The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannot...The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannotating and utilizing plastome sequences remain challenging.Therefore,a streamlined phylogenomic pipeline spanning plastome annotation,phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome.Here,we develop PlastidHub,a novel web application employing innovative tools to analyze plastome sequences.In comparison with existing tools,key novel functionalities in PlastidHub include:(1)standardization of quadripartite structure;(2)improvement of annotation flexibility and consistency;(3)quantitative assessment of annotation completeness;(4)diverse extraction modes for canonical and specialized sequences;(5)intelligent screening of molecular markers for biodiversity studies;(6)genelevel visual comparison of structural variations and annotation completeness.PlastidHub features cloud-based web applications that do not require users to install,update,or maintain tools;detailed help documents including user guides,test examples,a static pop-up prompt box,and dynamic pop-up warning prompts when entering unreasonable parameter values;batch processing capabilities for all tools;intermediate results for secondary use;and easy-to-operate task flows between fileupload and download.A key feature of PlastidHub is its interrelated task-based user interface design.Give that PlastidHub is easy to use without specialized computational skills or resources,this new platform should be widely used among botanists and evolutionary biologists,improving and expediting research employing the plastome.PlastidHub is available at https://www.plastidhub.cn.展开更多
Fusarium oxysporum f. sp. conglutinans （Foc） is the causal agent of Fusarium wilt disease of Brassica oleracea. A rapid, accurate, and reliable method to detect and identify plant pathogens is vitally important to i...Fusarium oxysporum f. sp. conglutinans （Foc） is the causal agent of Fusarium wilt disease of Brassica oleracea. A rapid, accurate, and reliable method to detect and identify plant pathogens is vitally important to integrated disease management. In this study, using a comparative genome analysis among Fusarium oxysporum （Fo）, we developed a Foc-specific primer set （Focs-l/Focs-2） and established a multiplex-PCR assay. In the assay, the Focs-1/Focs-2 and universal primers for Fusarium species （W106PJF106S） could be used to detect Foc isolates in a single PCR reaction. With the optimized PCR parameters, the multiplex-PCR assay showed a high specificity for detecting Foc and was very sensitive to detect as little as 100 pg of pure Foc genomic DNAor 1 000 spores in 1 g of twice-autoclaved soil. We also demonstrated that Foc isolates were easily detected from infected plant tissues, as well as from natural field soils, using the multiplex-PCR assay. To our knowledge, this is a first report on detection Fo by comparative genomic method.展开更多
Rice and wheat provide nearly 40%of human calorie and protein requirements.They share a common ancestor and belong to the Poaceae(grass)family.Characterizing their genetic homology is crucial for developing new cultiv...Rice and wheat provide nearly 40%of human calorie and protein requirements.They share a common ancestor and belong to the Poaceae(grass)family.Characterizing their genetic homology is crucial for developing new cultivars with enhanced traits.Several wheat genes and gene families have been characterized based on their rice orthologs.Rice–wheat orthology can identify genetic regions that regulate similar traits in both crops.Rice–wheat comparative genomics can identify candidate wheat genes in a genomic region identified by association or QTL mapping,deduce their putative functions and biochemical pathways,and develop molecular markers for marker-assisted breeding.A knowledge of gene homology facilitates the transfer between crops of genes or genomic regions associated with desirable traits by genetic engineering,gene editing,or wide crossing.展开更多
Powdery mildew,caused by Blumeria graminis f.sp.tritici,is one of the most severe wheat diseases.Mining powdery mildew resistance genes in wheat cultivars and their appliance in breeding program is a promising way to ...Powdery mildew,caused by Blumeria graminis f.sp.tritici,is one of the most severe wheat diseases.Mining powdery mildew resistance genes in wheat cultivars and their appliance in breeding program is a promising way to control this disease.Genetic analysis revealed that a single dominant resistance gene named PmTm4 originated from Chinese wheat line Tangmai 4 confers resistance to prevailing isolates of B.graminis f.sp.tritici isolate E09.Detailed comparative genomics analyses helped to develop closely linked markers to PmTm4 and a fine genetic map was constructed using large F2population,in which PmTm4 was located into a 0.66-c M genetic interval.The orthologous subgenome region of PmTm4in Aegilops tauschii was identified,and two resistance gene analogs（RGA）were characterized from the corresponding sequence scaffolds of Ae.tauschii draft assembly.The closely linked markers and identified Ae.tauschii orthologs in the mapping interval provide an entry point for chromosome landing and map-based cloning of PmTm4.展开更多
Clostridium tyrobutyricum is a promising microbial host for the anaerobic production of bio-based chemicals,especially butyric acid.However,the limited genetic traits of C.tyrobutyricum resulted in its constrained app...Clostridium tyrobutyricum is a promising microbial host for the anaerobic production of bio-based chemicals,especially butyric acid.However,the limited genetic traits of C.tyrobutyricum resulted in its constrained applicability in the food industry due to the absence of publicly available data.We performed a comparative genomic analysis of 13 C.tyrobutyricum strains isolated from different habitats to investigate the adaptation mechanisms and metabolic potentials of the C.tyrobutyricum strains isolated from fermentation environments(FE).The results showed that the genetic diversity of FE-associated C.tyrobutyricum strains was higher than that of strains isolated from non-fermentation environments(NFE).Based on evaluating safety-related genes,FE-associated strains were likely non-pathogenic to humans or animals.Many environmental adaptation-related genes involved in energy production and conversion,phosphotransferase system(PTS),etc.,were significantly enriched in FE-associated strains,which was conducive to their survival in the corresponding habitats.The analysis of carbohydrate-active enzymes revealed that the CAZyme categories of glycoside hydrolases(GHs)and carbohydrate esterases(CEs)were found to be significantly enriched in FE-associated strains,which was bene-ficial for carbohydrate utilization(including starch,cellulose,etc.).Fermentation experiments revealed that strains isolated from the Chinese liquor fermentation environment were capable of decomposing carbohydrates and producing organic acids.Collectively,this study provided insights into the genomic features of C.tyrobutyricum and the theoretical basis for further use,research,and development of these strains.展开更多
Bifidobacterium longum subsp.infantis(B.infantis)is the most active consumer of human milk oligosaccharides(HMOs),which can promote the development and maturation of the infant’s intestinal immune system.In this stud...Bifidobacterium longum subsp.infantis(B.infantis)is the most active consumer of human milk oligosaccharides(HMOs),which can promote the development and maturation of the infant’s intestinal immune system.In this study,we collected information on B.infantis isolated from human feces in the NCBI database to analyze their whole genome.We found that the whole genome of the tested strains and the functional genes utilizing the HMOs showed geographical clustering.Comparison of the genes encodingα-L-fucosidase between B.infantis H11 and BINF revealed that strain H11 had moreα-L-fucosidase genes,and further heterologous expression ofα-Lfucosidase showed that only the glycoside hydrolase(GH)95 family could hydrolyze 2’-fucosyllactose(2’-FL).At the same time,FUC95A(derived from strain H11)was more efficient in catalyzing 2’-FL than FUC95B(derived from strain BINF).In addition,metabolites in the 2’-FL fermentation supernatants were analyzed based on untargeted metabolomics,and it was found that strain H11 could utilize 2’-FL to produce more beneficial metabolites compared to strain BINF.In conclusion,we hypothesized that the enhancement ofα-L-fucosidase activity of B.infantis is one of the essential requirements to improve the utilization of 2’-FL and increase the contents of beneficial metabolites to perform the probiotic function.展开更多
Lactiplantibacillus plantarum is a nomadic species that displays adaptive variations in different habitats,partic-ularly in the intestines.Bile salts tolerance is crucial for L.plantarum to survive and exert beneficia...Lactiplantibacillus plantarum is a nomadic species that displays adaptive variations in different habitats,partic-ularly in the intestines.Bile salts tolerance is crucial for L.plantarum to survive and exert beneficial properties in this environment.L.plantarum exhibits varying growth capacities under bile salts exposure;however,the mo-lecular mechanisms responsible for this variation are not fully understood.In this study,comparative genomics analysis was used to elucidate the specific genes in bile salts-tolerant L.plantarum and further investigate the mechanisms that contribute to bacterial survival under bile salts.A total of eighty-seven specific genes were identified in the tolerant strains,which were primarily associated with the two-component system and carbo-hydrate metabolism.Notably,the mutation of a response regulator(agrA)in the two-component system decreased the growth rate of L.plantarum under bile salts exposure,whereas complementation increased tolerance.Metabolomic analysis suggested that the deletion of agrA resulted in the downregulation of pathways associated with bacterial energy metabolism.These findings indicate that L.plantarum responds to harsh envi-ronments by sensing bile salts as signaling molecules and subsequently adjusting complex metabolic pathways as a survival strategy.This provides novel insights into the molecular basis of the two-component system contributing to bile salts tolerance.展开更多
This study provides the first comprehensive analysis of antibiotic resistance&genomic characterization of Staphylococ-cus saprophyticus isolated from Southern Ocean.Antibiotic susceptibility profiling of S.saproph...This study provides the first comprehensive analysis of antibiotic resistance&genomic characterization of Staphylococ-cus saprophyticus isolated from Southern Ocean.Antibiotic susceptibility profiling of S.saprophyticus revealed complete resistance to Cefixime,Norfloxacin,Azithromycin,and Metronidazole,while susceptibility was observed for Ampicil-lin,Doxycycline,Tetracycline,Ciprofloxacin,and Co-trimoxazole.Whole-genome sequencing and comparative genomics analysis with 21 closely related strains identified antimicrobial resistance(AMR)genes viz a viz vanY(in the vanM cluster),sdrM,sepA,norC,salE,fusD,and fosBx1.Among these,vanY exhibited the highest prevalence,followed by sdrM and sepA.Study also showed varying AMR gene distributions,with some strains harboring all seven resistance genes.The presence of antibiotic-resistant S.saprophyticus in the Southern Ocean highlights the potential anthropogenic influence on microbial communities leading to AMR among native microbial communities and highlights the urgent need for further studies on AMR in remote marine environments and its mitigation strategies.The study enhances understanding of the global dis-semination of AMR by investigating S.saprophyticus in one of the pristine and isolated ecosystems on Earth.Our findings demonstrates that even remote environments are not immune to the spread of AMR.Furthermore,the study provides crucial insights into resistance mechanisms and the identification of resistance genes in a non-clinical,extreme environment puts light on microbial adaptability,and ecological resilience in response to environmental stressors.展开更多
Genomic compositions of representatives of thirteen S. dysenteriae serotypes were investigated by performing comparative genomic hybridization (CGH) with microarray containing the whole genomic ORFs (open reading fram...Genomic compositions of representatives of thirteen S. dysenteriae serotypes were investigated by performing comparative genomic hybridization (CGH) with microarray containing the whole genomic ORFs (open reading frames, ORFs) of E. coli K12 strain MG1655 and spe-cific ORFs of S. dysenteriae A1 strain Sd51197. The CGH results indicated the genomes of the serotypes contain 2654 conserved ORFs originating from E. coli. However, 219 intrinsic genes of E. coli including those prophage genes, molecular chaperones, synthesis of specific O antigen and so on were absent. Moreover, some specific genes such as type II secretion system associ-ated components, iron transport related genes and some others as well were acquired through horizontal transfer. According to phylogenic trees based on genetic composition, it was demon-strated that A1, A2, A8, A10 were distinct from the other S. dysenteriae serotypes. Our results in this report may provide new insights into the physiological process, pathogenicity and evolution of S. dysenteriae.展开更多
Bivalves are species-rich mollusks with prominent protective roles in coastal ecosystems.Across these ancient lineages,colony-founding larvae anchor themselves either by byssus production or by cemented attachment.The...Bivalves are species-rich mollusks with prominent protective roles in coastal ecosystems.Across these ancient lineages,colony-founding larvae anchor themselves either by byssus production or by cemented attachment.The latter mode of sessile life is strongly molded by left-right shell asymmetry during larval development of Ostreoida oysters such as Crassostrea hongkongensis.Here,we sequenced the genome of C.hongkongensis in high resolution and compared it to reference bivalve genomes to unveil genomic determinants driving cemented attachment and shell asymmetry.Importantly,loss of the homeobox gene Antennapedia(Antp)and broad expansion of lineagespecific extracellular gene families are implicated in a shift from byssal to cemented attachment in bivalves.Comparative transcriptomic analysis shows a conspicuous divergence between leftright asymmetrical C.hongkongensis and symmetrical Pinctada fucata in their expression profiles.Especially,a couple of orthologous transcription factor genes and lineage-specific shell-related gene families including that encoding tyrosinases are elevated,and may cooperatively govern asymmetrical shell formation in Ostreoida oysters.展开更多
Bi-directional BLAST is a simple approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. This procedure is usually confined to the realm of customized Perl scripts, usua...Bi-directional BLAST is a simple approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. This procedure is usually confined to the realm of customized Perl scripts, usually tuned for UNIX-like environments. Porting those scripts to other operating systems involves refactoring them, and also the installation of the Perl programming environment with the required libraries. To overcome these limitations, a data pipeline was implemented in Java. This application submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. GO Slim terms are attached to hits, several statistics are derived, and molecular evolution rates are estimated through PAML. The results are written to a set of delimited text tables intended for further analysis. The provided graphic user interface allows a friendly interaction with this application, which is documented and available to download at http：//moodle.fct.unl.pt/course/view.php？id=2079 or https：//sourceforge.net/projects/bidiblast/ under the GNU GPL license.展开更多
In recent years, much effort has been made in identifying microRNA （miRNA） genes from mammals insects, worms, plants, and viruses. Continuing the search for more miRNA genes is still important but difficult. This pa...In recent years, much effort has been made in identifying microRNA （miRNA） genes from mammals insects, worms, plants, and viruses. Continuing the search for more miRNA genes is still important but difficult. This paper presents a computational strategy based on comparative genomics analysis. The algorithm was used to scan four invertebrate genomes, Drosophila melangoster, Bombyx mori, Apis mellifera, and Anopheles gambiae, which are either model organisms or medically/economically important insects. 99 new miRNA genes were predicted from the four insect species which can be grouped into 17 miRNA gene families, of which 10 of the miRNA families are insect-specific. Sequence similarity analysis showed that 16 of the newly predicted insect miRNAs belong to the K-box, GY-box, and Brd-box miRNA families which are important participators in Notch-related pathways. To test the validity of the algorithm, 39 predicted insect miRNA genes from D. melangoster and A. mellifera were selected for further biological validation. 34 （87%） predicted miRNA genes＇ transcripts were successfully detected by reverse transcription-polymerase chain reaction experiments. Thus, this strategy can be used to efficiently screen for miRNA genes conserved cross species.展开更多
Liquorilactobacillus nagelii is a lactic acid bacterium frequently found in a variety of traditional fermented foods,where it contributes to their sensory properties and potential health benefits.However,research eval...Liquorilactobacillus nagelii is a lactic acid bacterium frequently found in a variety of traditional fermented foods,where it contributes to their sensory properties and potential health benefits.However,research evaluating the genetic and functional features of L.nagelii is scarce in the literature.In this study,we sequenced and assembled the genome of L.nagelii VUCC-R001,a strain isolated from kombucha tea,assessing its safety and exploring its biotechnological potential,mainly in terms of D-phenyllactic acid and dextran production,through a comparative genomic approach with 35 Liquorilactobacillus genomes and related phenotypic validation.Bioinformatic analysis revealed a good-quality draft genome(~2.4 Mb)of VUCC-R001 with a completeness around 99.7%(N50 of 151,630 bp).Comparative genomic analyses showed the correct identification of the new strain,the absence of genes encoding transmissible antibiotic resistance,virulence factors,and biogenic amine production,underlining its safety,also confirmed by phenotypic tests.We identified genes putatively associated with D-phenyllactic acid(PLA)production and verified the capability of this strain to produce a high concentration(52 mg/L)of PLA in vitro.To date,this is the first study reporting a Liquorilactibacillus strain that produces D-phenyllactic acid.Genome analyses of L.nagelii also elicited the presence of a dextransucrase GH70(EC 2.4.1.5),leading to the production of dextran from sucrose,an exopolysaccharide with applications in the food and biomedical industries.This investigation provides new insights into the genomic features and functional attributes of L.nagelii,opening new prospects for the biotechnological use of selected strains belonging to this species.展开更多
Lactobacillus johnsonii,as a microorganism widely presenting in the intestinal tract of mammals,dairy products,and poultry,possesses various probiotic characteristics.Currently,many research focused on the probiotic f...Lactobacillus johnsonii,as a microorganism widely presenting in the intestinal tract of mammals,dairy products,and poultry,possesses various probiotic characteristics.Currently,many research focused on the probiotic functions and industrial applications of L.johnsonii.In this study,98 strains of L.johnsonii were subjected to comparative genomic analyses to explore its genetic diversity.The results indicated that based on ANI values,d-DDH values,phylogenetic analysis,and whole-genome comparison,the 98 strains of L.johnsonii were classified into two phylogenetic clusters.The carbohydrate utilization genes,bacteriocin operon,extracellular polysaccharide gene cluster,and bile salt hydrolase encoding genes in L.johnsonii shared common features and exhibited systematic differences based on phylogenetic clustering.The main reason for the high intra-species gene diversity of L.johnsonii might be differences in phages and other mobile genetic elements.This study provides new insights into the genomic features and functional genes of L.johnsonii.展开更多
Lactococcus lactis,a major starter culture in the dairy industry,has been widely applied in food fermentation.While current research has primarily focused on evaluating its role during fermentation,genomic investigati...Lactococcus lactis,a major starter culture in the dairy industry,has been widely applied in food fermentation.While current research has primarily focused on evaluating its role during fermentation,genomic investigations into its genetic diversity and functional adaptability remain limited.In this study,199 L.lactis strains isolated from Chinese traditional artisanal cheeses(72 bovine,71 goat,and 56 yak milk cheese isolates)were subjected to comparative genomic analysis.Genomic characteristic analysis indicated that bovine milk strains possess larger genomes and the highest number of unique genes.Functional characterization further demonstrated notable differences in carbohydrate metabolism among strains from different sources,with yak milk strains enriched in enzymes involved in complex polysaccharide degradation,including members of the carbohydrate esterases family.Moreover,strains from different sources exhibit distinct strategies for lactose hydrolysis and metabolic utilization,reflecting adaptive evolution to their specific nutritional niches.Analysis of the antibiotic resistance profile suggests that L.lactis predominantly harbors glycopeptide and lincosamide resistance genes,encompassing four distinct resistance mechanisms.Collectively,this study reveals the genetic diversity and adaptive evolution of L.lactis strains from different sources and identifies key genes associated with carbohydrate degradation,lactose metabolism,and antibiotic resistance,providing concrete genetic evidence for the selection of efficient and safe industrial fermentation strains.展开更多
Alzheimer’s disease is initially thought to be caused by age-associated accumulation of plaques,in recent years,research has increasingly associated Alzheimer’s disease with lysosomal storage and metabolic disorders...Alzheimer’s disease is initially thought to be caused by age-associated accumulation of plaques,in recent years,research has increasingly associated Alzheimer’s disease with lysosomal storage and metabolic disorders,and the explanation of its pathogenesis has shifted from amyloid and tau accumulation to oxidative stress and impaired lipid and glucose metabolism aggravated by hypoxic conditions.However,the underlying mechanisms linking those cellular processes and conditions to disease progression have yet to be defined.Here,we applied a disease similarity approach to identify unknown molecular targets of Alzheimer’s disease by using transcriptomic data from congenital diseases known to increase Alzheimer’s disease risk,namely Down syndrome,Niemann-Pick type C disease,and mucopolysaccharidoses I.We uncovered common pathways,hub genes,and miRNAs across in vitro and in vivo models of these diseases as potential molecular targets for neuroprotection and amelioration of Alzheimer’s disease pathology,many of which have never been associated with Alzheimer’s disease.We then investigated common molecular alterations in brain samples from a Niemann-Pick type C disease mouse model by juxtaposing them with brain samples of both human and mouse models of Alzheimer’s disease.Detailed phenotypic,molecular,chronological,and biological aging analyses revealed that the Npc1tm(I1061T)Dso mouse model can serve as a potential short-lived in vivo model for brain aging and Alzheimer’s disease research.This research represents the first comprehensive approach to congenital disease association with neurodegeneration and a new perspective on Alzheimer’s disease research while highlighting shortcomings and lack of correlation in diverse in vitro models.Considering the lack of an Alzheimer’s disease mouse model that recapitulates the physiological hallmarks of brain aging,the short-lived Npc1^(tm(I1061T)Dso) mouse model can further accelerate the research in these fields and offer a unique model for understanding the molecular mechanisms of Alzheimer’s disease from a perspective of accelerated brain aging.展开更多
Finger millet(Eleusine coracana Gaertn.),a nutritionally rich and drought-resilient C4 cereal,possesses exceptional grain storage longevity(up to 50 years).Here,we report a high-quality genome assembly of the allotetr...Finger millet(Eleusine coracana Gaertn.),a nutritionally rich and drought-resilient C4 cereal,possesses exceptional grain storage longevity(up to 50 years).Here,we report a high-quality genome assembly of the allotetraploid cultivar C142,revealing extensive structural rearrangements between its two subgenomes(subA and subB),which are associated with asymmetric gene expression and subgenome dominance favoring subA.SubB diverged from subA and E.indica approximately 6.8 million years ago.Subsequently,two whole-genome duplication events shaped the current genome architecture,contributing to gene redundancy and adaptive potential.Notably,expansion of stress-related gene families,such as aldo-keto reductases,suggests a role in oxidative stress response and drought adaptation.Using genome-wide association studies,we identify several candidate genes associated with key agronomic traits.Among them,EcMDHAR,encoding monodehydroascorbate reductase,plays a critical role in enhancing drought tolerance.Different EcMDHAR haplotypes exhibit distinct expression profiles,supporting their functional relevance in drought adaptation.This genomic resource not only advances our understanding of polyploid genome evolution in millets,but also provides a foundation for genome-assisted improvement of drought resistance and nutritional quality in finger millet.展开更多
Trentepohliales is a completely terrestrial order within Ulvophyceae(the core Chlorophyta),and its closely related lineages are mainly marine macroalgae(green seaweeds).Despite the considerable interest in their biote...Trentepohliales is a completely terrestrial order within Ulvophyceae(the core Chlorophyta),and its closely related lineages are mainly marine macroalgae(green seaweeds).Despite the considerable interest in their biotechnological potential,little is known about their adaptations to challenging terrestrial habitats.Here,we assemble the high-quality reference genome of Trentepohlia odorata.This alga shows duplications of key genes associated with lipid metabolism and carotenoid synthesis,potentially facilitating intracellular accumulation of lipid droplets and carotenoids.We further reveal positive selection and expansion of gene families involved in vesicle trafficking and cell division regulation in T.odorata compared with other algae(cleavage furrow-mediated cell division)in Ulvophyceae,providing a genetic foundation for the evolution of phragmoplast-mediated cell division.The combined C_(4)-like and biophysical CO_(2)-concentrating mechanisms(CCMs)of T.odorata enable adaptation to fluctuating CO_(2) environments,and support efficient photosynthesis under CO_(2)-limited conditions.Adaptive strategies of T.odorata to terrestrial stressors,such as drought,intense light,and UV-B radiation,include horizontally acquired genes involved in cell wall synthesis and remodeling,homeostasis of aldehydes,and expanded genes associated with reactive oxygen species(ROS),DNA repair,and photoprotection.Our study provides a valuable genomic resource for studying aerial algae and improves understanding of plant terrestrialization.展开更多
基金the Natural Science Foundation of Shandong Province(ZR2020QC022)the Science and Technology Basic Resources Investigation Program of China(No.2019FY100900)+2 种基金the Major Program for Basic Research Project of Yunnan Province(202401BC070001)Yunnan Revitalization Talent Support Program:Yunling Scholar Project to Tingshuang Yithe open research project of“Cross Cooperative Team”of the Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences.
文摘The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannotating and utilizing plastome sequences remain challenging.Therefore,a streamlined phylogenomic pipeline spanning plastome annotation,phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome.Here,we develop PlastidHub,a novel web application employing innovative tools to analyze plastome sequences.In comparison with existing tools,key novel functionalities in PlastidHub include:(1)standardization of quadripartite structure;(2)improvement of annotation flexibility and consistency;(3)quantitative assessment of annotation completeness;(4)diverse extraction modes for canonical and specialized sequences;(5)intelligent screening of molecular markers for biodiversity studies;(6)genelevel visual comparison of structural variations and annotation completeness.PlastidHub features cloud-based web applications that do not require users to install,update,or maintain tools;detailed help documents including user guides,test examples,a static pop-up prompt box,and dynamic pop-up warning prompts when entering unreasonable parameter values;batch processing capabilities for all tools;intermediate results for secondary use;and easy-to-operate task flows between fileupload and download.A key feature of PlastidHub is its interrelated task-based user interface design.Give that PlastidHub is easy to use without specialized computational skills or resources,this new platform should be widely used among botanists and evolutionary biologists,improving and expediting research employing the plastome.PlastidHub is available at https://www.plastidhub.cn.
基金supported in part by the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, P.R.Chinathe National Natural Science Foundation of China (31571962, 31272003)+3 种基金the National Key Technology R&D Program of China (2012BAD19B06)the Special Fund for Agro-Scientific Research in the Public Interest, China (200903049-04)the National Staple Vegetable Industry Technology System Construction Project, China (CARS-25-B-01)the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences
文摘Fusarium oxysporum f. sp. conglutinans （Foc） is the causal agent of Fusarium wilt disease of Brassica oleracea. A rapid, accurate, and reliable method to detect and identify plant pathogens is vitally important to integrated disease management. In this study, using a comparative genome analysis among Fusarium oxysporum （Fo）, we developed a Foc-specific primer set （Focs-l/Focs-2） and established a multiplex-PCR assay. In the assay, the Focs-1/Focs-2 and universal primers for Fusarium species （W106PJF106S） could be used to detect Foc isolates in a single PCR reaction. With the optimized PCR parameters, the multiplex-PCR assay showed a high specificity for detecting Foc and was very sensitive to detect as little as 100 pg of pure Foc genomic DNAor 1 000 spores in 1 g of twice-autoclaved soil. We also demonstrated that Foc isolates were easily detected from infected plant tissues, as well as from natural field soils, using the multiplex-PCR assay. To our knowledge, this is a first report on detection Fo by comparative genomic method.
文摘Rice and wheat provide nearly 40%of human calorie and protein requirements.They share a common ancestor and belong to the Poaceae(grass)family.Characterizing their genetic homology is crucial for developing new cultivars with enhanced traits.Several wheat genes and gene families have been characterized based on their rice orthologs.Rice–wheat orthology can identify genetic regions that regulate similar traits in both crops.Rice–wheat comparative genomics can identify candidate wheat genes in a genomic region identified by association or QTL mapping,deduce their putative functions and biochemical pathways,and develop molecular markers for marker-assisted breeding.A knowledge of gene homology facilitates the transfer between crops of genes or genomic regions associated with desirable traits by genetic engineering,gene editing,or wide crossing.
基金financially supported by the National Natural Science Foundation of China (31371624, 31210103902)
文摘Powdery mildew,caused by Blumeria graminis f.sp.tritici,is one of the most severe wheat diseases.Mining powdery mildew resistance genes in wheat cultivars and their appliance in breeding program is a promising way to control this disease.Genetic analysis revealed that a single dominant resistance gene named PmTm4 originated from Chinese wheat line Tangmai 4 confers resistance to prevailing isolates of B.graminis f.sp.tritici isolate E09.Detailed comparative genomics analyses helped to develop closely linked markers to PmTm4 and a fine genetic map was constructed using large F2population,in which PmTm4 was located into a 0.66-c M genetic interval.The orthologous subgenome region of PmTm4in Aegilops tauschii was identified,and two resistance gene analogs（RGA）were characterized from the corresponding sequence scaffolds of Ae.tauschii draft assembly.The closely linked markers and identified Ae.tauschii orthologs in the mapping interval provide an entry point for chromosome landing and map-based cloning of PmTm4.
基金supported by the National Key Research and Development Program of China(grant numbers 2019YFA0905500)the National Natural Science Foundation of China(grant number 32370142)the China Postdoctoral Science Foundation(grant number 2023M741512).
文摘Clostridium tyrobutyricum is a promising microbial host for the anaerobic production of bio-based chemicals,especially butyric acid.However,the limited genetic traits of C.tyrobutyricum resulted in its constrained applicability in the food industry due to the absence of publicly available data.We performed a comparative genomic analysis of 13 C.tyrobutyricum strains isolated from different habitats to investigate the adaptation mechanisms and metabolic potentials of the C.tyrobutyricum strains isolated from fermentation environments(FE).The results showed that the genetic diversity of FE-associated C.tyrobutyricum strains was higher than that of strains isolated from non-fermentation environments(NFE).Based on evaluating safety-related genes,FE-associated strains were likely non-pathogenic to humans or animals.Many environmental adaptation-related genes involved in energy production and conversion,phosphotransferase system(PTS),etc.,were significantly enriched in FE-associated strains,which was conducive to their survival in the corresponding habitats.The analysis of carbohydrate-active enzymes revealed that the CAZyme categories of glycoside hydrolases(GHs)and carbohydrate esterases(CEs)were found to be significantly enriched in FE-associated strains,which was bene-ficial for carbohydrate utilization(including starch,cellulose,etc.).Fermentation experiments revealed that strains isolated from the Chinese liquor fermentation environment were capable of decomposing carbohydrates and producing organic acids.Collectively,this study provided insights into the genomic features of C.tyrobutyricum and the theoretical basis for further use,research,and development of these strains.
基金supported financially by the National Natural Science Foundation of China(No.32272291)Heilongjiang Province Key Research and Development Program(Innovation Base)(No.JD2023SJ15).
文摘Bifidobacterium longum subsp.infantis(B.infantis)is the most active consumer of human milk oligosaccharides(HMOs),which can promote the development and maturation of the infant’s intestinal immune system.In this study,we collected information on B.infantis isolated from human feces in the NCBI database to analyze their whole genome.We found that the whole genome of the tested strains and the functional genes utilizing the HMOs showed geographical clustering.Comparison of the genes encodingα-L-fucosidase between B.infantis H11 and BINF revealed that strain H11 had moreα-L-fucosidase genes,and further heterologous expression ofα-Lfucosidase showed that only the glycoside hydrolase(GH)95 family could hydrolyze 2’-fucosyllactose(2’-FL).At the same time,FUC95A(derived from strain H11)was more efficient in catalyzing 2’-FL than FUC95B(derived from strain BINF).In addition,metabolites in the 2’-FL fermentation supernatants were analyzed based on untargeted metabolomics,and it was found that strain H11 could utilize 2’-FL to produce more beneficial metabolites compared to strain BINF.In conclusion,we hypothesized that the enhancement ofα-L-fucosidase activity of B.infantis is one of the essential requirements to improve the utilization of 2’-FL and increase the contents of beneficial metabolites to perform the probiotic function.
基金supported by the National Natural Science Foundation of China[No.U23A20259,32394051 and 32122067]supported by the Fundamental Research Funds for the Central Universities JUSRP622013Collaborative innovation center of food safety and quality control in Jiangsu Province.
文摘Lactiplantibacillus plantarum is a nomadic species that displays adaptive variations in different habitats,partic-ularly in the intestines.Bile salts tolerance is crucial for L.plantarum to survive and exert beneficial properties in this environment.L.plantarum exhibits varying growth capacities under bile salts exposure;however,the mo-lecular mechanisms responsible for this variation are not fully understood.In this study,comparative genomics analysis was used to elucidate the specific genes in bile salts-tolerant L.plantarum and further investigate the mechanisms that contribute to bacterial survival under bile salts.A total of eighty-seven specific genes were identified in the tolerant strains,which were primarily associated with the two-component system and carbo-hydrate metabolism.Notably,the mutation of a response regulator(agrA)in the two-component system decreased the growth rate of L.plantarum under bile salts exposure,whereas complementation increased tolerance.Metabolomic analysis suggested that the deletion of agrA resulted in the downregulation of pathways associated with bacterial energy metabolism.These findings indicate that L.plantarum responds to harsh envi-ronments by sensing bile salts as signaling molecules and subsequently adjusting complex metabolic pathways as a survival strategy.This provides novel insights into the molecular basis of the two-component system contributing to bile salts tolerance.
基金conducted with the financial assistance of the Ministry of Earth Sciences(MOES),Govt.of India(MOES/REACHOUT/CNA/2022).
文摘This study provides the first comprehensive analysis of antibiotic resistance&genomic characterization of Staphylococ-cus saprophyticus isolated from Southern Ocean.Antibiotic susceptibility profiling of S.saprophyticus revealed complete resistance to Cefixime,Norfloxacin,Azithromycin,and Metronidazole,while susceptibility was observed for Ampicil-lin,Doxycycline,Tetracycline,Ciprofloxacin,and Co-trimoxazole.Whole-genome sequencing and comparative genomics analysis with 21 closely related strains identified antimicrobial resistance(AMR)genes viz a viz vanY(in the vanM cluster),sdrM,sepA,norC,salE,fusD,and fosBx1.Among these,vanY exhibited the highest prevalence,followed by sdrM and sepA.Study also showed varying AMR gene distributions,with some strains harboring all seven resistance genes.The presence of antibiotic-resistant S.saprophyticus in the Southern Ocean highlights the potential anthropogenic influence on microbial communities leading to AMR among native microbial communities and highlights the urgent need for further studies on AMR in remote marine environments and its mitigation strategies.The study enhances understanding of the global dis-semination of AMR by investigating S.saprophyticus in one of the pristine and isolated ecosystems on Earth.Our findings demonstrates that even remote environments are not immune to the spread of AMR.Furthermore,the study provides crucial insights into resistance mechanisms and the identification of resistance genes in a non-clinical,extreme environment puts light on microbial adaptability,and ecological resilience in response to environmental stressors.
文摘Genomic compositions of representatives of thirteen S. dysenteriae serotypes were investigated by performing comparative genomic hybridization (CGH) with microarray containing the whole genomic ORFs (open reading frames, ORFs) of E. coli K12 strain MG1655 and spe-cific ORFs of S. dysenteriae A1 strain Sd51197. The CGH results indicated the genomes of the serotypes contain 2654 conserved ORFs originating from E. coli. However, 219 intrinsic genes of E. coli including those prophage genes, molecular chaperones, synthesis of specific O antigen and so on were absent. Moreover, some specific genes such as type II secretion system associ-ated components, iron transport related genes and some others as well were acquired through horizontal transfer. According to phylogenic trees based on genetic composition, it was demon-strated that A1, A2, A8, A10 were distinct from the other S. dysenteriae serotypes. Our results in this report may provide new insights into the physiological process, pathogenicity and evolution of S. dysenteriae.
基金support from the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou),China(Grant No. GML2019ZD0407)the Key Deployment Project of Centre for Ocean Mega-Research of Science, Chinese Academy of Science (Grant No. COMS2019Q11)+6 种基金the National Natural Science Foundation of China (Grant Nos. 32073002 and 31902404)the China Agricultural Research System (Grant No. CARS-49)the Science and Technology Program of Guangzhou, China (Grant No. 201804020073)Natural Science Foundation of Guangdong, China (Grant No. 2020A1515011533)the Program of the Pearl River Young Talents of Science and Technology in Guangzhou of China (Grant No. 201806010003)the Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences (Grant Nos. ISEE2018PY01, ISEE2018PY03, and ISEE2018ZD01)the Science and Technology Planning Project of Guangdong Province, China (Grant Nos. 2017B030314052 and 201707010177)
文摘Bivalves are species-rich mollusks with prominent protective roles in coastal ecosystems.Across these ancient lineages,colony-founding larvae anchor themselves either by byssus production or by cemented attachment.The latter mode of sessile life is strongly molded by left-right shell asymmetry during larval development of Ostreoida oysters such as Crassostrea hongkongensis.Here,we sequenced the genome of C.hongkongensis in high resolution and compared it to reference bivalve genomes to unveil genomic determinants driving cemented attachment and shell asymmetry.Importantly,loss of the homeobox gene Antennapedia(Antp)and broad expansion of lineagespecific extracellular gene families are implicated in a shift from byssal to cemented attachment in bivalves.Comparative transcriptomic analysis shows a conspicuous divergence between leftright asymmetrical C.hongkongensis and symmetrical Pinctada fucata in their expression profiles.Especially,a couple of orthologous transcription factor genes and lineage-specific shell-related gene families including that encoding tyrosinases are elevated,and may cooperatively govern asymmetrical shell formation in Ostreoida oysters.
文摘Bi-directional BLAST is a simple approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. This procedure is usually confined to the realm of customized Perl scripts, usually tuned for UNIX-like environments. Porting those scripts to other operating systems involves refactoring them, and also the installation of the Perl programming environment with the required libraries. To overcome these limitations, a data pipeline was implemented in Java. This application submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. GO Slim terms are attached to hits, several statistics are derived, and molecular evolution rates are estimated through PAML. The results are written to a set of delimited text tables intended for further analysis. The provided graphic user interface allows a friendly interaction with this application, which is documented and available to download at http：//moodle.fct.unl.pt/course/view.php？id=2079 or https：//sourceforge.net/projects/bidiblast/ under the GNU GPL license.
基金the National Key Basic Research and Develop-ment (973) Program of China (No. 2004CB518605)the National Natural Science Foundation of China (Nos. 60405001 and 60572086)
文摘In recent years, much effort has been made in identifying microRNA （miRNA） genes from mammals insects, worms, plants, and viruses. Continuing the search for more miRNA genes is still important but difficult. This paper presents a computational strategy based on comparative genomics analysis. The algorithm was used to scan four invertebrate genomes, Drosophila melangoster, Bombyx mori, Apis mellifera, and Anopheles gambiae, which are either model organisms or medically/economically important insects. 99 new miRNA genes were predicted from the four insect species which can be grouped into 17 miRNA gene families, of which 10 of the miRNA families are insect-specific. Sequence similarity analysis showed that 16 of the newly predicted insect miRNAs belong to the K-box, GY-box, and Brd-box miRNA families which are important participators in Notch-related pathways. To test the validity of the algorithm, 39 predicted insect miRNA genes from D. melangoster and A. mellifera were selected for further biological validation. 34 （87%） predicted miRNA genes＇ transcripts were successfully detected by reverse transcription-polymerase chain reaction experiments. Thus, this strategy can be used to efficiently screen for miRNA genes conserved cross species.
文摘Liquorilactobacillus nagelii is a lactic acid bacterium frequently found in a variety of traditional fermented foods,where it contributes to their sensory properties and potential health benefits.However,research evaluating the genetic and functional features of L.nagelii is scarce in the literature.In this study,we sequenced and assembled the genome of L.nagelii VUCC-R001,a strain isolated from kombucha tea,assessing its safety and exploring its biotechnological potential,mainly in terms of D-phenyllactic acid and dextran production,through a comparative genomic approach with 35 Liquorilactobacillus genomes and related phenotypic validation.Bioinformatic analysis revealed a good-quality draft genome(~2.4 Mb)of VUCC-R001 with a completeness around 99.7%(N50 of 151,630 bp).Comparative genomic analyses showed the correct identification of the new strain,the absence of genes encoding transmissible antibiotic resistance,virulence factors,and biogenic amine production,underlining its safety,also confirmed by phenotypic tests.We identified genes putatively associated with D-phenyllactic acid(PLA)production and verified the capability of this strain to produce a high concentration(52 mg/L)of PLA in vitro.To date,this is the first study reporting a Liquorilactibacillus strain that produces D-phenyllactic acid.Genome analyses of L.nagelii also elicited the presence of a dextransucrase GH70(EC 2.4.1.5),leading to the production of dextran from sucrose,an exopolysaccharide with applications in the food and biomedical industries.This investigation provides new insights into the genomic features and functional attributes of L.nagelii,opening new prospects for the biotechnological use of selected strains belonging to this species.
基金supported by the National Natural Science Foundation of China(Nos.32021005,31820103010)111 project(BP0719028)the Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province。
文摘Lactobacillus johnsonii,as a microorganism widely presenting in the intestinal tract of mammals,dairy products,and poultry,possesses various probiotic characteristics.Currently,many research focused on the probiotic functions and industrial applications of L.johnsonii.In this study,98 strains of L.johnsonii were subjected to comparative genomic analyses to explore its genetic diversity.The results indicated that based on ANI values,d-DDH values,phylogenetic analysis,and whole-genome comparison,the 98 strains of L.johnsonii were classified into two phylogenetic clusters.The carbohydrate utilization genes,bacteriocin operon,extracellular polysaccharide gene cluster,and bile salt hydrolase encoding genes in L.johnsonii shared common features and exhibited systematic differences based on phylogenetic clustering.The main reason for the high intra-species gene diversity of L.johnsonii might be differences in phages and other mobile genetic elements.This study provides new insights into the genomic features and functional genes of L.johnsonii.
基金supported by the National Key Research and Development Project(2022YFD2100703)the National Natural Science Foundation of China(32394051 and U23A20259)the Fundamental Research Funds for the Central Universities(JUSRP622013).
文摘Lactococcus lactis,a major starter culture in the dairy industry,has been widely applied in food fermentation.While current research has primarily focused on evaluating its role during fermentation,genomic investigations into its genetic diversity and functional adaptability remain limited.In this study,199 L.lactis strains isolated from Chinese traditional artisanal cheeses(72 bovine,71 goat,and 56 yak milk cheese isolates)were subjected to comparative genomic analysis.Genomic characteristic analysis indicated that bovine milk strains possess larger genomes and the highest number of unique genes.Functional characterization further demonstrated notable differences in carbohydrate metabolism among strains from different sources,with yak milk strains enriched in enzymes involved in complex polysaccharide degradation,including members of the carbohydrate esterases family.Moreover,strains from different sources exhibit distinct strategies for lactose hydrolysis and metabolic utilization,reflecting adaptive evolution to their specific nutritional niches.Analysis of the antibiotic resistance profile suggests that L.lactis predominantly harbors glycopeptide and lincosamide resistance genes,encompassing four distinct resistance mechanisms.Collectively,this study reveals the genetic diversity and adaptive evolution of L.lactis strains from different sources and identifies key genes associated with carbohydrate degradation,lactose metabolism,and antibiotic resistance,providing concrete genetic evidence for the selection of efficient and safe industrial fermentation strains.
基金supported by the NIA/NIH(1K01AG060040).Studies performed by JN were funded by the NICHD/NIH(5R00HD096117)Microscopy Core Facility supported,in part,with funding from NIH-NCI Cancer Center Support Grant P30 CA016059.
文摘Alzheimer’s disease is initially thought to be caused by age-associated accumulation of plaques,in recent years,research has increasingly associated Alzheimer’s disease with lysosomal storage and metabolic disorders,and the explanation of its pathogenesis has shifted from amyloid and tau accumulation to oxidative stress and impaired lipid and glucose metabolism aggravated by hypoxic conditions.However,the underlying mechanisms linking those cellular processes and conditions to disease progression have yet to be defined.Here,we applied a disease similarity approach to identify unknown molecular targets of Alzheimer’s disease by using transcriptomic data from congenital diseases known to increase Alzheimer’s disease risk,namely Down syndrome,Niemann-Pick type C disease,and mucopolysaccharidoses I.We uncovered common pathways,hub genes,and miRNAs across in vitro and in vivo models of these diseases as potential molecular targets for neuroprotection and amelioration of Alzheimer’s disease pathology,many of which have never been associated with Alzheimer’s disease.We then investigated common molecular alterations in brain samples from a Niemann-Pick type C disease mouse model by juxtaposing them with brain samples of both human and mouse models of Alzheimer’s disease.Detailed phenotypic,molecular,chronological,and biological aging analyses revealed that the Npc1tm(I1061T)Dso mouse model can serve as a potential short-lived in vivo model for brain aging and Alzheimer’s disease research.This research represents the first comprehensive approach to congenital disease association with neurodegeneration and a new perspective on Alzheimer’s disease research while highlighting shortcomings and lack of correlation in diverse in vitro models.Considering the lack of an Alzheimer’s disease mouse model that recapitulates the physiological hallmarks of brain aging,the short-lived Npc1^(tm(I1061T)Dso) mouse model can further accelerate the research in these fields and offer a unique model for understanding the molecular mechanisms of Alzheimer’s disease from a perspective of accelerated brain aging.
基金supported by the National Crop Germplasm Resources Center(NCGRC-2024-056)the National Natural Science Foundation of China(32301813).
文摘Finger millet(Eleusine coracana Gaertn.),a nutritionally rich and drought-resilient C4 cereal,possesses exceptional grain storage longevity(up to 50 years).Here,we report a high-quality genome assembly of the allotetraploid cultivar C142,revealing extensive structural rearrangements between its two subgenomes(subA and subB),which are associated with asymmetric gene expression and subgenome dominance favoring subA.SubB diverged from subA and E.indica approximately 6.8 million years ago.Subsequently,two whole-genome duplication events shaped the current genome architecture,contributing to gene redundancy and adaptive potential.Notably,expansion of stress-related gene families,such as aldo-keto reductases,suggests a role in oxidative stress response and drought adaptation.Using genome-wide association studies,we identify several candidate genes associated with key agronomic traits.Among them,EcMDHAR,encoding monodehydroascorbate reductase,plays a critical role in enhancing drought tolerance.Different EcMDHAR haplotypes exhibit distinct expression profiles,supporting their functional relevance in drought adaptation.This genomic resource not only advances our understanding of polyploid genome evolution in millets,but also provides a foundation for genome-assisted improvement of drought resistance and nutritional quality in finger millet.
基金supported by the National Natural Science Foundation of China(W2511024,32370228,32470232)the Natural Science Foundation of Jiangsu Province(BK20250004)+3 种基金the Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry,the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)the fund of Taxonomy Scientist Program'of the Chinese Academy of Sciences(CAS-TAX-24-038)the Youth Innovation Promotion Association CAS(2023355)Postgraduate Research&Practice Innovation Program of Jiangsu Province(KYCX24_1846).
文摘Trentepohliales is a completely terrestrial order within Ulvophyceae(the core Chlorophyta),and its closely related lineages are mainly marine macroalgae(green seaweeds).Despite the considerable interest in their biotechnological potential,little is known about their adaptations to challenging terrestrial habitats.Here,we assemble the high-quality reference genome of Trentepohlia odorata.This alga shows duplications of key genes associated with lipid metabolism and carotenoid synthesis,potentially facilitating intracellular accumulation of lipid droplets and carotenoids.We further reveal positive selection and expansion of gene families involved in vesicle trafficking and cell division regulation in T.odorata compared with other algae(cleavage furrow-mediated cell division)in Ulvophyceae,providing a genetic foundation for the evolution of phragmoplast-mediated cell division.The combined C_(4)-like and biophysical CO_(2)-concentrating mechanisms(CCMs)of T.odorata enable adaptation to fluctuating CO_(2) environments,and support efficient photosynthesis under CO_(2)-limited conditions.Adaptive strategies of T.odorata to terrestrial stressors,such as drought,intense light,and UV-B radiation,include horizontally acquired genes involved in cell wall synthesis and remodeling,homeostasis of aldehydes,and expanded genes associated with reactive oxygen species(ROS),DNA repair,and photoprotection.Our study provides a valuable genomic resource for studying aerial algae and improves understanding of plant terrestrialization.
