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
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
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
Objective： In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as an- timicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork qual...Objective： In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as an- timicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. Methods： The genome sequence of L. p/antarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palin- dromic repeats （CRISPRs）. Results： We identified genes that encode proteins related to genetic adaptation and pro- biotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid bio- synthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall exopolysaccharide （EPS） biosynthesis, and bacteriocin biosynthesis. Conclusions： Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate.展开更多
Bread wheat （Triticum aestivum, AABBDD） is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the whe...Bread wheat （Triticum aestivum, AABBDD） is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path （MTP） of 3176 BAC clones from the short arm ofAe. tauschii chromosome 3 （At3DS）. The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a 247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3DS contains 38.67% more genes. In comparison to At3DS, the short arm sequence of wheat chromosome 3B （Ta3BS） is 95-Mb large in size, which is primarily due to the expansion of the non-centromeric region, suggesting that transposable element （TE） bursts in Ta3B likely occurred there. Also, the size increase is accompanied by a proportional increase in gene number in Ta3BS. We found that in the sequence of short arm of wheat chromosome 3D （Ta3DS）, there was only less than 0.27% gene loss compared to At3DS. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.展开更多
Genome dynamics of pathogenic organisms are driven by plant host and pathogenic organism co-evolution, in which patho- gen genomes areused to overcome stresses imposed by hosts with various genetic backgrounds through...Genome dynamics of pathogenic organisms are driven by plant host and pathogenic organism co-evolution, in which patho- gen genomes areused to overcome stresses imposed by hosts with various genetic backgrounds through generation of a range of field isolates. This model also applies to the rice host and its fungal pathogen Magnaporthe oryzae. To better understand genetic variation of M. oryzae in nature, the field isolate V86010 from the Philippines was sequenced and ana- lyzed. Genome annotation found that the assembled V86010 genome was composed of 1 931 scaffolds with a combined length of 38.9 Mb. The average GC ratio is 51.3% and repetitive elements constitute 5.1% of the genome. A total of 11 857 genes including 616 effector protein genes were predicted using a combined analysis pipeline. All predicted genes and effector protein genes of isolate V86010 distribute on the eight chromosomes when aligned with the assembled genome of isolate 70-15. Effector protein genes are located disproportionately at several chromosomal ends. The Pot2 elements are abundant in V86010. Seven V86010-specific effector proteins were found to suppress programmed cell death induced by BAX in tobacco leaves using an Agrobacterium-mediated transient assay. Our results may provide useful information for further study of the molecular and genomic dynamics in the evolution of M. oryzae and rice host interactions, and for characterizing novel effectors and AVR genes in the rice blast pathogen.展开更多
Common wheat(Triticum aestivum) is a hexaploid plant(AABBDD) derived from genetically related tetraploid wheat T. turgidum(AABB) and a diploid goatgrass Aegilops tauschii(DD). Recent advances in sequencing technology ...Common wheat(Triticum aestivum) is a hexaploid plant(AABBDD) derived from genetically related tetraploid wheat T. turgidum(AABB) and a diploid goatgrass Aegilops tauschii(DD). Recent advances in sequencing technology and genome assembly strategies allow the acquisition of multiple wheat genomes, calling for a centralized database to store, manage and query the genomics information in a manner to reflect their evolutionary relationship and to perform effective comparative genome analysis. Here,we built WheatGene, a database that contains five wheat genomes of 318,102 genes and 945,900 transcripts and their expression information in 998 RNA-seq samples that can be searched and compared in an interactive manner. WheatGene was developed with Drupal, a popular content management system and the toolkit Tripal managed the biological information. The database was accessible through a web browser with species, search, gene expression, tools, and literature entries. Tools available were BLAST,synteny viewer, map viewer, JBrowse, data downloads, gene expression heatmap and bar chart, and homologs viewer. Moreover, the map viewer connected genomics data with genetic maps and QTL that can be searched for markers for molecular breeding. WheatGene was developed with open-source modules and libraries. WheatGene is available at http://wheatgene.agrinome.org.展开更多
Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most devastating wheat diseases. Wild emmer wheat（Triticum turgidum ssp. dicoccoides） is a promising source of disease resistance for wheat. ...Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most devastating wheat diseases. Wild emmer wheat（Triticum turgidum ssp. dicoccoides） is a promising source of disease resistance for wheat. A powdery mildew resistance gene conferring resistance to B. graminis f. sp. tritici isolate E09, originating from wild emmer wheat, has been transferred into the hexaploid wheat line WE4 through crossing and backcrossing. Genetic analyses indicated that the powdery mildew resistance was controlled by a single dominant gene, temporarily designated Ml WE4. By mean of comparative genomics and bulked segregant analysis, a genetic linkage map of Ml WE4 was constructed, and Ml WE4 was mapped on the distal region of chromosome arm 5BL. Comparative genetic linkage maps showed that genes Ml WE4, Pm36 and Ml3D232 were co-segregated with markers XBD37670 and XBD37680, indicating they are likely the same gene or alleles in the same locus. The co-segregated markers provide a starting point for chromosome landing and map-based cloning of Ml WE4, Pm36 and Ml3D232.展开更多
Plant hormones are small molecules that play important roles throughout the life span of a plant, known as auxin, gibberellin, cyto- kinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. ...Plant hormones are small molecules that play important roles throughout the life span of a plant, known as auxin, gibberellin, cyto- kinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Genetic and molecular studies in the model organism Arabidopsis thaliana have revealed the individual pathways of various plant hormone responses. In this study, we selected 479 genes that were convincingly associated with various hormone actions based on genetic evidence. By using these 479 genes as queries, a genome-wide search for their orthologues in several species （microorganisms, plants and animals） was performed. Meanwhile, a com- parative analysis was conducted to evaluate their evolutionary relationship. Our analysis revealed that the metabolisms and functions of plant hormones are generally more sophisticated and diversified in higher plant species. In particular, we found that several phytohor- mone receptors and key signaling components were not present in lower plants or animals. Meanwhile, as the genome complexity in- creases, the orthologue genes tend to have more copies and probably gain more diverse functions. Our study attempts to introduce the classification and phylogenic analysis of phytohormone related genes, from metabolism enzymes to receptors and signaling components, in different species.展开更多
The green seaweeds Ulva linza and U.prolifera are closely related species.They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone.In the Yellow Sea,...The green seaweeds Ulva linza and U.prolifera are closely related species.They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone.In the Yellow Sea,a genetically unique floating ecotype of U.prolifera even bloomed to cause serious green tides.However,there is still a lack of appropriate molecular markers to distinguish these two species,partially due to limited evaluations on the intraspecific variations in U.prolifera among dif ferent ecotypes.Since organelle genomes could provide rich genetic resources for phylogenetic analysis and development of genetic markers,in this study,the chloroplast genome from one attached population of U.prolifera was completely sequenced,and comparative genomic analyses were performed with other existing chloroplast genomes from U.linza and the floating ecotype of U.prolifera.The results showed that in spite of the high level of collinearity among three genomes,there were plenty of genetic variations especially within the non-coding regions,including introns and gene spacer regions.A strategy was proposed that only those signals of variation,which were identical between two ecotypes of U.prolifera but divergent between U.linza and U.prolifera,were selected to develop the interspecific markers for U.linza and U.prolifera.Two candidate markers,psa B and pet B,were shown to be able to distinguish these two closely related species and were applicable to more attached populations of U.prolifera from a wide range of geographical sources.In addition to the interspecific marker,this study would also provide resources for the development of intraspecific markers for U.prolifera.These markers might contribute to the surveys for Ulva species composition and green tide monitoring especially in the Yellow Sea region.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.
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 International Science&Technology Cooperation Program of China(No.2013DFA32330)the National Natural Science Foundation of China(Nos.31540044 and 31271821)+1 种基金the National High-Tech R&D Program(863)of China(No.2014AA022210-08)Natural Science Foundation of Zhejiang Province(No.LY16C200002),China
文摘Objective： In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as an- timicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. Methods： The genome sequence of L. p/antarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palin- dromic repeats （CRISPRs）. Results： We identified genes that encode proteins related to genetic adaptation and pro- biotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid bio- synthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall exopolysaccharide （EPS） biosynthesis, and bacteriocin biosynthesis. Conclusions： Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate.
基金supported by funding from the National Natural Science Foundation of China(Nos.31290210,31210103902)the Unites States National Science Foundation grant(No.IOS 1238231)+1 种基金the USDA-Agricultural Research Service CRIS project(No.5325-21000-019)the Ministry of Education of China(111 project)
文摘Bread wheat （Triticum aestivum, AABBDD） is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path （MTP） of 3176 BAC clones from the short arm ofAe. tauschii chromosome 3 （At3DS）. The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a 247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3DS contains 38.67% more genes. In comparison to At3DS, the short arm sequence of wheat chromosome 3B （Ta3BS） is 95-Mb large in size, which is primarily due to the expansion of the non-centromeric region, suggesting that transposable element （TE） bursts in Ta3B likely occurred there. Also, the size increase is accompanied by a proportional increase in gene number in Ta3BS. We found that in the sequence of short arm of wheat chromosome 3D （Ta3DS）, there was only less than 0.27% gene loss compared to At3DS. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.
基金supported by the grants from the National Natural Science Foundation of China (31528017 and 31461143019)
文摘Genome dynamics of pathogenic organisms are driven by plant host and pathogenic organism co-evolution, in which patho- gen genomes areused to overcome stresses imposed by hosts with various genetic backgrounds through generation of a range of field isolates. This model also applies to the rice host and its fungal pathogen Magnaporthe oryzae. To better understand genetic variation of M. oryzae in nature, the field isolate V86010 from the Philippines was sequenced and ana- lyzed. Genome annotation found that the assembled V86010 genome was composed of 1 931 scaffolds with a combined length of 38.9 Mb. The average GC ratio is 51.3% and repetitive elements constitute 5.1% of the genome. A total of 11 857 genes including 616 effector protein genes were predicted using a combined analysis pipeline. All predicted genes and effector protein genes of isolate V86010 distribute on the eight chromosomes when aligned with the assembled genome of isolate 70-15. Effector protein genes are located disproportionately at several chromosomal ends. The Pot2 elements are abundant in V86010. Seven V86010-specific effector proteins were found to suppress programmed cell death induced by BAX in tobacco leaves using an Agrobacterium-mediated transient assay. Our results may provide useful information for further study of the molecular and genomic dynamics in the evolution of M. oryzae and rice host interactions, and for characterizing novel effectors and AVR genes in the rice blast pathogen.
基金financially supported by National Key Research and Development Program of China (2016YFD0101004)Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciencessupported by the Chinese Government Scholarship。
文摘Common wheat(Triticum aestivum) is a hexaploid plant(AABBDD) derived from genetically related tetraploid wheat T. turgidum(AABB) and a diploid goatgrass Aegilops tauschii(DD). Recent advances in sequencing technology and genome assembly strategies allow the acquisition of multiple wheat genomes, calling for a centralized database to store, manage and query the genomics information in a manner to reflect their evolutionary relationship and to perform effective comparative genome analysis. Here,we built WheatGene, a database that contains five wheat genomes of 318,102 genes and 945,900 transcripts and their expression information in 998 RNA-seq samples that can be searched and compared in an interactive manner. WheatGene was developed with Drupal, a popular content management system and the toolkit Tripal managed the biological information. The database was accessible through a web browser with species, search, gene expression, tools, and literature entries. Tools available were BLAST,synteny viewer, map viewer, JBrowse, data downloads, gene expression heatmap and bar chart, and homologs viewer. Moreover, the map viewer connected genomics data with genetic maps and QTL that can be searched for markers for molecular breeding. WheatGene was developed with open-source modules and libraries. WheatGene is available at http://wheatgene.agrinome.org.
基金financially supported by the National HighTech R&D Program of China (2011AA100104)the National Basic Research Program of China (2013CB127705)+1 种基金the National Natural Science Foundation of China (31030056, 31210103902)the Introducing Talents of Disciplines to Universities,Ministry of Education (MOE) of China (111-02-3)
文摘Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most devastating wheat diseases. Wild emmer wheat（Triticum turgidum ssp. dicoccoides） is a promising source of disease resistance for wheat. A powdery mildew resistance gene conferring resistance to B. graminis f. sp. tritici isolate E09, originating from wild emmer wheat, has been transferred into the hexaploid wheat line WE4 through crossing and backcrossing. Genetic analyses indicated that the powdery mildew resistance was controlled by a single dominant gene, temporarily designated Ml WE4. By mean of comparative genomics and bulked segregant analysis, a genetic linkage map of Ml WE4 was constructed, and Ml WE4 was mapped on the distal region of chromosome arm 5BL. Comparative genetic linkage maps showed that genes Ml WE4, Pm36 and Ml3D232 were co-segregated with markers XBD37670 and XBD37680, indicating they are likely the same gene or alleles in the same locus. The co-segregated markers provide a starting point for chromosome landing and map-based cloning of Ml WE4, Pm36 and Ml3D232.
基金supported by the National Science Foundation of China (No.30625003,and 30730011)the China Ministry of Education (No.20060047)
文摘Plant hormones are small molecules that play important roles throughout the life span of a plant, known as auxin, gibberellin, cyto- kinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Genetic and molecular studies in the model organism Arabidopsis thaliana have revealed the individual pathways of various plant hormone responses. In this study, we selected 479 genes that were convincingly associated with various hormone actions based on genetic evidence. By using these 479 genes as queries, a genome-wide search for their orthologues in several species （microorganisms, plants and animals） was performed. Meanwhile, a com- parative analysis was conducted to evaluate their evolutionary relationship. Our analysis revealed that the metabolisms and functions of plant hormones are generally more sophisticated and diversified in higher plant species. In particular, we found that several phytohor- mone receptors and key signaling components were not present in lower plants or animals. Meanwhile, as the genome complexity in- creases, the orthologue genes tend to have more copies and probably gain more diverse functions. Our study attempts to introduce the classification and phylogenic analysis of phytohormone related genes, from metabolism enzymes to receptors and signaling components, in different species.
基金Supported by the Science&Technology Basic Resources Investigation Program of China(No.2018FY100205)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA23050302)+2 种基金the National Key R&D Program of China(No.2018YFD0901500)the National Natural Science Foundation of China(No.41776153)the Key R&D Program of Shandong Province(No.2019GSF107012)。
文摘The green seaweeds Ulva linza and U.prolifera are closely related species.They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone.In the Yellow Sea,a genetically unique floating ecotype of U.prolifera even bloomed to cause serious green tides.However,there is still a lack of appropriate molecular markers to distinguish these two species,partially due to limited evaluations on the intraspecific variations in U.prolifera among dif ferent ecotypes.Since organelle genomes could provide rich genetic resources for phylogenetic analysis and development of genetic markers,in this study,the chloroplast genome from one attached population of U.prolifera was completely sequenced,and comparative genomic analyses were performed with other existing chloroplast genomes from U.linza and the floating ecotype of U.prolifera.The results showed that in spite of the high level of collinearity among three genomes,there were plenty of genetic variations especially within the non-coding regions,including introns and gene spacer regions.A strategy was proposed that only those signals of variation,which were identical between two ecotypes of U.prolifera but divergent between U.linza and U.prolifera,were selected to develop the interspecific markers for U.linza and U.prolifera.Two candidate markers,psa B and pet B,were shown to be able to distinguish these two closely related species and were applicable to more attached populations of U.prolifera from a wide range of geographical sources.In addition to the interspecific marker,this study would also provide resources for the development of intraspecific markers for U.prolifera.These markers might contribute to the surveys for Ulva species composition and green tide monitoring especially in the Yellow Sea region.
