(relative intensity of 34728.67),some of which were contributed by L.plantarum,such as ethyl acetate(relative intensities of 583.33 and 588.33 for the LP and LS groups,respectively)and benzaldehyde(relative intensities of 786.67 and 909.00 for the LP and LS groups,respectively),and several of which were generated by S.simulans,such as ethyl propionate(relative intensities of 214.67 and 136.67 for the SS and LS groups,respectively)and benzyl alcohol(relative intensities of 720.00 and 656.00 for the SS and LS groups,respectively).Furthermore,L.plantarum was found to possess more genes encoding peptidases(48)and carbohydrate-active enzymes(124),while S.simulans had more genes related to lipid hydrolysis(12).In conclusion,differences in the properties and combinations of indigenous strains play a crucial role in the generation of flavor metabolites in sausages.
基金supported by the Joint Funds of the National Natural Science Foundation of China(Grant No.U22A20494)the 1+9 Open Competition Project of Sichuan Academy of Agricultural Sciences(1+9KJGGo02)+4 种基金the National Key R&D Program of China(2024YFA130670O)the“5+1”Agricultural Frontier Technology Research Initiative of Sichuan Academy of Agricultural Sciences(5+1QYGG003)the Project of Sichuan Province Engineering Technology Research Center of Vegetables(2023PZSC0303)the 14th Five-Year Plan Vegetable Breeding Project of Sichuan Province(2021YFYZ0022)the Experts of Sichuan Vegetable Innovation Team(SCCXTD-2025-05).
文摘Radish(Raphanus sativus L.)is an important cruciferous root vegetable,with bolting regulated by multiple genes.However,the genetic mechanisms underlying bolting regulation remain unclear.Here,the genome of the cultivar C60213 is assembled into a high-quality,gap-free telomere-to-telomere structure,spanning nine chromosomes and totaling 472.71 Mb,using a combination of Oxford Nanopore,PacBio,and Hi-C sequencing technologies.It identifies 49,768 protein-coding genes,97.38%of which are functionally annotated.Repetitive sequences constitute 59.72%of the genome,primarily comprising long terminal repeats.A high-density genetic linkage map is constructed using an F2 population derived from a cross between early-and late-bolting radishes,identifying seven major quantitative trait loci associated with bolting and flowering.RNA-seq and quantitative real-time PCR analysis reveal that the RsMIPS3 gene is found to be associated with bolting,with its expression decreasing during this process.Notably,RsMIPS3 overexpression in Arabidopsis delays bolting,confirming its role in regulating bolting time.These findings advance radish genome research and provide a valuable target for breeding late-bolting varieties.
基金supported by grants from the Agriculture Seed Improvement Projects of Shandong Province(Nos.2022LZGCQY010,2021ZLGX03,and 2021TSGC 1240)the China Agriculture Research System Project(No.CARS-49)。
文摘The Chamidae are widely distributed in the tropical to temperate seas,with>70 known species.Currently,their classification relies mainly on traditional morphological methods and identification primarily on small fragment genes,such as COI.The intrafamily phylogenetic relationships are ambiguous,lacking support from reliable molecular data.In this study,the mitochondrial genomes of eight species of Chamidae were sequenced for the first time and then annotated.Their structures and compositional characteristics were analyzed.The mitochondrial gene order in this family differed significantly.Concurrently,the evolutionary position and phylogenetic relationship among Chamidae species were explored,and the Veneroida phylogenetic tree was recreated.Maximum Likelihood and Bayesian Inference analyses supported the monophyly of Chamidae.Additionally,the divergence time within Chamidae was estimated based on mitochondrial DNA sequences,with the most ancient divergence estimated to occur during the early Cretaceous period,128 MYA.This phylogeny is significant for understanding the diversity and taxonomic status of Chamidae.
基金funded by the Shenzhen Science and Technology Program(Grant No.JCYJ20241202130723030)the National Natural Science Foundation of China(Grant No.32170238)+2 种基金the Guangdong Pearl River Talent Program(Grant No.2021QN02N792)the Shenzhen Fundamental Research Program(Grant No.JCYJ20220818103212025)the Chinese Academy of Agricultural Sciences Elite Youth Program(110243160001007)to Z.W.
文摘Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data.To dissect this classic cyto-nuclear conflict,we developed the‘PhyloForensics’framework,a novel diagnostic approach to systematically identify sources of phylogenetic instability.This framework revealed that signal heterogeneity(topological entropy variance)and information content(the proportion of informative sites)are the primary drivers of gene-tree conflict.Empirically validating this,we show that removing a small subset of“loudly conflicted”genes resolves deep-level incongruence,yielding a single,highly-supported topology previously obscured by noise.Finally,complementing this sequence-based resolution,we demonstrate that mitogenome architecture provides powerful phylogenetic signals,revealing predictable,mitogenome-wide evolutionary patterns,such as a significant negative correlation between branch length and both GC content and RNA editing sites.By integrating a validated conflict-resolution framework with architectural genomics,our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories.
基金supported by the National Natural Science Foundation of China(31970344)Joint Funds of the Natural Science Foundation of Hainan Province,China(2021JJLH0065).
文摘Soybean(Glycine max L.)is a globally vital crop for oil production and food security.High-quality genomic resources are instrumental for both functional genomics and breeding.Here,we report a near-complete,high-quality genome assembly of the elite cultivar Tianlong 1(TL1),featuring fully resolved telomeres and centromeres,as well as a gap-free assembly of 14 of its 20 chromosomes.On the basis of the genome assembly,we generate an ethyl methanesulfonate(EMS)-mutagenized population comprising 2555 M7 plants.Whole-genome resequencing of 288 EMS mutants uncovers 1,163,869 high-confidence single-nucleotide polymorphisms(SNPs)and 542,709 insertions/deletions(InDels),achieving 91.89%coverage of predicted protein-coding genes.Phenotypic screening demonstrates robust genotype–phenotype associations,with two nonsynonymous mutants displaying pronounced defects in seed and leaf development.Collectively,the chromosome-scale TL1 genome assembly and the extensively characterized mutant population establish valuable resources for functional genomics and precision breeding in soybean and related legume species.
基金supported by the National Crop Germplasm Resources Center(NCGRC-2024-056)the National Natural Science Foundation of China(32301813).
文摘Finger millet(Eleusine coracana Gaertn.),a nutritionally rich and drought-resilient C4 cereal,possesses exceptional grain storage longevity(up to 50 years).Here,we report a high-quality genome assembly of the allotetraploid cultivar C142,revealing extensive structural rearrangements between its two subgenomes(subA and subB),which are associated with asymmetric gene expression and subgenome dominance favoring subA.SubB diverged from subA and E.indica approximately 6.8 million years ago.Subsequently,two whole-genome duplication events shaped the current genome architecture,contributing to gene redundancy and adaptive potential.Notably,expansion of stress-related gene families,such as aldo-keto reductases,suggests a role in oxidative stress response and drought adaptation.Using genome-wide association studies,we identify several candidate genes associated with key agronomic traits.Among them,EcMDHAR,encoding monodehydroascorbate reductase,plays a critical role in enhancing drought tolerance.Different EcMDHAR haplotypes exhibit distinct expression profiles,supporting their functional relevance in drought adaptation.This genomic resource not only advances our understanding of polyploid genome evolution in millets,but also provides a foundation for genome-assisted improvement of drought resistance and nutritional quality in finger millet.
基金supported by the National Natural Science Foundation of China(W2511024,32370228,32470232)the Natural Science Foundation of Jiangsu Province(BK20250004)+3 种基金the Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry,the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)the fund of Taxonomy Scientist Program'of the Chinese Academy of Sciences(CAS-TAX-24-038)the Youth Innovation Promotion Association CAS(2023355)Postgraduate Research&Practice Innovation Program of Jiangsu Province(KYCX24_1846).
文摘Trentepohliales is a completely terrestrial order within Ulvophyceae(the core Chlorophyta),and its closely related lineages are mainly marine macroalgae(green seaweeds).Despite the considerable interest in their biotechnological potential,little is known about their adaptations to challenging terrestrial habitats.Here,we assemble the high-quality reference genome of Trentepohlia odorata.This alga shows duplications of key genes associated with lipid metabolism and carotenoid synthesis,potentially facilitating intracellular accumulation of lipid droplets and carotenoids.We further reveal positive selection and expansion of gene families involved in vesicle trafficking and cell division regulation in T.odorata compared with other algae(cleavage furrow-mediated cell division)in Ulvophyceae,providing a genetic foundation for the evolution of phragmoplast-mediated cell division.The combined C_(4)-like and biophysical CO_(2)-concentrating mechanisms(CCMs)of T.odorata enable adaptation to fluctuating CO_(2) environments,and support efficient photosynthesis under CO_(2)-limited conditions.Adaptive strategies of T.odorata to terrestrial stressors,such as drought,intense light,and UV-B radiation,include horizontally acquired genes involved in cell wall synthesis and remodeling,homeostasis of aldehydes,and expanded genes associated with reactive oxygen species(ROS),DNA repair,and photoprotection.Our study provides a valuable genomic resource for studying aerial algae and improves understanding of plant terrestrialization.
基金supported by the National Natural Science Foundation of China(No.51974128)the National Key Research and Development Program of China(No.2023YFC3009105)。
文摘Early prevention and control of coal spontaneous combustion have emerged as a critical research area in coal mine safety.Due to their sustainability and environmental friendliness,microorganisms have gained attention.A filamentous fungus was collected in the coal mine and identified as Absidia spinosa.Results indicated that the mycelium effectively covered and repaired many coal pores.The oxygen consumption ratio of A.spinosa was higher in coal-containing environments than in coal-free conditions.The fungus significantly impacted aliphatic functional groups,disrupting bridging bonds and side chains connected to aromatic structures and reducing the relative content of C—O bonds.Additionally,A.spinosa increases the ignition temperature by 25.34℃.The total heat release was decreased by approximately 32.58%,and the activation energies were increased.The genome of Absidia spinosa revealed genes related to oxygen consumption,small molecule degradation,and secretion of metabolic products,such as those annotated under GO ID:0140657,etc.The pathways involved in the degradation of small organic molecules(e.g.,ko00626,etc.),carbon fixation,and nitrogen cycling,all linked to coal decomposition.Through oxygen consumption and the alteration of coal-active structures,A.spinosa effectively inhibits CSC,providing an experimental basis for exploring eco-friendly biological control methods in the goaf.
基金supported by the National Natural Science Foundation of China(U23A20160,32360336)Guizhou Provincial Key Technology R&D Program(Qian KeHe ZhiCheng[2023]YiBan035).
文摘Natural hybridization is known to play a vital role in speciation;however,the mechanisms underlying the early stages of natural hybridization remain unclear.Where two plant species come into contact,two driving forces may balance the dynamic consequences of hybridization:fusion by hybridization-mediated gene flow,and separation by reproductive isolation(RI)(Ma et al.,2010a,b;Chang et al.,2022).
文摘The demand for extended electric vehicle(EV)range necessitates advanced lightweighting strategies.This study introduces a materials genome approach,augmented by machine learning(ML),for optimizing lightweight composite designs for EVs.A comprehensive materials genome database was developed,encompassing composites based on carbon,glass,and natural fibers.This database systematically records critical parameters such as mechanical properties,density,cost,and environmental impact.Machine learning models,including Random Forest,Support Vector Machines,and Artificial Neural Networks,were employed to construct a predictive system for material performance.Subsequent material composition optimization was performed using amulti-objective genetic algorithm.Experimental validation demonstrated that an optimized carbon fiber/bio-based resin composite achieved a 45%weight reduction compared to conventional steel,while maintaining equivalent structural strength.The predictive accuracy of the models reached 94.2%.A cost-benefit analysis indicated that despite a 15%increase in material cost,the overall vehicle energy consumption decreased by 12%,leading to an 18%total cost saving over a five-year operational lifecycle,under a representative mid-size battery electric vehicle(BEV)operational scenario.
