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
Multi-agent reinforcement learning(MARL)has proven its effectiveness in cooperative multi-agent systems(MASs)but still faces issues on the curse of dimensionality and learning efficiency.The main difficulty is caused ...Multi-agent reinforcement learning(MARL)has proven its effectiveness in cooperative multi-agent systems(MASs)but still faces issues on the curse of dimensionality and learning efficiency.The main difficulty is caused by the strong inter-agent coupling nature embedded in an MARL problem,which is yet to be fully exploited in existing algorithms.In this work,we recognize a learning graph characterizing the dependence between individual rewards and individual policies.Then we propose a graph-based reward aggregation(GRA)method,which utilizes the inherent coupling relationship among agents to eliminate redundant information.Specifically,GRA passes information among cooperating agents through graph attention networks to obtain aggregated rewards that contribute to the fitting of the value function,making each agent learn a decentralized executable cooperation policy.In addition,we propose a variant of GRA,named GRA-decen,which achieves decentralized training and decentralized execution(DTDE)when each agent only has access to information of partial agents in the learning process.We conduct experiments in different environments and demonstrate the practicality and scalability of our algorithms.展开更多
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
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
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
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
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
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
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
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
The advantages of genome selection(GS) in animal and plant breeding are self-evident.Traditional parametric models have disadvantage in better fit the increasingly large sequencing data and capture complex effects acc...The advantages of genome selection(GS) in animal and plant breeding are self-evident.Traditional parametric models have disadvantage in better fit the increasingly large sequencing data and capture complex effects accurately.Machine learning models have demonstrated remarkable potential in addressing these challenges.In this study,we introduced the concept of mixed kernel functions to explore the performance of support vector machine regression(SVR) in GS.Six single kernel functions(SVR_L,SVR_C,SVR_G,SVR_P,SVR_S,SVR_L) and four mixed kernel functions(SVR_GS,SVR_GP,SVR_LS,SVR_LP) were used to predict genome breeding values.The prediction accuracy,mean squared error(MSE) and mean absolute error(MAE) were used as evaluation indicators to compare with two traditional parametric models(GBLUP,BayesB) and two popular machine learning models(RF,KcRR).The results indicate that in most cases,the performance of the mixed kernel function model significantly outperforms that of GBLUP,BayesB and single kernel function.For instance,for T1 in the pig dataset,the predictive accuracy of SVR_GS is improved by 10% compared to GBLUP,and by approximately 4.4 and 18.6% compared to SVR_G and SVR_S respectively.For E1 in the wheat dataset,SVR_GS achieves 13.3% higher prediction accuracy than GBLUP.Among single kernel functions,the Laplacian and Gaussian kernel functions yield similar results,with the Gaussian kernel function performing better.The mixed kernel function notably reduces the MSE and MAE when compared to all single kernel functions.Furthermore,regarding runtime,SVR_GS and SVR_GP mixed kernel functions run approximately three times faster than GBLUP in the pig dataset,with only a slight increase in runtime compared to the single kernel function model.In summary,the mixed kernel function model of SVR demonstrates speed and accuracy competitiveness,and the model such as SVR_GS has important application potential for GS.展开更多
This study examined the potential response mechanisms of Ligilactobacillus salivarius AR612 to glucose stress through whole-genome and comparative transcriptome analysis.We obtained the basic genome information of L.s...This study examined the potential response mechanisms of Ligilactobacillus salivarius AR612 to glucose stress through whole-genome and comparative transcriptome analysis.We obtained the basic genome information of L.salivarius AR612.The full genome length of L.salivarius AR612 was 1970245 bp,with a GC content of 33.01%and 1894 coding genes.Moreover,we identified many genes associated with genetic adaptations to various stress factors,including temperature,p H,osmotic pressure,bile salts,and oxidative stress.Physiological analysis revealed that the growth and morphology of AR612 changed significantly under glucose stress,with a decrease in the maximum growth and irregular cell morphology.Furthermore,a comparison of transcriptome data indicated that glucose stress induced changes in the number of differential genes.Moreover,AR612 could respond to extracellular glucose stress by changing the expression of genes related to cell morphology,carbohydrate metabolism,amino acid metabolism,fatty acid synthesis,and nucleotide metabolism.This study provides valuable theoretical insights for future research on the adaptation of L.salivarius AR612 to nutritional stress and its application in industrial processes.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
Brain organoids are artificial neural tissues derived in vitro,containing a variety of cell types,as well as structural and/or functional brain regions.They can partially mimic brain physiological activities and disea...Brain organoids are artificial neural tissues derived in vitro,containing a variety of cell types,as well as structural and/or functional brain regions.They can partially mimic brain physiological activities and diseased processes.Owing to their operability and sample accessibility,brain organoids serve as a bridge between in vitro monolayer cell culture models and in vivo animal models.An increasing number of induction protocols for brain organoids have been developed over the preceding decade.A key future research direction will focus on ensuring the complexity and quality of brain organoids.The integration of powerful technologies,such as the CRISP R/Cas9 genome editing and lineage tra cing systems,shall precipitate practical and broad applications of brain organoids.In this review,we discuss the generation and application of brain organoids,as well as their integration with genome editing technologies,in the study of neural development,disease modeling,and mechanistic investigations.The innovative combination of these two technologies may offer a fresh perspective for exploring the fundamental aspects of the human nervous system and related diseases.展开更多
The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported...The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported a high-quality genome assembly of G.latifolium.Comparative genome analyses revealed substantial variations in both gene group composition and genomic sequences across 13 cotton genomes,including the expansion of photosynthesis-related gene groups in G.latifolium compared with other races and the pivotal contribution of structural variations(SVs)to G.hirsutum domestication.Based on the resequencing reads and constructed pan-genome of upland cotton,co-selection regions and SVs with significant frequency differences among different populations were identified.Genes located in these regions or affected by these variations may characterize the differences between G.latifolium and other races,and could be involved in maintenance of upland cotton domestication phenotypes.These findings may assist in mining genes for upland cotton improvement and improving the understanding of the genetic basis of upland cotton domestication.展开更多
Chinese chestnut is an important economic forest tree species with enormous application value in the wood,medical,and chemical industries.Currently,the limited genome-wide SSR molecular marker information on chestnut ...Chinese chestnut is an important economic forest tree species with enormous application value in the wood,medical,and chemical industries.Currently,the limited genome-wide SSR molecular marker information on chestnut resources significantly restricts research on the genetic diversity and identification of chestnut resources.To address this issue,we used GMATA to screen simple sequence repeat(SSR)markers throughout the Chinese chestnut genome.A total of 312,302 molecular markers were obtained with a density of 434.38 Mb-1.Subsequently,all SSR markers were examined for polymorphism using the Hip STR program and 138,208 polymorphic loci were ultimately obtained.To verify the capability of the developed SSR for identification,we randomly selected 36 markers on 12 chromosomes to construct fingerprint maps of 96 ancient Chinese chestnut resources from the Yanshan Mountains.The results showed that only six pairs of primers were required to create a unique DNA fingerprint of the tested ancient trees,showing that the developed markers have good potential for identification.We then evaluated the inter-specific universality and polymorphism of these markers using 91 Castanea plants of three different species.The molecular markers amplified 94%of the interspecies with a polymorphic information content(PIC)value of 0.859.Cluster analysis revealed that the resources can be well differentiated using these developed markers,and these markers can be widely used to identify interspecific boundaries.The results of this study proved that the developed molecular markers have the potential for assessing genotypic diversity,which can provide references for genetic diversity research,variety identification,kinship analysis,the selection of good products,and the construction of core germplasm resources of chestnut and even chestnut plants.Also these markers provide a solid foundation for the molecular design of hybrids,improved breeding and development of germplasm resources.展开更多
Background India harbors the world’s largest cattle population,encompassing over 50 distinct Bos indicus breeds.This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the...Background India harbors the world’s largest cattle population,encompassing over 50 distinct Bos indicus breeds.This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle.To comprehensively characterize the genomic variation within Bos indicus and,specifically,dairy breeds,we aim to identify non-reference sequences and construct a comprehensive pangenome.Results Five representative genomes of prominent dairy breeds,including Gir,Kankrej,Tharparkar,Sahiwal,and Red Sindhi,were sequenced using 10X Genomics‘linked-read’technology.Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb,comparable to the Bos indicus Brahman reference genome.A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods,revealing 8 Mb and 17.7 Mb of novel sequence respectively.A confident set of 6,844 Non-reference Unique Insertions(NUIs)spanning 7.57 Mb was identified through both methods,representing the pange-nome of Indian Bos indicus breeds.Comparative analysis with previously published pangenomes unveiled 2.8 Mb(37%)commonality with the Chinese indicine pangenome and only 1%commonality with the Bos taurus pange-nome.Among these,2,312 NUIs encompassing~2 Mb,were commonly found in 98 samples of the 5 breeds and des-ignated as Bos indicus Common Insertions(BICIs)in the population.Furthermore,926 BICIs were identified within 682 protein-coding genes,54 long non-coding RNAs(lncRNA),and 18 pseudogenes.These protein-coding genes were enriched for functions such as chemical synaptic transmission,cell junction organization,cell-cell adhesion,and cell morphogenesis.The protein-coding genes were found in various prominent quantitative trait locus(QTL)regions,suggesting potential roles of BICIs in traits related to milk production,reproduction,exterior,health,meat,and carcass.Notably,63.21%of the bases within the BICIs call set contained interspersed repeats,predominantly Long Inter-spersed Nuclear Elements(LINEs).Additionally,70.28%of BICIs are shared with other domesticated and wild species,highlighting their evolutionary significance.Conclusions This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India.The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.展开更多
In-depth knowledge of the microbes responsible for biogenic amine(BA)production during soy sauce fermentation remains limited.Herein,the variations in the BA profiles,microbial communities,and microbes involved in BA ...In-depth knowledge of the microbes responsible for biogenic amine(BA)production during soy sauce fermentation remains limited.Herein,the variations in the BA profiles,microbial communities,and microbes involved in BA production during the fermentation of soy sauce through Japanese-type(JP)and Cantonese-type(CP)processes were compared.BA analysis revealed that the most abundant BA species were putrescine,tyramine,and histamine in the later three stages(1187.68,785.16,and 193.20 mg/kg on average,respectively).The BA profiles differed significantly,with CP samples containing higher contents of putrescine,tyramine,and histamine(P<0.05)at the end of fermentation.Metagenomic analysis indicated that BA-producing genes exhibited different abundance profiles,with most genes,including spe A,spe B,arg,spe E,and tyr DC,having higher abundances in microbial communities during the CP process.In total,15 high-quality metagenome-assembled genomes(MAGs)were retrieved,of which 10 encoded at BA production-related genes.Enterococcus faecium(MAG10)and Weissella paramesenteroides(MAG5)might be the major tyramine producers.The high putrescine content in CP might be associated with the high abundance of Staphylococcus gallinarum(MAG8).This study provides a comprehensive understanding of the diversity and abundance of genes involved in BA synthesis,especially at the species level,during food fermentation.展开更多
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 in part by the National Natural Science Foundation of China(grants 62203073 and 62573068)the Natural Science Foundation of Chongqing,China(grant CSTB2022NSCQMSX0577)。
文摘Multi-agent reinforcement learning(MARL)has proven its effectiveness in cooperative multi-agent systems(MASs)but still faces issues on the curse of dimensionality and learning efficiency.The main difficulty is caused by the strong inter-agent coupling nature embedded in an MARL problem,which is yet to be fully exploited in existing algorithms.In this work,we recognize a learning graph characterizing the dependence between individual rewards and individual policies.Then we propose a graph-based reward aggregation(GRA)method,which utilizes the inherent coupling relationship among agents to eliminate redundant information.Specifically,GRA passes information among cooperating agents through graph attention networks to obtain aggregated rewards that contribute to the fitting of the value function,making each agent learn a decentralized executable cooperation policy.In addition,we propose a variant of GRA,named GRA-decen,which achieves decentralized training and decentralized execution(DTDE)when each agent only has access to information of partial agents in the learning process.We conduct experiments in different environments and demonstrate the practicality and scalability of our algorithms.
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.
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 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 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(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 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(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.
基金supported by the China Agriculture Research System of MOF and MARAthe National Natural Science Foundation of China (31872337 and 31501919)the Agricultural Science and Technology Innovation Project,China (ASTIP-IAS02)。
文摘The advantages of genome selection(GS) in animal and plant breeding are self-evident.Traditional parametric models have disadvantage in better fit the increasingly large sequencing data and capture complex effects accurately.Machine learning models have demonstrated remarkable potential in addressing these challenges.In this study,we introduced the concept of mixed kernel functions to explore the performance of support vector machine regression(SVR) in GS.Six single kernel functions(SVR_L,SVR_C,SVR_G,SVR_P,SVR_S,SVR_L) and four mixed kernel functions(SVR_GS,SVR_GP,SVR_LS,SVR_LP) were used to predict genome breeding values.The prediction accuracy,mean squared error(MSE) and mean absolute error(MAE) were used as evaluation indicators to compare with two traditional parametric models(GBLUP,BayesB) and two popular machine learning models(RF,KcRR).The results indicate that in most cases,the performance of the mixed kernel function model significantly outperforms that of GBLUP,BayesB and single kernel function.For instance,for T1 in the pig dataset,the predictive accuracy of SVR_GS is improved by 10% compared to GBLUP,and by approximately 4.4 and 18.6% compared to SVR_G and SVR_S respectively.For E1 in the wheat dataset,SVR_GS achieves 13.3% higher prediction accuracy than GBLUP.Among single kernel functions,the Laplacian and Gaussian kernel functions yield similar results,with the Gaussian kernel function performing better.The mixed kernel function notably reduces the MSE and MAE when compared to all single kernel functions.Furthermore,regarding runtime,SVR_GS and SVR_GP mixed kernel functions run approximately three times faster than GBLUP in the pig dataset,with only a slight increase in runtime compared to the single kernel function model.In summary,the mixed kernel function model of SVR demonstrates speed and accuracy competitiveness,and the model such as SVR_GS has important application potential for GS.
基金supported by the Natural Science Foundation of China(32272364)the Shanghai Education Committee Scientific Research Innovation Projects,China(2101070007800120)+2 种基金National Science Foundation for Distinguished Young Scholars(32025029)Shanghai Key Project in Synthetic Biology(23HC1400900)the Shanghai Engineering Research Center of 460 Food Microbiology Program(19DZ2281100).
文摘This study examined the potential response mechanisms of Ligilactobacillus salivarius AR612 to glucose stress through whole-genome and comparative transcriptome analysis.We obtained the basic genome information of L.salivarius AR612.The full genome length of L.salivarius AR612 was 1970245 bp,with a GC content of 33.01%and 1894 coding genes.Moreover,we identified many genes associated with genetic adaptations to various stress factors,including temperature,p H,osmotic pressure,bile salts,and oxidative stress.Physiological analysis revealed that the growth and morphology of AR612 changed significantly under glucose stress,with a decrease in the maximum growth and irregular cell morphology.Furthermore,a comparison of transcriptome data indicated that glucose stress induced changes in the number of differential genes.Moreover,AR612 could respond to extracellular glucose stress by changing the expression of genes related to cell morphology,carbohydrate metabolism,amino acid metabolism,fatty acid synthesis,and nucleotide metabolism.This study provides valuable theoretical insights for future research on the adaptation of L.salivarius AR612 to nutritional stress and its application in industrial processes.
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.
基金Special Projectfor Clinical Research of Shanghai Municipal Health Commission,No.202140403Key Disciplines Group Construction Project of Pudong Health Bureau of Shanghai,No.PWZxq2022-05+2 种基金Natural Science Foundation of Ningxia Hui Autonomous Region,No.2024AAC05084Ningxia Hui Autonomous Region Key Research and Development Program,No.2021BEG03084National Natural Science Foundation of China,Nos.32370895,32070862。
文摘Brain organoids are artificial neural tissues derived in vitro,containing a variety of cell types,as well as structural and/or functional brain regions.They can partially mimic brain physiological activities and diseased processes.Owing to their operability and sample accessibility,brain organoids serve as a bridge between in vitro monolayer cell culture models and in vivo animal models.An increasing number of induction protocols for brain organoids have been developed over the preceding decade.A key future research direction will focus on ensuring the complexity and quality of brain organoids.The integration of powerful technologies,such as the CRISP R/Cas9 genome editing and lineage tra cing systems,shall precipitate practical and broad applications of brain organoids.In this review,we discuss the generation and application of brain organoids,as well as their integration with genome editing technologies,in the study of neural development,disease modeling,and mechanistic investigations.The innovative combination of these two technologies may offer a fresh perspective for exploring the fundamental aspects of the human nervous system and related diseases.
基金supported by the National Natural Science Foundation of China(32201873)the Key Research and Development Plan of Hubei Province(2023BBB050)。
文摘The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported a high-quality genome assembly of G.latifolium.Comparative genome analyses revealed substantial variations in both gene group composition and genomic sequences across 13 cotton genomes,including the expansion of photosynthesis-related gene groups in G.latifolium compared with other races and the pivotal contribution of structural variations(SVs)to G.hirsutum domestication.Based on the resequencing reads and constructed pan-genome of upland cotton,co-selection regions and SVs with significant frequency differences among different populations were identified.Genes located in these regions or affected by these variations may characterize the differences between G.latifolium and other races,and could be involved in maintenance of upland cotton domestication phenotypes.These findings may assist in mining genes for upland cotton improvement and improving the understanding of the genetic basis of upland cotton domestication.
基金supported by the National Key Research&Development Program of China(2024YFD2200602)the National Natural Science Foundation of China(32471917)。
文摘Chinese chestnut is an important economic forest tree species with enormous application value in the wood,medical,and chemical industries.Currently,the limited genome-wide SSR molecular marker information on chestnut resources significantly restricts research on the genetic diversity and identification of chestnut resources.To address this issue,we used GMATA to screen simple sequence repeat(SSR)markers throughout the Chinese chestnut genome.A total of 312,302 molecular markers were obtained with a density of 434.38 Mb-1.Subsequently,all SSR markers were examined for polymorphism using the Hip STR program and 138,208 polymorphic loci were ultimately obtained.To verify the capability of the developed SSR for identification,we randomly selected 36 markers on 12 chromosomes to construct fingerprint maps of 96 ancient Chinese chestnut resources from the Yanshan Mountains.The results showed that only six pairs of primers were required to create a unique DNA fingerprint of the tested ancient trees,showing that the developed markers have good potential for identification.We then evaluated the inter-specific universality and polymorphism of these markers using 91 Castanea plants of three different species.The molecular markers amplified 94%of the interspecies with a polymorphic information content(PIC)value of 0.859.Cluster analysis revealed that the resources can be well differentiated using these developed markers,and these markers can be widely used to identify interspecific boundaries.The results of this study proved that the developed molecular markers have the potential for assessing genotypic diversity,which can provide references for genetic diversity research,variety identification,kinship analysis,the selection of good products,and the construction of core germplasm resources of chestnut and even chestnut plants.Also these markers provide a solid foundation for the molecular design of hybrids,improved breeding and development of germplasm resources.
基金the project “Genomics for Conservation of Indigenous Cattle Breeds and for Enhancing Milk Yield, Phase-I” [BT/ PR26466/AAQ/1/704/2017], funded by the Department of Biotechnology (DBT ), Indiathe project “Identification of key molecular factors involved in resistance/susceptibility to paratuberculosis infection in indigenous breeds of cows” [BT/PR32758/AAQ/1/760/2019], which was also funded by Department of Biotechnology (DBT ), India。
文摘Background India harbors the world’s largest cattle population,encompassing over 50 distinct Bos indicus breeds.This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle.To comprehensively characterize the genomic variation within Bos indicus and,specifically,dairy breeds,we aim to identify non-reference sequences and construct a comprehensive pangenome.Results Five representative genomes of prominent dairy breeds,including Gir,Kankrej,Tharparkar,Sahiwal,and Red Sindhi,were sequenced using 10X Genomics‘linked-read’technology.Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb,comparable to the Bos indicus Brahman reference genome.A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods,revealing 8 Mb and 17.7 Mb of novel sequence respectively.A confident set of 6,844 Non-reference Unique Insertions(NUIs)spanning 7.57 Mb was identified through both methods,representing the pange-nome of Indian Bos indicus breeds.Comparative analysis with previously published pangenomes unveiled 2.8 Mb(37%)commonality with the Chinese indicine pangenome and only 1%commonality with the Bos taurus pange-nome.Among these,2,312 NUIs encompassing~2 Mb,were commonly found in 98 samples of the 5 breeds and des-ignated as Bos indicus Common Insertions(BICIs)in the population.Furthermore,926 BICIs were identified within 682 protein-coding genes,54 long non-coding RNAs(lncRNA),and 18 pseudogenes.These protein-coding genes were enriched for functions such as chemical synaptic transmission,cell junction organization,cell-cell adhesion,and cell morphogenesis.The protein-coding genes were found in various prominent quantitative trait locus(QTL)regions,suggesting potential roles of BICIs in traits related to milk production,reproduction,exterior,health,meat,and carcass.Notably,63.21%of the bases within the BICIs call set contained interspersed repeats,predominantly Long Inter-spersed Nuclear Elements(LINEs).Additionally,70.28%of BICIs are shared with other domesticated and wild species,highlighting their evolutionary significance.Conclusions This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India.The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.
基金supported by the Natural Science Foundation of Guangdong Province(2022A1515012158)the National Science Foundation of China(41977138)+3 种基金the Construction Project of Teaching Quality and Teaching Reform in Guangdong Province(SJD202001)the General University Project of Guangdong Provincial Department of Education(2021KCXTD070 and 2021ZDZX4072)the Key Project of Social Welfare and Basic Research of Zhongshan City(2020B2010)the Start-up Fund from the Zhongshan Institute at the University of Electronic Science and Technology in China(419YKQN12)。
文摘In-depth knowledge of the microbes responsible for biogenic amine(BA)production during soy sauce fermentation remains limited.Herein,the variations in the BA profiles,microbial communities,and microbes involved in BA production during the fermentation of soy sauce through Japanese-type(JP)and Cantonese-type(CP)processes were compared.BA analysis revealed that the most abundant BA species were putrescine,tyramine,and histamine in the later three stages(1187.68,785.16,and 193.20 mg/kg on average,respectively).The BA profiles differed significantly,with CP samples containing higher contents of putrescine,tyramine,and histamine(P<0.05)at the end of fermentation.Metagenomic analysis indicated that BA-producing genes exhibited different abundance profiles,with most genes,including spe A,spe B,arg,spe E,and tyr DC,having higher abundances in microbial communities during the CP process.In total,15 high-quality metagenome-assembled genomes(MAGs)were retrieved,of which 10 encoded at BA production-related genes.Enterococcus faecium(MAG10)and Weissella paramesenteroides(MAG5)might be the major tyramine producers.The high putrescine content in CP might be associated with the high abundance of Staphylococcus gallinarum(MAG8).This study provides a comprehensive understanding of the diversity and abundance of genes involved in BA synthesis,especially at the species level,during food fermentation.
