Wheat(Triticum aestivum)faces significant threats from diseases such as powdery mildew(Blumeria graminis)and Fusarium head blight(FHB;caused by Fusarium graminearum),which cause severe yield losses.Moreover,the antago...Wheat(Triticum aestivum)faces significant threats from diseases such as powdery mildew(Blumeria graminis)and Fusarium head blight(FHB;caused by Fusarium graminearum),which cause severe yield losses.Moreover,the antagonism between yield-related traits and disease resistance makes yield resistance coordination a major challenge in wheat breeding.The lack of genetic resources combining both disease resistance and high yield constrains the elucidation of underlying resistance-yield trade-off mechanisms,thereby hindering the development of high-yield and disease-resistant wheat cultivars.Remarkably,Yangmai 33(YM33),a notable wheat cultivar with resistance to both powdery mildew and FHB as well as high-yield performance,was recently developed.It offers a unique opportunity to dissect the genomic architecture underlying the coordination between disease resistance and yield.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
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
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
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
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
Populus species,important economic species combining rapid growth with broad ecological adaptability,play a critical role in sustainable forestry and bioenergy production.In this study,we performed whole-genome resequ...Populus species,important economic species combining rapid growth with broad ecological adaptability,play a critical role in sustainable forestry and bioenergy production.In this study,we performed whole-genome resequencing of 707 individuals from a full-sib family to develop comprehensive single nucleotide polymorphism(SNP)markers and constructed a high-density genetic linkage map of 19 linkage groups.The total genetic length of the map reached 3623.65 cM with an average marker interval of 0.34 cM.By integrating multidimensional phenotypic data,89 quantitative trait loci(QTL)associated with growth,wood physical and chemical properties,disease resistance,and leaf morphology traits were identified,with logarithm of odds(LOD)scores ranging from 3.13 to 21.72 Notably,pleiotropic analysis revealed significant colocaliza and phenotypic variance explained between 1.7% and 11.6%.-tion hotspots on chromosomes LG1,LG5,LG6,LG8,and LG14,with epistatic interaction network analysis confirming genetic basis of coordinated regulation across multiple traits.Functional annotation of 207 candidate genes showed that R2R3-MYB and bHLH transcription factors and pyruvate kinase-encoding genes were significantly enriched,suggesting crucial roles in lignin biosynthesis and carbon metabolic pathways.Allelic effect analysis indicated that the frequency of favorable alleles associated with target traits ranged from 0.20 to 0.55.Incorporation of QTL-derived favorable alleles as random effects into Bayesian-based genomic selection models led to an increase in prediction accuracy ranging from 1% to 21%,with Bayesian ridge regression as the best predictive model.This study provides valuable genomic resources and genetic insights for deciphering complex trait architecture and advancing molecular breeding in poplar.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
Rice, a global staple food, is critical for food security. The cultivated Oryza sativa, domesticated from wild O. rufipogon, derives~80%of its 993 identified domestication-related genes from O. rufipogon and 20%from S...Rice, a global staple food, is critical for food security. The cultivated Oryza sativa, domesticated from wild O. rufipogon, derives~80%of its 993 identified domestication-related genes from O. rufipogon and 20%from South/Southeast Asian wild O. nivara(Jing et al., 2023). Genes like An-1, BH4, PROG1,SH4, Rc, Rd, and GS3—which regulate awn length, hull color,til er angle, seed shattering, pericarp color, seed length, and thousand-grain weight, respectively—were selected against during domestication to form modern O. sativa(Yu et al., 2021).However, domestication and yield-focused breeding eliminated wild rice's valuable genes(e.g., for disease resistance, stress tolerance, nutrition), narrowing genetic diversity and impeding efforts to meet growing societal demands.展开更多
Background Multibreed genomic prediction(MBGP)is crucial for improving prediction accuracy for breeds with small populations,for which limited data are often available.Recent studies have demonstrated that partitionin...Background Multibreed genomic prediction(MBGP)is crucial for improving prediction accuracy for breeds with small populations,for which limited data are often available.Recent studies have demonstrated that partitioning the genome into nonoverlapping blocks to model heterogeneous genetic(co)variance in multitrait models can achieve higher joint prediction accuracy.However,the block partitioning method,a key factor influencing model performance,has not been extensively explored.Results We introduce mbBayesABLD,a novel Bayesian MBGP model that partitions each chromosome into nonoverlapping blocks on the basis of linkage disequilibrium(LD)patterns.In this model,marker effects within each block are assumed to follow normal distributions with block-specific parameters.We employ simulated data as well as empirical datasets from pigs and beans to assess genomic prediction accuracy across different models using cross-validation.The results demonstrate that mbBayesABLD significantly outperforms conventional MBGP models,such as GBLUP and BayesR.For the meat marbling score trait in pigs,compared with GBLUP,which does not account for heterogeneous genetic(co)variance,mbBayesABLD improves the prediction accuracy for the small-population breed Landrace by 15.6%.Furthermore,our findings indicate that a moderate level of similarity in LD patterns between breeds(with an average correlation of 0.6)is sufficient to improve the prediction accuracy of the target breed.Conclusions This study presents a novel LD block-based approach for multibreed genomic prediction.Our work provides a practical tool for livestock breeding programs and offers new insights into leveraging genetic diversity across breeds for improved genomic prediction.展开更多
Objective The basic helix-loop-helix(bHLH)transcription factors(TFs)are pivotal in regulating fungal growth,development,and secondary metabolism.However,the knowledge about the Ganoderma lucidum bHLHs(GlbHLHs)in ganod...Objective The basic helix-loop-helix(bHLH)transcription factors(TFs)are pivotal in regulating fungal growth,development,and secondary metabolism.However,the knowledge about the Ganoderma lucidum bHLHs(GlbHLHs)in ganoderic acid(GA)biosynthesis of G.lucidum was limited.This study aimed to explore the functions of bHLH genes in ganoderic acid biosynthesis during G.lucidum growth development.Methods First,the genome-wide identification of GlbHLHs was performed through Hidden Markov model searches and Two-way blast.Furthermore,through physicochemical properties,gene structure,and phylogenetic analysis,as well as combining the transcriptome and metabolome data from different developmental stages of G.lucidum,candidate GlbHLHs were screened.Subsequently,their regulatory roles in ganoderic acid biosynthesis were explored using yeast one-hybrid and dual-luciferase reporter assays.Results A total of 11 GlbHLH members were characterized in G.lucidum.The upstream promoter regions of these genes enriched hormones and abiotic stress responsive elements.Although individual ganoderic acid monomers demonstrated marked differences in accumulation patterns across specific growth phases and tissue types,overall,the total GA content was consistently higher in caps than in stipes throughout development.In addition,all GlbHLHs exhibited high expression in whole G.lucidum from the primordium to maturation stages.Among them,GlbHLH5 and GlbHLH7 showed the highest expression in any stage and highly correlated with key genes associated with GA pathway.Functional validation through dual-luciferase assays and yeast one-hybrid experiments had demonstrated that GlbHLH5 activated the P2 region of the lanosterol synthase promoter,while GlbHLH7 activated the promoters of squalene epoxidase and squalene synthase.Conclusion Compared to plants,G.lucidum harbored a small number of bHLH members but all high expression in any stages.Additionally,GlbHLH5 and GlbHLH7 with the highest expression among GlbHLHs showed activation in regulating the biosynthesis of GA.These results provide a theoretical reference for further research on ganoderic acid regulation in G.lucidum,and thereby providing a molecular foundation for enhancing ganoderic acid yield to optimize the medicinal value of G.lucidum.展开更多
Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,199...Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,1999;One Thousand Plant Transcriptomes Initiative,2019).Due to its unique phylogenetic status,it holds tremendous interest for botanists.The nuclear and mitochondrial genomes of Amborella were first published in 2013,providing valuable resources for studies on genome and gene family evolution,phylogenomics,and flower development,despite the fact that the assembly is heavily fragmented(Amborella Genome Project,2013;Rice et al.,2013).In 2024,a haplotype-resolved Amborella genome assembly was published,showing significant improvement in quality and completeness(Carey et al.,2024).展开更多
Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural...Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural variations and other annotation information.B:The second type of visualization map was simple and only showed the synteny relationship between the chromosomes of two or three genomes.C:Multiplatform general GenomeSyn submission page,applicable to Windows,MAC and web platforms;other analysis files can be entered in the"other"option.The publisher would like to apologise for any inconvenience caused.展开更多
The genus Oryza consists of two cultivated species (O. sativa L. and O. glaberrima Steud.) and approximately 20 wild relative species widely distributed in the pan-tropics. These species have been classified into four...The genus Oryza consists of two cultivated species (O. sativa L. and O. glaberrima Steud.) and approximately 20 wild relative species widely distributed in the pan-tropics. These species have been classified into four complexes following the Vaughan's taxonomic system([1]). The O. officinalis complex is the largest complex in the genus, which includes ten species, having BE, CC, on, and EE genomes in the diploids as well as BBCC and CCDD genomes in the tetraploids. The relationships among the BE, CC, and EE genomes still remain unclear, although previous studies have indicated certain affinities of these genomes([2-4]). Genomic in situ hybridization (GISH) is a powerful technique to detect the relationships among the related genomes at chromosome and DNA levels. The objective of the present study was to investigate the relationships among the BE, CC and EE genomes in the genus Oryza by the two-probe GISH.展开更多
Selaginella moellendorffii Hieron.,a lycophyte of significant medicinal and evolutionary importance,is recognized as one of the earliest vascular plants.However,the absence of a high-quality reference genome has hinde...Selaginella moellendorffii Hieron.,a lycophyte of significant medicinal and evolutionary importance,is recognized as one of the earliest vascular plants.However,the absence of a high-quality reference genome has hindered the comprehensive exploration of its unique phylogenetic position and therapeutic potential,thereby limiting our understanding of its genomic structure and metabolic capabilities.In this study,we present the first chromosome-level,telomere-to-telomere(T2T)genome assembly of S.moellendorffii,constructed utilizing PacBio HiFi,Oxford Nanopore(ONT),and Hi-C technologies.The assembled genome,spanning 112.83 Mb across 10 chromosomes with a contig N50 of 11.11 Mb,exhibited exceptional completeness(BUSCO score:95.7%)and accuracy(QV=48.11).Comparative genomic analysis identified 3515 gene families unique to S.moellendorffii,with significant enrichment in secondary metabolismpathways,including those related to flavonoid biosynthesis.Phylogenetic analysis revealed that S.moellendorffii diverged from Isoetes approximately 339.6 million years ago(MYA),representing a key evolutionary transition in early vascular plants.By integrating tissue-specific transcriptome and metabolome analyses,we uncovered the molecular basis of biflavone biosynthesis,identifying key enzymes and regulatory networks that govern the production of these bioactive compounds.We observed a correlation between the tissue-specific accumulation patterns of six major biflavones,including amentoflavone and ginkgetin,and the expression of their biosynthetic genes.This high-quality genome assembly,coupled with multi-omics analyses,offers unprecedented insights into the evolution of early vascular plants and elucidates the molecular mechanisms behind their specialized metabolism.展开更多
基金supported by the National Key R&D Program of China(2024YFD1201100)the research program from the Zhongshan Biological Breeding Laboratory(ZSBBL-KY2023-02)the National Natural Science Foundation of China(32341037).
文摘Wheat(Triticum aestivum)faces significant threats from diseases such as powdery mildew(Blumeria graminis)and Fusarium head blight(FHB;caused by Fusarium graminearum),which cause severe yield losses.Moreover,the antagonism between yield-related traits and disease resistance makes yield resistance coordination a major challenge in wheat breeding.The lack of genetic resources combining both disease resistance and high yield constrains the elucidation of underlying resistance-yield trade-off mechanisms,thereby hindering the development of high-yield and disease-resistant wheat cultivars.Remarkably,Yangmai 33(YM33),a notable wheat cultivar with resistance to both powdery mildew and FHB as well as high-yield performance,was recently developed.It offers a unique opportunity to dissect the genomic architecture underlying the coordination between disease resistance and yield.
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.
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 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.
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 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).
基金supported by the National Key Research and Development Plan of China(2021YFD2200202)the Key Research and Development Project of Jiangsu Province,China(BE2021366).
文摘Populus species,important economic species combining rapid growth with broad ecological adaptability,play a critical role in sustainable forestry and bioenergy production.In this study,we performed whole-genome resequencing of 707 individuals from a full-sib family to develop comprehensive single nucleotide polymorphism(SNP)markers and constructed a high-density genetic linkage map of 19 linkage groups.The total genetic length of the map reached 3623.65 cM with an average marker interval of 0.34 cM.By integrating multidimensional phenotypic data,89 quantitative trait loci(QTL)associated with growth,wood physical and chemical properties,disease resistance,and leaf morphology traits were identified,with logarithm of odds(LOD)scores ranging from 3.13 to 21.72 Notably,pleiotropic analysis revealed significant colocaliza and phenotypic variance explained between 1.7% and 11.6%.-tion hotspots on chromosomes LG1,LG5,LG6,LG8,and LG14,with epistatic interaction network analysis confirming genetic basis of coordinated regulation across multiple traits.Functional annotation of 207 candidate genes showed that R2R3-MYB and bHLH transcription factors and pyruvate kinase-encoding genes were significantly enriched,suggesting crucial roles in lignin biosynthesis and carbon metabolic pathways.Allelic effect analysis indicated that the frequency of favorable alleles associated with target traits ranged from 0.20 to 0.55.Incorporation of QTL-derived favorable alleles as random effects into Bayesian-based genomic selection models led to an increase in prediction accuracy ranging from 1% to 21%,with Bayesian ridge regression as the best predictive model.This study provides valuable genomic resources and genetic insights for deciphering complex trait architecture and advancing molecular breeding in poplar.
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 Biological BreedingMajor Projects(2023ZD04076)the National Natural Science Foundation of China(32300312)+2 种基金the Innovation Program of Chinses Academy of Agricultural Sciences(CAAS-CSIAF-202303)the Guangdong Basic and Applied Basic Research Foundation(2020B1515120086)the KeyArea Research and Development Program of Guangdong Province(2021B0707010006)。
文摘Rice, a global staple food, is critical for food security. The cultivated Oryza sativa, domesticated from wild O. rufipogon, derives~80%of its 993 identified domestication-related genes from O. rufipogon and 20%from South/Southeast Asian wild O. nivara(Jing et al., 2023). Genes like An-1, BH4, PROG1,SH4, Rc, Rd, and GS3—which regulate awn length, hull color,til er angle, seed shattering, pericarp color, seed length, and thousand-grain weight, respectively—were selected against during domestication to form modern O. sativa(Yu et al., 2021).However, domestication and yield-focused breeding eliminated wild rice's valuable genes(e.g., for disease resistance, stress tolerance, nutrition), narrowing genetic diversity and impeding efforts to meet growing societal demands.
基金supported by the Biological Breeding-Major Projects in National Science and Technology(No.2023ZD0404405)the Earmarked Fund for China Agriculture Research System(No.CARS-pig-35)+2 种基金the National Natural Science Foundation of China(No.3227284,32302708)the 2115 Talent Development Program of China Agricultural University,the Chinese Universities Scientific Fund(No.2023TC196)the Seed Industry Revitalization Action Project of Guangdong Province(No.2024-XPY-06-001)。
文摘Background Multibreed genomic prediction(MBGP)is crucial for improving prediction accuracy for breeds with small populations,for which limited data are often available.Recent studies have demonstrated that partitioning the genome into nonoverlapping blocks to model heterogeneous genetic(co)variance in multitrait models can achieve higher joint prediction accuracy.However,the block partitioning method,a key factor influencing model performance,has not been extensively explored.Results We introduce mbBayesABLD,a novel Bayesian MBGP model that partitions each chromosome into nonoverlapping blocks on the basis of linkage disequilibrium(LD)patterns.In this model,marker effects within each block are assumed to follow normal distributions with block-specific parameters.We employ simulated data as well as empirical datasets from pigs and beans to assess genomic prediction accuracy across different models using cross-validation.The results demonstrate that mbBayesABLD significantly outperforms conventional MBGP models,such as GBLUP and BayesR.For the meat marbling score trait in pigs,compared with GBLUP,which does not account for heterogeneous genetic(co)variance,mbBayesABLD improves the prediction accuracy for the small-population breed Landrace by 15.6%.Furthermore,our findings indicate that a moderate level of similarity in LD patterns between breeds(with an average correlation of 0.6)is sufficient to improve the prediction accuracy of the target breed.Conclusions This study presents a novel LD block-based approach for multibreed genomic prediction.Our work provides a practical tool for livestock breeding programs and offers new insights into leveraging genetic diversity across breeds for improved genomic prediction.
基金funding from the Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences(No.CI2021A04008)National Key Research and Development Project(No.2023YFC3504104)+2 种基金Hangzhou Joint Fund of the Zhejiang Provincial Natural Science Foundation of China(No.LHZSZ24H280003)Technology Major Program on Agricultural New Variety Breeding(No.2021C02073)Central Guiding Local Science and Technology Development Fund Project(No.2024ZY01009).
文摘Objective The basic helix-loop-helix(bHLH)transcription factors(TFs)are pivotal in regulating fungal growth,development,and secondary metabolism.However,the knowledge about the Ganoderma lucidum bHLHs(GlbHLHs)in ganoderic acid(GA)biosynthesis of G.lucidum was limited.This study aimed to explore the functions of bHLH genes in ganoderic acid biosynthesis during G.lucidum growth development.Methods First,the genome-wide identification of GlbHLHs was performed through Hidden Markov model searches and Two-way blast.Furthermore,through physicochemical properties,gene structure,and phylogenetic analysis,as well as combining the transcriptome and metabolome data from different developmental stages of G.lucidum,candidate GlbHLHs were screened.Subsequently,their regulatory roles in ganoderic acid biosynthesis were explored using yeast one-hybrid and dual-luciferase reporter assays.Results A total of 11 GlbHLH members were characterized in G.lucidum.The upstream promoter regions of these genes enriched hormones and abiotic stress responsive elements.Although individual ganoderic acid monomers demonstrated marked differences in accumulation patterns across specific growth phases and tissue types,overall,the total GA content was consistently higher in caps than in stipes throughout development.In addition,all GlbHLHs exhibited high expression in whole G.lucidum from the primordium to maturation stages.Among them,GlbHLH5 and GlbHLH7 showed the highest expression in any stage and highly correlated with key genes associated with GA pathway.Functional validation through dual-luciferase assays and yeast one-hybrid experiments had demonstrated that GlbHLH5 activated the P2 region of the lanosterol synthase promoter,while GlbHLH7 activated the promoters of squalene epoxidase and squalene synthase.Conclusion Compared to plants,G.lucidum harbored a small number of bHLH members but all high expression in any stages.Additionally,GlbHLH5 and GlbHLH7 with the highest expression among GlbHLHs showed activation in regulating the biosynthesis of GA.These results provide a theoretical reference for further research on ganoderic acid regulation in G.lucidum,and thereby providing a molecular foundation for enhancing ganoderic acid yield to optimize the medicinal value of G.lucidum.
基金supported by the National Natural Science Foundation of China(32270217,31970205,31770211)Metasequoia funding of Nanjing Forestry University to YY。
文摘Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,1999;One Thousand Plant Transcriptomes Initiative,2019).Due to its unique phylogenetic status,it holds tremendous interest for botanists.The nuclear and mitochondrial genomes of Amborella were first published in 2013,providing valuable resources for studies on genome and gene family evolution,phylogenomics,and flower development,despite the fact that the assembly is heavily fragmented(Amborella Genome Project,2013;Rice et al.,2013).In 2024,a haplotype-resolved Amborella genome assembly was published,showing significant improvement in quality and completeness(Carey et al.,2024).
文摘Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural variations and other annotation information.B:The second type of visualization map was simple and only showed the synteny relationship between the chromosomes of two or three genomes.C:Multiplatform general GenomeSyn submission page,applicable to Windows,MAC and web platforms;other analysis files can be entered in the"other"option.The publisher would like to apologise for any inconvenience caused.
文摘The genus Oryza consists of two cultivated species (O. sativa L. and O. glaberrima Steud.) and approximately 20 wild relative species widely distributed in the pan-tropics. These species have been classified into four complexes following the Vaughan's taxonomic system([1]). The O. officinalis complex is the largest complex in the genus, which includes ten species, having BE, CC, on, and EE genomes in the diploids as well as BBCC and CCDD genomes in the tetraploids. The relationships among the BE, CC, and EE genomes still remain unclear, although previous studies have indicated certain affinities of these genomes([2-4]). Genomic in situ hybridization (GISH) is a powerful technique to detect the relationships among the related genomes at chromosome and DNA levels. The objective of the present study was to investigate the relationships among the BE, CC and EE genomes in the genus Oryza by the two-probe GISH.
基金funded by the National Natural Science Foundation of China(Grant No.81903921)the Key project at central government level:The ability establishment of sustainable use for valuable Chinese medicine resources(2060302)the Distinguished Young Scholars of Hubei University of Chinese Medicine(Grant No.2022ZZXJ002).
文摘Selaginella moellendorffii Hieron.,a lycophyte of significant medicinal and evolutionary importance,is recognized as one of the earliest vascular plants.However,the absence of a high-quality reference genome has hindered the comprehensive exploration of its unique phylogenetic position and therapeutic potential,thereby limiting our understanding of its genomic structure and metabolic capabilities.In this study,we present the first chromosome-level,telomere-to-telomere(T2T)genome assembly of S.moellendorffii,constructed utilizing PacBio HiFi,Oxford Nanopore(ONT),and Hi-C technologies.The assembled genome,spanning 112.83 Mb across 10 chromosomes with a contig N50 of 11.11 Mb,exhibited exceptional completeness(BUSCO score:95.7%)and accuracy(QV=48.11).Comparative genomic analysis identified 3515 gene families unique to S.moellendorffii,with significant enrichment in secondary metabolismpathways,including those related to flavonoid biosynthesis.Phylogenetic analysis revealed that S.moellendorffii diverged from Isoetes approximately 339.6 million years ago(MYA),representing a key evolutionary transition in early vascular plants.By integrating tissue-specific transcriptome and metabolome analyses,we uncovered the molecular basis of biflavone biosynthesis,identifying key enzymes and regulatory networks that govern the production of these bioactive compounds.We observed a correlation between the tissue-specific accumulation patterns of six major biflavones,including amentoflavone and ginkgetin,and the expression of their biosynthetic genes.This high-quality genome assembly,coupled with multi-omics analyses,offers unprecedented insights into the evolution of early vascular plants and elucidates the molecular mechanisms behind their specialized metabolism.
