The analysis of ancient genomics provides opportunities to explore human population history across both temporal and geographic dimensions(Haak et al.,2015;Wang et al.,2021,2024)to enhance the accessibility and utilit...The analysis of ancient genomics provides opportunities to explore human population history across both temporal and geographic dimensions(Haak et al.,2015;Wang et al.,2021,2024)to enhance the accessibility and utility of these ancient genomic datasets,a range of databases and advanced statistical models have been developed,including the Allen Ancient DNA Resource(AADR)(Mallick et al.,2024)and AdmixTools(Patterson et al.,2012).While upstream processes such as sequencing and raw data processing have been streamlined by resources like the AADR,the downstream analysis of these datasets-encompassing population genetics inference and spatiotemporal interpretation-remains a significant challenge.The AADR provides a unified collection of published ancient DNA(aDNA)data,yet its file-based format and reliance on command-line tools,such as those in Admix-Tools(Patterson et al.,2012),require advanced computational expertise for effective exploration and analysis.These requirements can present significant challenges forresearchers lackingadvanced computational expertise,limiting the accessibility and broader application of these valuable genomic resources.展开更多
A brief review on the development of wheat germplasm with introduced powdery mildew and scab resistance from Haynaldia villosa Sch. and Leymus racemosus Lam., Roegneria ciliaris (Trin.) Nevski as well as R. kamoji C. ...A brief review on the development of wheat germplasm with introduced powdery mildew and scab resistance from Haynaldia villosa Sch. and Leymus racemosus Lam., Roegneria ciliaris (Trin.) Nevski as well as R. kamoji C. Koch respectively was made. In the course of germplasm development, genome analysis by means of chromosome banding, genomic in situ hybridization (GISH) or fluorescence in situ hybridization (FISH), molecular markers, particularly restriction fragment length polymorphism (RFLP) coupled with aneuploid analysis was employed for the purpose of improving breeding efficiency. Potential use of such germplasm in wheat breeding practice, basic studies and some related problems were also discussed.展开更多
Enterococci bacteria are important in environmental, food and clinical microbiology. Enterococcus faecium is a nosocomial pathogen that causes bacteremia, endocarditis and other infections. It is among the most preval...Enterococci bacteria are important in environmental, food and clinical microbiology. Enterococcus faecium is a nosocomial pathogen that causes bacteremia, endocarditis and other infections. It is among the most prevalent organisms encountered in hospital-associated infections accounting for approximately 12% of nosocomial infections in the USA （Linden and Miller, 1999）. However, certain strains of E. faecium are not only non-pathogenic but also have beneficial effects on human health with probiotic potential. For example, E. faecium T-110 is a consortium member in several probiotic products including BIO-THREE~ which is widely prescribed for human, animal and aqua-cultural use. This strain was originally developed by TOA Pharmaceuticals in Japan, and later used in the probiotic products of several other companies.展开更多
The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported...The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported a high-quality genome assembly of G.latifolium.Comparative genome analyses revealed substantial variations in both gene group composition and genomic sequences across 13 cotton genomes,including the expansion of photosynthesis-related gene groups in G.latifolium compared with other races and the pivotal contribution of structural variations(SVs)to G.hirsutum domestication.Based on the resequencing reads and constructed pan-genome of upland cotton,co-selection regions and SVs with significant frequency differences among different populations were identified.Genes located in these regions or affected by these variations may characterize the differences between G.latifolium and other races,and could be involved in maintenance of upland cotton domestication phenotypes.These findings may assist in mining genes for upland cotton improvement and improving the understanding of the genetic basis of upland cotton domestication.展开更多
Limosilactobacillus reuteri is a microbe intricately linked to humans and animal health.A thorough assessment of its safety and potential benefits is imperative prior to its application in human and animals.In this in...Limosilactobacillus reuteri is a microbe intricately linked to humans and animal health.A thorough assessment of its safety and potential benefits is imperative prior to its application in human and animals.In this investigation,we performed a comprehensive analysis encompassing genome sequencing,genomic analysis,and phenotypic characterization of L.reuteri Q35,an exceptionally proficient producer of reuterin.The whole genome sequencing results showed that the complete genome sequence spans 2145158 bp with a GC content of 38.9%and encompasses 2121 genes.Initial identification of antibiotic-resistant genes,virulence factors,and toxin-coding genes in the genome substantiated the strain’s low-risk status.Subsequent tests for antibiotic resistance,acute oral toxicology,and hemolysis further confirmed its elevated safety level.The genome of L.reuteri Q35 was found to contain genes associated with adhesion and stress tolerance.Following exposure to artificial gastric juice and bile salt,the strain exhibited a higher survival rate and demonstrated a strong scavenging ability for hydroxyl free radicals in antioxidant capacity tests.These findings suggested that L.reuteri Q35 possesses unique probiotic properties.Additionally,the genome of strain Q35 harbors three truncated oxaloyl-CoA decarboxylase genes(oxc1,oxc2 and oxc3),overexpression of which resulted in a significant increase in ammonium oxalate degradation from 29.5%to 48.8%.These findings highlight that L.reuteri Q35 exhibits both favorable safety characteristics alongside beneficial properties,making it a promising candidate for treating metabolic disorders such as hyperoxaluria.展开更多
Pseudoalteromonas is a group of marine bacteria widespread in diverse marine sediments,producing a wide range of bioactive compounds.However,only a limited number of Pseudoalteromonas phages have been isolated and stu...Pseudoalteromonas is a group of marine bacteria widespread in diverse marine sediments,producing a wide range of bioactive compounds.However,only a limited number of Pseudoalteromonas phages have been isolated and studied.In this study,a novel lytic Pseudoalteromonas phage,denoted as vB_PalP_Y7,was isolated from sewage samples collected at the Seafood Market in Qingdao,China.vB_PalP_Y7 remained stable across a wide range of temperatures(-20–50℃)and a wide pH range(3–12).The vB_PalP_Y7 phage harbors a linear double-stranded DNA molecule of 57699 base pairs(bp)with a G+C content of 45.90%.Furthermore,it is predicted to contain 58 open reading frames(ORFs).Phylogenetic analysis and protein network relationship analysis revealed low similarity between vB_PalP_Y7 and viruses in the ICTV and IMG/VR4 database,suggesting that vB_PalP_Y7 may be a potential new genus,Miuvirus.This study contributed valuable insights to comprehend the relationship between Pseudoalteromonas phages and their host organisms.展开更多
OBJECTIVE:To investigate the molecular effect of Socheongryong Tang(SCRT,Xiaoqinglong Tang in Chinese) on whole genome level in asthma mouse model by microarray technology.METHODS:Asthma was induced by intranasal inst...OBJECTIVE:To investigate the molecular effect of Socheongryong Tang(SCRT,Xiaoqinglong Tang in Chinese) on whole genome level in asthma mouse model by microarray technology.METHODS:Asthma was induced by intranasal instillation of ovalbumin in mouse.After administration of SCRT on asthma-induced mouse,the expression of genes in lung tissue was measured using whole genome microarray.The functional implication of differentially expressed genes was performed using ontological analysis and the similarity of promoter structure of genes was also analyzed.RESULTS:Treatment of SCRT restored expression level of many up- or down-regulated genes in asthma model,and this recovery rate means SCRT could regulate a set of genes having specific TFBS binding sites.CONCLUSION:In this study,we identified a set of genes subjected to similar regulation by SCRT in asthma model in mice.展开更多
The high intraspecies heterogeneity of Baciillus coagulans leads to significant phenotypic differences among different strains.Thus,6 B.coagulans strains were tested in the present study using an irritable bowel syndr...The high intraspecies heterogeneity of Baciillus coagulans leads to significant phenotypic differences among different strains.Thus,6 B.coagulans strains were tested in the present study using an irritable bowel syndrome(IBS)animal model to determine whether the IBS-alleviating effects of B.coagulans strains are strain-specific.The results of this study showed that the ingestion of B.coagulans GBI-30,6086,and B.coagulans CCFM1041 significantly alleviated IBS symptoms in mice.In contrast,other B.coagulans strains showed no or limited alleviating effects on IBS symptoms.According to our experimental results,the two main common features of these strains were as follows:1)The resistance of vegetative cells to bile salts,and 2)ability to synthesize specific lipids and secondary metabolites.Screening strains based on these two indicators may greatly reduce costs and provide a basis for mining new functional B.coagulans strains.Our results also suggest that administration of B.coagulans could significantly regulate microbiota dysbiosis in animal models.Moreover,the close relationships between the gut microbiota,gut microbiota metabolites,and IBS were further confirmed in this study.展开更多
Human adenovirus type 3 （HAdV-3） is widely prevalent all over the world, especially in Asia. The objective of this study is to carry out complete genomic DNA sequencing and the phylogenetic analysis for two strains ...Human adenovirus type 3 （HAdV-3） is widely prevalent all over the world, especially in Asia. The objective of this study is to carry out complete genomic DNA sequencing and the phylogenetic analysis for two strains （Guangzhou01 and Guangzhou02） of HAdV-3 wild virus isolated from South China. Nasopharyngeal secretion aspirate specimens of sick children were inoculated into HEp-2 and HeLa culture tubes, and the cultures were identified by neutralization assay with type-specific reference rabbit antiserum. Type-specific primers were also utilized to confirm the serotype. The restriction fragments of HAdV genome DNA were cloned into pBlueScript SK （ ＋ ） vectors and sequenced, and the 5＇ and 3＇ ends of the linear HAdV-3 genome were directly sequenced with double purified genomic DNA as templates. General features of the HAdV-3 genome sequences were explored by using several bio-software. Phylogenetic analysis was done with MEGA 3.0 software. The genomic sequences of Guangzhou01 and Guangzhou02 possess the same 4 early regions and 5 late regions and have 39 coding sequences and two RNA coding sequences. Other non-coding regions are conservative. Inverted repeats and palindromes were identified in the genome sequences. The genomes of group B human adenovirus as well as HAdV-3 have close phylogenetic relationship with that of chimpanzee adenovirus type 21. The genomic lengths of these two isolated strains are 35 273 bp and 35 269 bp, respectively. The phylogenetic analysis showed that HAdV-B species has some relationship with certain types of chimpanzee adenovirus.展开更多
Fowl adenovirus serotype 4(FAdV-4)strain SD1511 was isolated from chickens with severe inclusion body hepatitis and hydropericardium syndrome in Shandong Province,China.The isolate was cultured in primary chicken embr...Fowl adenovirus serotype 4(FAdV-4)strain SD1511 was isolated from chickens with severe inclusion body hepatitis and hydropericardium syndrome in Shandong Province,China.The isolate was cultured in primary chicken embryo kidney cells.A study of pathogenicity indicated that SD1511 readily infected 7–35-d-old chickens by intramuscular injection and intranasal and oral routes,causing 50%–100%mortality.The 35-d-old chickens suffered more severe infection than 7-and 21-d-old chickens with mortality highest in the intramuscular injection group.The serum from surviving chickens showed potent viral neutralizing capability.The complete genome of SD1511 was sequenced and analyzed.The strain was found to belong to the FAdV-4 cluster with more than 99%identity with the virulent FAdV-4 strains isolated in China in recent years except for some distinct variations,including deletions of open reading frame 27(ORF27),ORF48,and part of ORF19.Our findings suggest that SD1511 might be used as a prototype strain for the study of pathogenesis and vaccine development.展开更多
Erianthus arundinaceus is a wild relative of sugarcane(Saccharum officinarum L.)with many desirable agronomic traits for sugarcane genetic improvement.However,limited knowledge of the complex genome of hexaploid E.aru...Erianthus arundinaceus is a wild relative of sugarcane(Saccharum officinarum L.)with many desirable agronomic traits for sugarcane genetic improvement.However,limited knowledge of the complex genome of hexaploid E.arundinaceus has impeded the development of required molecular tools.Dissecting complex genomes into single chromosomes can simplify analyses.The flow-cytometric sorting of a single chromosome of E.arundinaceus in a Saccharum-Erianthus introgression line is reported.A novel approach called genomic in situ hybridization in suspension was used to discriminate the alien chromosome from sugarcane chromosomes at the same size.A total of 218,000 E.arundinaceus chromosome 1(EaC1)were sorted to>97%purity and amplified DNA was sequenced using Illumina and Pac Bio technologies.The resulting assembly had a 70.93 Mb contig sequence with an N50 of 19.62 kb.A total of 56.69 Mb repeat sequences were predicted,accounting for 79.1%of the chromosome and 2646 genes having a total length of 1.84 Mb that represented 2.59%of the chromosome.Of these genes,1877(70.9%)genes were functionally annotated.The phylogenetic relationship of E.arundinaceus with other species using the chromosome1 sequence revealed that E.arundinaceus was distantly related to Oryza sativa and Zea mays,followed by Sorghum bicolor,and was closely related to S.spontaneum and Saccharum spp.hybrids.This study provides the first insights into the characteristics of EaC1,and the results will provide tools to support molecular improvement and alien introgression breeding of sugarcane.展开更多
African cultivated rice(Oryza glaberrima)was domesticated from its wild progenitor,Oryza barthii.The transition from long-awn to short-awn or awnless glumes was an important evolutionary event during domestication.A Q...African cultivated rice(Oryza glaberrima)was domesticated from its wild progenitor,Oryza barthii.The transition from long-awn to short-awn or awnless glumes was an important evolutionary event during domestication.A QTL analysis of 331 recombinant inbred lines(RILs)using 194 InDel markers identified five quantitative trait loci(QTL)associated with awn length.Locus qObAwn5 made the highest contribution in regulating awn length and was fine-mapped to a 260-kb genomic interval.RNA-seq and RT-qPCR analyses,combined with CRISPR/Cas9-mediated knockout that disruption of gene G12 caused a significant reduction in awn length indicating that G12 was ObAwn5.Genomic analysis revealed a large structural variation(SV)between W1411 and IRGC104165 within this region,characterized by an inversion and two large deletions.Population genomic analyses revealed that all the cultivated African accessions exhibit a domestication-like(Dom-like)pattern,whereas non-cultivated accessions consisted of two distinct types:W1050-like and W1411-like.The W1411-like type was exclusively found in the AA genome of African wild rice.This discovery of ObAwn5 newly substantiates the independent origin of African cultivated rice.展开更多
In the present study,the complete genomes of four common（4/EV71/Wenzhou/CHN/2014,15/EV71/Wenzhou/CHN/2014,116/EV71/Wenzhou/CHN/2014,and 120/EV71/Wenzhou/CHN/2014）and two virulent（11/EV71/Wenzhou/CHN/2014and 109/EV7...In the present study,the complete genomes of four common（4/EV71/Wenzhou/CHN/2014,15/EV71/Wenzhou/CHN/2014,116/EV71/Wenzhou/CHN/2014,and 120/EV71/Wenzhou/CHN/2014）and two virulent（11/EV71/Wenzhou/CHN/2014and 109/EV71/Wenzhou/CHN/2014）enterovirus 71（EV71）isolates were sequenced and described.They are 7405 bp in length and belong to EV71 sub-genotype C4 （C4a cluster）.展开更多
The first decade since the completion of the Human Genome Project has been marked with rapid development of genomic technologies and their immediate clinical applications. Genomic analysis using oligonucleotide array ...The first decade since the completion of the Human Genome Project has been marked with rapid development of genomic technologies and their immediate clinical applications. Genomic analysis using oligonucleotide array comparative genomic hybridization （aCGH） or single nucleotide polymorphism （SNP） chips has been applied to pediatric patients with developmental and intellectual disabilities （DD/ ID）, multiple congenital anomalies （MCA） and autistic spectrum disorders （ASD）. Evaluation of analytical and clinical validities of aCGH showed 〉 99% sensitivity and specificity and increased analytical resolution by higher density probe coverage. Reviews of case series, multi-center comparison and large patient-control studies demonstrated a diagnostic yield of 12%--20%; approximately 60% of these abnormalities were recurrent genomic disorders. This pediatric experience has been extended toward prenatal diagnosis. A series of reports indicated approximately 10% of pregnancies with ultrasound-detected structural anomalies and normal cytogenetic findings had genomic abnormalities, and 30% of these abnormalities were syndromic genomic disorders. Evidence-based practice guidelines and standards for implementing genomic analysis and web-delivered knowledge resources for interpreting genomic findings have been established. The progress from this technology-driven and evidence-based genomic analysis provides not only opportunities to dissect disease-causing mechanisms and develop rational therapeutic interventions but also important lessons for integrating genomic sequencing into pediatric and prenatal genetic evaluation.展开更多
Emerging evidence shows that some Lactobacillus fermentum(L.fermentum)strains can contribute to the prevention and treatment of ulcerative colitis(UC).In this study,105 isolates of L.fermentum strains were separated f...Emerging evidence shows that some Lactobacillus fermentum(L.fermentum)strains can contribute to the prevention and treatment of ulcerative colitis(UC).In this study,105 isolates of L.fermentum strains were separated from fecal samples of populations in different regions in China and their draft genomes were sequenced.Pan-genomic and phylogenetic characterizations of these strains and four model strains(L.fermentum 3872,CECT5716,IF03956,and VRI003)were performed.Phylogenetic analysis ind icated that there was no significant adaptive evolution between the genomes of L.fermentum strains and the geographical location,sex,ethnicity,and age of the hosts.Three L.fermentum strains(FWXBH115,FGDLZR121,and FXJCJ61)from different branches of the phylogenetic tree and strain type L.fermentum CECT5716 were selected and their anti-inflammatory and immune modulatory activities in a dextran sulphate sodium(DSS)-induced colitis mouse model were further investigated.Both L.fermentum FXJCJ61 and CECT5716 significantly alleviated UC by reducing all colitis-associated histological indices,maintaining mucosal integrity,and stimulating replenishment of short-chain fatty acids(SCFAs),while the other two strains failed to offer similar protection.The anti-inflammato ry mechanisms of L.fermentum FXJCJ61 and CECT5716 were related to the inhibition of nuclear factor kappa-B(NF-κB)signaling pathway activation and enhancement of interleukin 10(IL-10)production.Comparative genomic analysis of these strains identified candidate genes that may contribute to the anti-inflammatory effects of specific L.fermentum strains.展开更多
Magnetotactic bacteria(MTB)display magnetotaxis ability because of biomineralization of intracellular nanometer-sized,membrane-bound organelles termed magnetosomes.Despite having been discovered more than half a centu...Magnetotactic bacteria(MTB)display magnetotaxis ability because of biomineralization of intracellular nanometer-sized,membrane-bound organelles termed magnetosomes.Despite having been discovered more than half a century,only a few representatives of MTB have been isolated and cultured in the laboratory.In this study,we report the genomic characterization of a novel marine magnetotactic spirillum strain SH-1 belonging to the genus Terasakiella that was recently isolated.A gene encoding haloalkane dehalogenase,which is involved in the degradation of chlorocyclohexane,chlorobenzene,chloroalkane,and chloroalkene,was identified.SH-1 genome contained cysCHI and soxBAZYX genes,thus potentially capable of assimilatory sulfate reduction to H_(2)S and using thiosulfate as electron donors and oxidizing it to sulfate.Genome of SH-1 also contained genes encoding periplasmic dissimilatory nitrate reductases(napAB),assimilatory nitrate reductase(nasA)and assimilatory nitrite reductases(nasB),suggesting that it is capable of gaining energy by converting nitrate to ammonia.The pure culture of Terasakiella sp.SH-1 together with its genomic results off ers new opportunities to examine biology,physiology,and biomineralization mechanisms of MTB.展开更多
The genetic base that cotton breeders commonly use to improve Upland cultivars is very narrow.The AD-genome species Gossypium barbadense,G.tomentosum,and G.mustelinum are part of
A continuous co-evolutionary arms-race between pathogens and their host plants promotes the development of pathogenic factors by microbes, including carbohydrate esterase(CE) genes to overcome the barriers in plant ce...A continuous co-evolutionary arms-race between pathogens and their host plants promotes the development of pathogenic factors by microbes, including carbohydrate esterase(CE) genes to overcome the barriers in plant cell walls. Identification of CEs is essential to facilitate their functional and evolutionary investigations; however, current methods may have a limit in detecting some conserved domains, and ignore evolutionary relationships of CEs, as well as do not distinguish CEs from proteases. Here, candidate CEs were annotated using conserved functional domains, and orthologous gene detection and phylogenetic relationships were used to identify new CEs in 16 oomycete genomes, excluding genes with protease domains. In our method, 41 new putative CEs were discovered comparing to current methods, including three CE4, 14 CE5, eight CE12, five CE13, and 11 CE14. We found that significantly more CEs were identified in Phytophthora than in Hyaloperonospora and Pythium, especially CE8, CE12, and CE13 that are putatively involved in pectin degradation. The abundance of these CEs in Phytophthora may be due to a high frequency of multiple-copy genes, supporting by the phylogenetic distribution of CE13 genes, which showed five units of Phytophthora CE13 gene clusters each displaying a species tree like topology, but without any gene from Hyaloperonospora or Pythium species. Additionally, diverse proteins associated with products of CE13 genes were identified in Phytophthora strains. Our analyses provide a highly effective method for CE discovery, complementing current methods, and have the potential to advance our understanding of function and evolution of CEs.展开更多
supported by the China Animal Disease Prevention and Control Center;the China Agriculture Research System Poultry-Related Science and Technology Innovation Team of Peking, China （CARS-PSTP）
Background:The Genotype-Tissue Expression was used to expanded normal tissue of the Cancer Genome Atlas database.This study aimed to investigate genes associated with the pathogenesis and prognosis of prostate cancer....Background:The Genotype-Tissue Expression was used to expanded normal tissue of the Cancer Genome Atlas database.This study aimed to investigate genes associated with the pathogenesis and prognosis of prostate cancer.Methods:We conducted prognostic related genes for prostate cancer by using transcriptome data from the Genotype-Tissue Expression Project and the Cancer Genome Atlas data sources,which were analyzed using an integrated bioinformatics strategy.Clinically significant modules were distinguished,and GO and KEGG analysis were used to Database for Annotation,Visualization and Integrated Discovery.Further annotation was performed through Gene set enrichment analysis.Logistic regression was carried out to analyze the associations between clinicopathologic characteristics and the hub genes.Logistic regression model and survival analysis were performed.Results:By using data available from the Cancer Genome Atlas and the Genotype-Tissue Expression databases,we here show that 53 differential expression genes were identified.Through GO and KEGG analysis a prognostic related gene signature consisted of GOLM1,EIF4A1,ABCC4,RPL7P16,NPIPB12 and PCA3 was constructed with a good performance in predicting overall survivals.The majority of the six hub genes were associated with clinical characteristics of prostate cancer.Conclusion:These genes might be considered as new targets for further investigating the diagnostic and prognostic biomarkers to facilitate the molecular targeting therapy since they showed differently expressed in prostate cancer and correlate with overall survival prognosis.展开更多
基金by the National Key Research and Development Program of China(2023YFC3303701-02 and 2024YFC3306701)the National Natural Science Foundation of China(T2425014 and 32270667)+3 种基金the Natural Science Foundation of Fujian Province of China(2023J06013)the Major Project of the National Social Science Foundation of China granted to Chuan-Chao Wang(21&ZD285)Open Research Fund of State Key Laboratory of Genetic Engineering at Fudan University(SKLGE-2310)Open Research Fund of Forensic Genetics Key Laboratory of the Ministry of Public Security(2023FGKFKT07).
文摘The analysis of ancient genomics provides opportunities to explore human population history across both temporal and geographic dimensions(Haak et al.,2015;Wang et al.,2021,2024)to enhance the accessibility and utility of these ancient genomic datasets,a range of databases and advanced statistical models have been developed,including the Allen Ancient DNA Resource(AADR)(Mallick et al.,2024)and AdmixTools(Patterson et al.,2012).While upstream processes such as sequencing and raw data processing have been streamlined by resources like the AADR,the downstream analysis of these datasets-encompassing population genetics inference and spatiotemporal interpretation-remains a significant challenge.The AADR provides a unified collection of published ancient DNA(aDNA)data,yet its file-based format and reliance on command-line tools,such as those in Admix-Tools(Patterson et al.,2012),require advanced computational expertise for effective exploration and analysis.These requirements can present significant challenges forresearchers lackingadvanced computational expertise,limiting the accessibility and broader application of these valuable genomic resources.
文摘A brief review on the development of wheat germplasm with introduced powdery mildew and scab resistance from Haynaldia villosa Sch. and Leymus racemosus Lam., Roegneria ciliaris (Trin.) Nevski as well as R. kamoji C. Koch respectively was made. In the course of germplasm development, genome analysis by means of chromosome banding, genomic in situ hybridization (GISH) or fluorescence in situ hybridization (FISH), molecular markers, particularly restriction fragment length polymorphism (RFLP) coupled with aneuploid analysis was employed for the purpose of improving breeding efficiency. Potential use of such germplasm in wheat breeding practice, basic studies and some related problems were also discussed.
文摘Enterococci bacteria are important in environmental, food and clinical microbiology. Enterococcus faecium is a nosocomial pathogen that causes bacteremia, endocarditis and other infections. It is among the most prevalent organisms encountered in hospital-associated infections accounting for approximately 12% of nosocomial infections in the USA （Linden and Miller, 1999）. However, certain strains of E. faecium are not only non-pathogenic but also have beneficial effects on human health with probiotic potential. For example, E. faecium T-110 is a consortium member in several probiotic products including BIO-THREE~ which is widely prescribed for human, animal and aqua-cultural use. This strain was originally developed by TOA Pharmaceuticals in Japan, and later used in the probiotic products of several other companies.
基金supported by the National Natural Science Foundation of China(32201873)the Key Research and Development Plan of Hubei Province(2023BBB050)。
文摘The genetic basis for Gossypium hirsutum race latifolium,the putative ancestor of cultivated upland cotton,emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown.Here,we reported a high-quality genome assembly of G.latifolium.Comparative genome analyses revealed substantial variations in both gene group composition and genomic sequences across 13 cotton genomes,including the expansion of photosynthesis-related gene groups in G.latifolium compared with other races and the pivotal contribution of structural variations(SVs)to G.hirsutum domestication.Based on the resequencing reads and constructed pan-genome of upland cotton,co-selection regions and SVs with significant frequency differences among different populations were identified.Genes located in these regions or affected by these variations may characterize the differences between G.latifolium and other races,and could be involved in maintenance of upland cotton domestication phenotypes.These findings may assist in mining genes for upland cotton improvement and improving the understanding of the genetic basis of upland cotton domestication.
文摘Limosilactobacillus reuteri is a microbe intricately linked to humans and animal health.A thorough assessment of its safety and potential benefits is imperative prior to its application in human and animals.In this investigation,we performed a comprehensive analysis encompassing genome sequencing,genomic analysis,and phenotypic characterization of L.reuteri Q35,an exceptionally proficient producer of reuterin.The whole genome sequencing results showed that the complete genome sequence spans 2145158 bp with a GC content of 38.9%and encompasses 2121 genes.Initial identification of antibiotic-resistant genes,virulence factors,and toxin-coding genes in the genome substantiated the strain’s low-risk status.Subsequent tests for antibiotic resistance,acute oral toxicology,and hemolysis further confirmed its elevated safety level.The genome of L.reuteri Q35 was found to contain genes associated with adhesion and stress tolerance.Following exposure to artificial gastric juice and bile salt,the strain exhibited a higher survival rate and demonstrated a strong scavenging ability for hydroxyl free radicals in antioxidant capacity tests.These findings suggested that L.reuteri Q35 possesses unique probiotic properties.Additionally,the genome of strain Q35 harbors three truncated oxaloyl-CoA decarboxylase genes(oxc1,oxc2 and oxc3),overexpression of which resulted in a significant increase in ammonium oxalate degradation from 29.5%to 48.8%.These findings highlight that L.reuteri Q35 exhibits both favorable safety characteristics alongside beneficial properties,making it a promising candidate for treating metabolic disorders such as hyperoxaluria.
基金the National Natural Science Foundation of China(Nos.42188102,42120104006,41976117,42176111)the Fundamental Research Funds for the Central Universities(Nos.202172002,201812002)the funding from Andrew Mc Minn。
文摘Pseudoalteromonas is a group of marine bacteria widespread in diverse marine sediments,producing a wide range of bioactive compounds.However,only a limited number of Pseudoalteromonas phages have been isolated and studied.In this study,a novel lytic Pseudoalteromonas phage,denoted as vB_PalP_Y7,was isolated from sewage samples collected at the Seafood Market in Qingdao,China.vB_PalP_Y7 remained stable across a wide range of temperatures(-20–50℃)and a wide pH range(3–12).The vB_PalP_Y7 phage harbors a linear double-stranded DNA molecule of 57699 base pairs(bp)with a G+C content of 45.90%.Furthermore,it is predicted to contain 58 open reading frames(ORFs).Phylogenetic analysis and protein network relationship analysis revealed low similarity between vB_PalP_Y7 and viruses in the ICTV and IMG/VR4 database,suggesting that vB_PalP_Y7 may be a potential new genus,Miuvirus.This study contributed valuable insights to comprehend the relationship between Pseudoalteromonas phages and their host organisms.
文摘OBJECTIVE:To investigate the molecular effect of Socheongryong Tang(SCRT,Xiaoqinglong Tang in Chinese) on whole genome level in asthma mouse model by microarray technology.METHODS:Asthma was induced by intranasal instillation of ovalbumin in mouse.After administration of SCRT on asthma-induced mouse,the expression of genes in lung tissue was measured using whole genome microarray.The functional implication of differentially expressed genes was performed using ontological analysis and the similarity of promoter structure of genes was also analyzed.RESULTS:Treatment of SCRT restored expression level of many up- or down-regulated genes in asthma model,and this recovery rate means SCRT could regulate a set of genes having specific TFBS binding sites.CONCLUSION:In this study,we identified a set of genes subjected to similar regulation by SCRT in asthma model in mice.
基金supported by the Natural Science Foundation of Jiangsu Province(BK20200084)the National Natural Science Foundation of China(31871773 and 31820103010)+1 种基金the Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province and Key Talents Project of“Strengthening Health through Science and Education”of Wuxi Health and Family Planning Commission(ZDRC039)Top Talents Project of“Six-one Project”for High-level Health Talents in Jiangsu Province(LGY2018016)。
文摘The high intraspecies heterogeneity of Baciillus coagulans leads to significant phenotypic differences among different strains.Thus,6 B.coagulans strains were tested in the present study using an irritable bowel syndrome(IBS)animal model to determine whether the IBS-alleviating effects of B.coagulans strains are strain-specific.The results of this study showed that the ingestion of B.coagulans GBI-30,6086,and B.coagulans CCFM1041 significantly alleviated IBS symptoms in mice.In contrast,other B.coagulans strains showed no or limited alleviating effects on IBS symptoms.According to our experimental results,the two main common features of these strains were as follows:1)The resistance of vegetative cells to bile salts,and 2)ability to synthesize specific lipids and secondary metabolites.Screening strains based on these two indicators may greatly reduce costs and provide a basis for mining new functional B.coagulans strains.Our results also suggest that administration of B.coagulans could significantly regulate microbiota dysbiosis in animal models.Moreover,the close relationships between the gut microbiota,gut microbiota metabolites,and IBS were further confirmed in this study.
文摘Human adenovirus type 3 （HAdV-3） is widely prevalent all over the world, especially in Asia. The objective of this study is to carry out complete genomic DNA sequencing and the phylogenetic analysis for two strains （Guangzhou01 and Guangzhou02） of HAdV-3 wild virus isolated from South China. Nasopharyngeal secretion aspirate specimens of sick children were inoculated into HEp-2 and HeLa culture tubes, and the cultures were identified by neutralization assay with type-specific reference rabbit antiserum. Type-specific primers were also utilized to confirm the serotype. The restriction fragments of HAdV genome DNA were cloned into pBlueScript SK （ ＋ ） vectors and sequenced, and the 5＇ and 3＇ ends of the linear HAdV-3 genome were directly sequenced with double purified genomic DNA as templates. General features of the HAdV-3 genome sequences were explored by using several bio-software. Phylogenetic analysis was done with MEGA 3.0 software. The genomic sequences of Guangzhou01 and Guangzhou02 possess the same 4 early regions and 5 late regions and have 39 coding sequences and two RNA coding sequences. Other non-coding regions are conservative. Inverted repeats and palindromes were identified in the genome sequences. The genomes of group B human adenovirus as well as HAdV-3 have close phylogenetic relationship with that of chimpanzee adenovirus type 21. The genomic lengths of these two isolated strains are 35 273 bp and 35 269 bp, respectively. The phylogenetic analysis showed that HAdV-B species has some relationship with certain types of chimpanzee adenovirus.
基金the National Key Technology Research and Development Program of China(No.2015BAD12B01)the China Agriculture Research System(No.CARS-40-K13)
文摘Fowl adenovirus serotype 4(FAdV-4)strain SD1511 was isolated from chickens with severe inclusion body hepatitis and hydropericardium syndrome in Shandong Province,China.The isolate was cultured in primary chicken embryo kidney cells.A study of pathogenicity indicated that SD1511 readily infected 7–35-d-old chickens by intramuscular injection and intranasal and oral routes,causing 50%–100%mortality.The 35-d-old chickens suffered more severe infection than 7-and 21-d-old chickens with mortality highest in the intramuscular injection group.The serum from surviving chickens showed potent viral neutralizing capability.The complete genome of SD1511 was sequenced and analyzed.The strain was found to belong to the FAdV-4 cluster with more than 99%identity with the virulent FAdV-4 strains isolated in China in recent years except for some distinct variations,including deletions of open reading frame 27(ORF27),ORF48,and part of ORF19.Our findings suggest that SD1511 might be used as a prototype strain for the study of pathogenesis and vaccine development.
基金funded by the National Natural Science Foundation of China(31771863)Science and Technology Major Project of the Fujian Province of China(2015NZ0002-2)+3 种基金Special Fund for Scientific and Technological Innovation of the Fujian Agriculture and Forestry University(KFA17168A)Doctoral Students of Fujian Agriculture and Forestry University Going Abroad to Cooperative Research(324-112110082)Key Laboratory of Conservation and Utilization of Subtropical Agricultural Biological Resources(SKLCUSA-a201912)supported by ERDF Project“Plants as a tool for sustainable global development”(CZ.02.1.01/0.0/0.0/16_019/0000827)。
文摘Erianthus arundinaceus is a wild relative of sugarcane(Saccharum officinarum L.)with many desirable agronomic traits for sugarcane genetic improvement.However,limited knowledge of the complex genome of hexaploid E.arundinaceus has impeded the development of required molecular tools.Dissecting complex genomes into single chromosomes can simplify analyses.The flow-cytometric sorting of a single chromosome of E.arundinaceus in a Saccharum-Erianthus introgression line is reported.A novel approach called genomic in situ hybridization in suspension was used to discriminate the alien chromosome from sugarcane chromosomes at the same size.A total of 218,000 E.arundinaceus chromosome 1(EaC1)were sorted to>97%purity and amplified DNA was sequenced using Illumina and Pac Bio technologies.The resulting assembly had a 70.93 Mb contig sequence with an N50 of 19.62 kb.A total of 56.69 Mb repeat sequences were predicted,accounting for 79.1%of the chromosome and 2646 genes having a total length of 1.84 Mb that represented 2.59%of the chromosome.Of these genes,1877(70.9%)genes were functionally annotated.The phylogenetic relationship of E.arundinaceus with other species using the chromosome1 sequence revealed that E.arundinaceus was distantly related to Oryza sativa and Zea mays,followed by Sorghum bicolor,and was closely related to S.spontaneum and Saccharum spp.hybrids.This study provides the first insights into the characteristics of EaC1,and the results will provide tools to support molecular improvement and alien introgression breeding of sugarcane.
基金supported by the National Natural Science Foundation of China (31925029,32401815)
文摘African cultivated rice(Oryza glaberrima)was domesticated from its wild progenitor,Oryza barthii.The transition from long-awn to short-awn or awnless glumes was an important evolutionary event during domestication.A QTL analysis of 331 recombinant inbred lines(RILs)using 194 InDel markers identified five quantitative trait loci(QTL)associated with awn length.Locus qObAwn5 made the highest contribution in regulating awn length and was fine-mapped to a 260-kb genomic interval.RNA-seq and RT-qPCR analyses,combined with CRISPR/Cas9-mediated knockout that disruption of gene G12 caused a significant reduction in awn length indicating that G12 was ObAwn5.Genomic analysis revealed a large structural variation(SV)between W1411 and IRGC104165 within this region,characterized by an inversion and two large deletions.Population genomic analyses revealed that all the cultivated African accessions exhibit a domestication-like(Dom-like)pattern,whereas non-cultivated accessions consisted of two distinct types:W1050-like and W1411-like.The W1411-like type was exclusively found in the AA genome of African wild rice.This discovery of ObAwn5 newly substantiates the independent origin of African cultivated rice.
基金funded by Natural Science Foundation of Zhejiang(LQ14C010006)National Natural Science Foundation of China(81501363)Planned Science and Technology Project of Zhejiang(2014C33261)
文摘In the present study,the complete genomes of four common（4/EV71/Wenzhou/CHN/2014,15/EV71/Wenzhou/CHN/2014,116/EV71/Wenzhou/CHN/2014,and 120/EV71/Wenzhou/CHN/2014）and two virulent（11/EV71/Wenzhou/CHN/2014and 109/EV71/Wenzhou/CHN/2014）enterovirus 71（EV71）isolates were sequenced and described.They are 7405 bp in length and belong to EV71 sub-genotype C4 （C4a cluster）.
基金supported in part by fellowship award from the China Scholarship Council to Yuan Wei
文摘The first decade since the completion of the Human Genome Project has been marked with rapid development of genomic technologies and their immediate clinical applications. Genomic analysis using oligonucleotide array comparative genomic hybridization （aCGH） or single nucleotide polymorphism （SNP） chips has been applied to pediatric patients with developmental and intellectual disabilities （DD/ ID）, multiple congenital anomalies （MCA） and autistic spectrum disorders （ASD）. Evaluation of analytical and clinical validities of aCGH showed 〉 99% sensitivity and specificity and increased analytical resolution by higher density probe coverage. Reviews of case series, multi-center comparison and large patient-control studies demonstrated a diagnostic yield of 12%--20%; approximately 60% of these abnormalities were recurrent genomic disorders. This pediatric experience has been extended toward prenatal diagnosis. A series of reports indicated approximately 10% of pregnancies with ultrasound-detected structural anomalies and normal cytogenetic findings had genomic abnormalities, and 30% of these abnormalities were syndromic genomic disorders. Evidence-based practice guidelines and standards for implementing genomic analysis and web-delivered knowledge resources for interpreting genomic findings have been established. The progress from this technology-driven and evidence-based genomic analysis provides not only opportunities to dissect disease-causing mechanisms and develop rational therapeutic interventions but also important lessons for integrating genomic sequencing into pediatric and prenatal genetic evaluation.
基金supported by the National Natural Science Foundation of China(31820103010,31530056,and 31871773)National Key Research and Development Project(2018YFC1604206)+3 种基金Projects of Innovation and Development Pillar Program for Key Industries in Southern Xinjiang of Xinjiang Production and Construction Corps(2018DB002)National FirstClass Discipline Program of Food Science and Technology(JUFSTR20180102)BBSRC Newton Fund Joint Centre Award(BB/J004529/1)Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province。
文摘Emerging evidence shows that some Lactobacillus fermentum(L.fermentum)strains can contribute to the prevention and treatment of ulcerative colitis(UC).In this study,105 isolates of L.fermentum strains were separated from fecal samples of populations in different regions in China and their draft genomes were sequenced.Pan-genomic and phylogenetic characterizations of these strains and four model strains(L.fermentum 3872,CECT5716,IF03956,and VRI003)were performed.Phylogenetic analysis ind icated that there was no significant adaptive evolution between the genomes of L.fermentum strains and the geographical location,sex,ethnicity,and age of the hosts.Three L.fermentum strains(FWXBH115,FGDLZR121,and FXJCJ61)from different branches of the phylogenetic tree and strain type L.fermentum CECT5716 were selected and their anti-inflammatory and immune modulatory activities in a dextran sulphate sodium(DSS)-induced colitis mouse model were further investigated.Both L.fermentum FXJCJ61 and CECT5716 significantly alleviated UC by reducing all colitis-associated histological indices,maintaining mucosal integrity,and stimulating replenishment of short-chain fatty acids(SCFAs),while the other two strains failed to offer similar protection.The anti-inflammato ry mechanisms of L.fermentum FXJCJ61 and CECT5716 were related to the inhibition of nuclear factor kappa-B(NF-κB)signaling pathway activation and enhancement of interleukin 10(IL-10)production.Comparative genomic analysis of these strains identified candidate genes that may contribute to the anti-inflammatory effects of specific L.fermentum strains.
基金Supported by the National Natural Science Foundation of China-Shandong Joint Fund(No.U1706208)the National Natural Science Foundation of China(Nos.41776131,41776130)。
文摘Magnetotactic bacteria(MTB)display magnetotaxis ability because of biomineralization of intracellular nanometer-sized,membrane-bound organelles termed magnetosomes.Despite having been discovered more than half a century,only a few representatives of MTB have been isolated and cultured in the laboratory.In this study,we report the genomic characterization of a novel marine magnetotactic spirillum strain SH-1 belonging to the genus Terasakiella that was recently isolated.A gene encoding haloalkane dehalogenase,which is involved in the degradation of chlorocyclohexane,chlorobenzene,chloroalkane,and chloroalkene,was identified.SH-1 genome contained cysCHI and soxBAZYX genes,thus potentially capable of assimilatory sulfate reduction to H_(2)S and using thiosulfate as electron donors and oxidizing it to sulfate.Genome of SH-1 also contained genes encoding periplasmic dissimilatory nitrate reductases(napAB),assimilatory nitrate reductase(nasA)and assimilatory nitrite reductases(nasB),suggesting that it is capable of gaining energy by converting nitrate to ammonia.The pure culture of Terasakiella sp.SH-1 together with its genomic results off ers new opportunities to examine biology,physiology,and biomineralization mechanisms of MTB.
文摘The genetic base that cotton breeders commonly use to improve Upland cultivars is very narrow.The AD-genome species Gossypium barbadense,G.tomentosum,and G.mustelinum are part of
基金supported by the Special Fund for Agro-scientific Research in the Public Interest,China(201303018)the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS-ASTIP-IVFCAAS)the emarked fund for the China Agriculture Research System(CARS-25-B-01)
文摘A continuous co-evolutionary arms-race between pathogens and their host plants promotes the development of pathogenic factors by microbes, including carbohydrate esterase(CE) genes to overcome the barriers in plant cell walls. Identification of CEs is essential to facilitate their functional and evolutionary investigations; however, current methods may have a limit in detecting some conserved domains, and ignore evolutionary relationships of CEs, as well as do not distinguish CEs from proteases. Here, candidate CEs were annotated using conserved functional domains, and orthologous gene detection and phylogenetic relationships were used to identify new CEs in 16 oomycete genomes, excluding genes with protease domains. In our method, 41 new putative CEs were discovered comparing to current methods, including three CE4, 14 CE5, eight CE12, five CE13, and 11 CE14. We found that significantly more CEs were identified in Phytophthora than in Hyaloperonospora and Pythium, especially CE8, CE12, and CE13 that are putatively involved in pectin degradation. The abundance of these CEs in Phytophthora may be due to a high frequency of multiple-copy genes, supporting by the phylogenetic distribution of CE13 genes, which showed five units of Phytophthora CE13 gene clusters each displaying a species tree like topology, but without any gene from Hyaloperonospora or Pythium species. Additionally, diverse proteins associated with products of CE13 genes were identified in Phytophthora strains. Our analyses provide a highly effective method for CE discovery, complementing current methods, and have the potential to advance our understanding of function and evolution of CEs.
基金supported by the China Animal Disease Prevention and Control Centerthe China Agriculture Research System Poultry-Related Science and Technology Innovation Team of Peking, China (CARS-PSTP)
文摘supported by the China Animal Disease Prevention and Control Center;the China Agriculture Research System Poultry-Related Science and Technology Innovation Team of Peking, China （CARS-PSTP）
基金grants from the National Natural Science Foundation of China(No.81603438 and 81802568).
文摘Background:The Genotype-Tissue Expression was used to expanded normal tissue of the Cancer Genome Atlas database.This study aimed to investigate genes associated with the pathogenesis and prognosis of prostate cancer.Methods:We conducted prognostic related genes for prostate cancer by using transcriptome data from the Genotype-Tissue Expression Project and the Cancer Genome Atlas data sources,which were analyzed using an integrated bioinformatics strategy.Clinically significant modules were distinguished,and GO and KEGG analysis were used to Database for Annotation,Visualization and Integrated Discovery.Further annotation was performed through Gene set enrichment analysis.Logistic regression was carried out to analyze the associations between clinicopathologic characteristics and the hub genes.Logistic regression model and survival analysis were performed.Results:By using data available from the Cancer Genome Atlas and the Genotype-Tissue Expression databases,we here show that 53 differential expression genes were identified.Through GO and KEGG analysis a prognostic related gene signature consisted of GOLM1,EIF4A1,ABCC4,RPL7P16,NPIPB12 and PCA3 was constructed with a good performance in predicting overall survivals.The majority of the six hub genes were associated with clinical characteristics of prostate cancer.Conclusion:These genes might be considered as new targets for further investigating the diagnostic and prognostic biomarkers to facilitate the molecular targeting therapy since they showed differently expressed in prostate cancer and correlate with overall survival prognosis.
