Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the...Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the community by immune evasion mechanisms. Due to mutation within S gene, most Omicron variants have reported S gene target failure (SGTF) with some commercially available PCR kits. Such diagnostic features can be used as markers to screen Omicron. However, Whole Genome Sequencing (WGS) is the only gold standard approach to confirm novel microorganisms at genetically level as similar mutations can also be found in other variants that are circulating at low frequencies worldwide. This Retrospective study is aimed to assess RT-PCR sensitivity in the detection of S gene target failure in comparison with whole genome sequencing to detect variants of Omicron. Methods: We have analysed retrospective data of SARS-CoV-2 positive RT-PCR samples for S gene target failure (SGTF) with TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) and combined with sequencing technologies to study the emerged pattern of SARS-CoV-2 variants during third wave at the tertiary care centre, Surat. Results: From the first day of December 2021 till the end of February 2022, a total of 321,803 diagnostic RT-PCR tests for SARS-CoV-2 were performed, of which 20,566 positive cases were reported at our tertiary care centre with an average cumulative positivity of 6.39% over a period of three months. In the month of December 21 samples characterized by the SGTF (70/129) were suggestive of being infected by the Omicron variant and identified as Omicron (B.1.1.529 lineage) when sequence. In the month of January, we analysed a subset of samples (n = 618) with SGTF (24%) and without SGTF (76%) with Ct values Conclusions: During the COVID-19 pandemic, it took almost more than 15 days to diagnose infection and identify pathogen by sequencing technology. In contrast to that molecular assay provided quick identification with the help of SGTF phenomenon within 5 hours of duration. This strategy helps scientists and health policymakers for the quick isolation and identification of clusters. That ultimately results in a decreased transmission of pathogen among the community.展开更多
Dental implants have restored masticatory function to over 100000000 individuals,yet almost 1000000 implants fail each year due to peri-implantitis,a disease triggered by peri-implant microbial dysbiosis.Our ability t...Dental implants have restored masticatory function to over 100000000 individuals,yet almost 1000000 implants fail each year due to peri-implantitis,a disease triggered by peri-implant microbial dysbiosis.Our ability to prevent and treat peri-implantitis is hampered by a paucity of knowledge of how these biomes are acquired and the factors that engender normobiosis.Therefore,we combined a 3-month interventional study of 15 systemically and periodontally healthy adults with whole genome sequencing,finescale enumeration and graph theoretics to interrogate colonization dynamics in the pristine peri-implant sulcus.We discovered that colonization trajectories of implants differ substantially from adjoining teeth in acquisition of new members and development of functional synergies.Source-tracking algorithms revealed that this niche is initially seeded by bacteria trapped within the coverscrew chamber during implant placement.These pioneer species stably colonize the microbiome and exert a sustained influence on the ecosystem by serving as anchors of influential hubs and by providing functions that enable cell replication and biofilm maturation.Unlike the periodontal microbiome,recruitment of new members to the peri-implant community occurs on nepotistic principles.Maturation is accompanied by a progressive increase in anaerobiosis,however,the predominant functionalities are oxygen-dependent over the 12-weeks.The peri-implant community is easily perturbed following crown placement,but demonstrates remarkable resilience;returning to pre-perturbation states within three weeks.This study highlights important differences in the development of the periodontal and peri-implant ecosystems,and signposts the importance of placing implants in periodontally healthy individuals or following the successful resolution of periodontal disease.展开更多
Objective Pseudomonas aeruginosa(P.aeruginosa)is a prevalent pathogenic bacterium involved in meningitis;however,the virulence factors contributing to this disease remain poorly understood.Methods The virulence of the...Objective Pseudomonas aeruginosa(P.aeruginosa)is a prevalent pathogenic bacterium involved in meningitis;however,the virulence factors contributing to this disease remain poorly understood.Methods The virulence of the P.aeruginosa A584,isolated from meningitis samples,was evaluated by constructing in vitro blood-brain barrier and in vivo systemic infection models.qPCR,whole-genome sequencing,and drug efflux assays of A584 were performed to analyze the virulence factors.Results Genomic sequencing showed that A584 formed a phylogenetic cluster with the reference strains NY7610,DDRC3,Pa58,and Pa124.Its genome includes abundant virulence factors,such as hemolysin,the Type IV secretion system,and pyoverdine.A584 is a multidrug-resistant strain,and its wide-spectrum resistance is associated with enhanced drug efflux.Moreover,this strain caused significantly more severe damage to the blood-brain barrier than the standard strain,PAO1.qPCR assays further revealed the downregulation of the blood-brain barrier-associated proteins Claudin-5 and Occludin by A584.During systemic infection,A584 exhibited a higher capacity of brain colonization than PAO1(37.1×10^(6) CFU/g brain versus 2.5×10^(6) CFU/g brain),leading to higher levels of the proinflammatory factors IL-1βand TNF-α.Conclusion This study sheds light on the virulence factors of P.aeruginosa involved in meningitis.展开更多
The potherb mustard Xuecai(XC)cultivar is a cruciferous vegetable that is popular either fresh or pickled.Due to the deep notches in the edges of leaves in mustard XC,this plant can be said to have multipinnately lobe...The potherb mustard Xuecai(XC)cultivar is a cruciferous vegetable that is popular either fresh or pickled.Due to the deep notches in the edges of leaves in mustard XC,this plant can be said to have multipinnately lobed leaves.The net photosynthesis of lobed leaves is significantly greater than that of simple leaves.However,the molecular mechanism of leaf shape variation has not been determined.Here,we used HiFi and Hi-C data to assemble the XC genome.The genome was 961.72 Mb in size,with a contig N50 value of 6.565 Mb.The XC genome was compared with four previously sequenced mustard genomes,and the genomic collinearity regions,SNPs,and indels were identified.Five BjRCO genes were found on chromosome(Chr.)A10 in potherb mustard XC when the BjRCO gene locus was compared against other sequenced B.juncea genomes.Segmental duplication was found to contribute to the BjRCO gene copy number.The transcript expression of BjRCO genes was greater in multipinnately lobed leaves than in sawtooth-like leaves.Together,these findings indicate that both the greater copy number and the expression level of BjRCO genes regulate leaf shape from simple to complex in B.juncea.Gene editing of the BjRCO gene from XC changed the leaf shape from multipinnately lobed to simple.The high-quality XC genome sequence not only provides new insight into B.juncea leaf-type genomics but also helps in deciphering leaf shape variation.Our study provides insights into the variation and evolution of important traits in Brassica plants through a comparative analysis of the sequenced genomes.展开更多
Ectromelia virus(ECTV),a member of the Orthopoxvirus genus,serves as both a causative agent of mousepox and a pivotal surrogate model for studying highly pathogenic orthopoxviruses.Although genomic data on ECTV remain...Ectromelia virus(ECTV),a member of the Orthopoxvirus genus,serves as both a causative agent of mousepox and a pivotal surrogate model for studying highly pathogenic orthopoxviruses.Although genomic data on ECTV remains limited,we report the isolation and characterization of a novel strain,ECTV-C-Tan-GD01,obtained from rodents in Guangdong Province,China.Nanopore sequencing yielded a complete genome(199 annotated genes,including one gene truncated at the C-terminus)with inverted terminal repeats(ITRs)harboring a conserved hairpin structure.Notably,a frameshift-inducing“G”deletion in the EV159 gene resulted in the truncation of a semaphorin-like protein.In vitro assays demonstrated cell-associated viral replication kinetics,with maximum titers achieved earlier in Vero/HeLa cells(72 h)than in BHK-21/CEF cells(84 h).Murine challenge experiments revealed extreme virulence(LD50<1 plaque-forming unit(PFU)via intranasal/footpad routes)and hepatosplenic tropism.Furthermore,ECTV-C-Tan-GD01 exhibited utility in evaluating orthopoxvirus countermeasures:a single dose of vaccinia virus Tiantan(VTT)or non-replicating vaccinia virus Tiantan(NTV)conferred cross-protection,while tecovirimat(ST-246),cidofovir(CDV),and brincidofovir(initially CMX001)significantly reduced viral loads and pathology.This study establishes ECTV-C-Tan-GD01 as a dual-purpose resource for probing orthopoxvirus evolution and advancing therapeutic development.展开更多
The inappropriate use of cephalosporins lead to the occurrence and global spread of bacteria resistant to these antimicrobials.In this study,we isolated four Escherichia albertii strains from broilers in eastern China...The inappropriate use of cephalosporins lead to the occurrence and global spread of bacteria resistant to these antimicrobials.In this study,we isolated four Escherichia albertii strains from broilers in eastern China.The antimicrobial susceptibility and genomic characterization of these E.albertii isolates were determined.Our results revealed that these four E.albertii isolates exhibited resistance to tetracyclines,chloramphenicol,β-lactams,aminoglycosides,polymyxin B,sulfonamides,quinolones,and other antimicrobials.Among them,EA04 isolate was multidrug resistant and harbored extended-spectrumβ-lactamases(ESBL)genes blaCTX-Mand blaTEM.Whole genome sequencing and core-genome multilocus sequence typing(cgMLST)based on all ST4638 E.albertii for EA04 inferred highly probable epidemiological links between selected human isolates.Additionally,the ESBL genes blaTEM-141and blaCTX-M-55were coexistent in an approximately 75 kb Inc FII plasmid pEA04.2 in EA04.Comparative analysis indicated that genes blaTEM-141and blaCTX-M-55were located in IS15-blaCTX-M-55-wbu C-blaTEM-141-IS26 region,which similar structures were identified in various bacteria.Furthermore,the plasmid pEA04.2 could be transferable to E.coli EC600 and lead to the resistance to third-generation cephalosporins.These results suggested that chicken potentially serve as a reservoir for multidrug resistant E.albertii,which increases the risk of horizontal transfer of antimicrobial resistance between humans,animals and environment.展开更多
Lactiplantibacillus plantarum MWFLp-182 was originally isolated from the feces of long-living elderly individuals in Hezhou city,Guangxi,China.L.plantarum MWFLp-182 showed favorable gastric and intestinal tolerance co...Lactiplantibacillus plantarum MWFLp-182 was originally isolated from the feces of long-living elderly individuals in Hezhou city,Guangxi,China.L.plantarum MWFLp-182 showed favorable gastric and intestinal tolerance compared with Lactiplantibacillus rhamnosus GG(LGG).L.plantarum MWFLp-182 was further examined for its antioxidant and anti-inflammatory activity in ABAP-treated HT-29 cells.Importantly,it enhanced the expression of anti-inflammatory factor(interleukin-10(IL-10)),antioxidant cytokines(superoxide dismutase(SOD),glutathione peroxidase(GPx),nuclear factor erythroid 2-related factor(Nrf2),and hemeoxygenase 1(HO-1)),B-cell lymphoma-2(Bcl-2),and tight junction(Zonula occludens protein 1(ZO-1),Claudin-1,and Occludin)proteins and genes,and reduced reactive oxygen species(ROS).The complete genome of L.plantarum MWFLp-182 contained a single circular chromosome that was 3257196 bp long,with a G+C content of 44.49%,and a single circular plasmid that was 53560 bp long.The genes tpx,trx A,trx B,npr,nrd H,dps,rec A,gpx,gsh A and ars C in this strain were related to antioxidant function;the key genes involved in antioxidant function were further investigated.In this study,we identified a probiotic candidate with antioxidant properties.展开更多
Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and h...Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.展开更多
Drought stress is an important factor affecting soybean yield.Improving drought tolerance of soybean varieties can increase yield and yield stability when the stress occurs.Identifying QTL related to drought tolerance...Drought stress is an important factor affecting soybean yield.Improving drought tolerance of soybean varieties can increase yield and yield stability when the stress occurs.Identifying QTL related to drought tolerance using molecular marker-assisted selection is able to facilitate the development of drought-tolerant soybean varieties.In this study,we used a high-yielding and drought-sensitive cultivar‘Zhonghuang 35’and a drought-tolerant cultivar‘Jindou 21’to establish F6:9 recombinant inbred lines.We constructed a highdensity genetic map using specific locus amplified fragment sequencing(SLAF-Seq)technology.The genetic map contained 8078 SLAF markers distributing across 20 soybean chromosomes with a total genetic distance of 3780.98 c M and an average genetic distance of0.59 c M between adjacent markers.Two treatments(irrigation and drought)were used in the field tests,the Additive-Inclusive Composite Interval Mapping(ICIM-ADD)was used to call QTL,and plant height and seed weight per plant were used as the indicators of drought tolerance.We identified a total of 23 QTL related to drought tolerance.Among them,seven QTL(q PH2,q PH6,q PH7,q PH17,q PH19-1,q PH19-2,and q PH19-3)on chromosomes 2,6,7,17,and 19 were related to plant height,and five QTL(q SWPP2,q SWPP6,q SWPP13,q SWPP17,and q SWPP19)on chromosomes 2,6,13,17,and 19 were related to seed weight and could be considered as the major QTL.In addition,three common QTL(q PH6/q SWPP6,q PH17/q SWPP17,and q PH19-3/q SWPP19)for both plant height and seed weight per plant were located in the same genomic regions on the same chromosomes.Three(q PH2,q PH17,and q PH19-2)and four novel QTL(q SWPP2,q SWPP13,q SWPP17,and q SWPP19)were identified for plant height and seed weight per plant,respectively.Two pairs of QTL(q PH2/q SWPP2 and q PH17/q SWPP17)were also common for both plant height and seed weight per plant.These QTL and closely linked SLAF markers could be used to accelerate breeding for drought tolerant cultivars via MAS.展开更多
Objective:Epithelial cancers often originate from progenitor cells,while the origin of hepatocellular carcinoma(HCC)is still controversial.HCC,one of the deadliest cancers,is closely linked with liver injuries and chr...Objective:Epithelial cancers often originate from progenitor cells,while the origin of hepatocellular carcinoma(HCC)is still controversial.HCC,one of the deadliest cancers,is closely linked with liver injuries and chronic inflammation,which trigger massive infiltration of bone marrow-derived cells(BMDCs)during liver repair.Methods:To address the possible roles of BMDCs in HCC origination,we established a diethylnitrosamine(DEN)-induced HCC model in bone marrow transplanted mice.Immunohistochemistry and frozen tissue immunofluorescence were used to verify DENinduced HCC in the pathology of the disease.The cellular origin of DEN-induced HCC was further studied by single cell sequencing,single-cell nested PCR,and immunofluorescence-fluorescence in situ hybridization.Results:Studies by using single cell sequencing and biochemical analysis revealed that HCC cells in these mice were coming from donor mice BMDCs,and not from recipient mice.Furthermore,the copy numbers of mouse orthologs of several HCC-related genes previously reported in human HCC were also altered in our mouse model.DEN-induced HCCs exhibited a similar histological phenotype and genomic profile as human HCCs.Conclusions:These results suggested that BMDCs are an important origin of HCC,which provide important clues to HCC prevention,detection,and treatments.展开更多
As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome （BAC） by BAC strategy. The current physical contigs are expec...As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome （BAC） by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa.展开更多
Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1%of azoospermia or severe oligospermia.However,the underlying mechanisms of pathogenesis and...Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1%of azoospermia or severe oligospermia.However,the underlying mechanisms of pathogenesis and etiologies are still largely unknown.Herein,we investigated apparently balanced interchromosomal structural rearrangements in six cases with azoospermia/severe oligospermia to comprehensively identify and delineate cryptic structural rearrangements and the related copy number variants.In addition,high read-depth genome sequencing(GS)(30-fold)was performed to investigate point mutations causative of male infertility.Mate-pair GS(4-fold)revealed additional structural rearrangements and/or copy number changes in 5 of 6 cases and detected a total of 48 rearrangements.Overall,the breakpoints caused truncations of 30 RefSeq genes,five of which were associated with spermatogenesis.Furthermore,the breakpoints disrupted 43 topological-associated domains.Direct disruptions or potential dysregulations of genes,which play potential roles in male germ cell development,apoptosis,and spermatogenesis,were found in all cases(n=6).In addition,high read-depth GS detected dual molecular findings in case MI6,involving a complex rearrangement and two point mutations in the gene DNAH1.Overall,our study provided the molecular characteristics of apparently balanced interchromosomal structural rearrangements in patients with male infertility.We demonstrated the complexity of chromosomal structural rearrangements,potential gene disruptions/dysregulation and single-gene mutations could be the contributing mechanisms underlie male infertility.展开更多
Due to evolving molecular and informatics technologies,modern genome sequencing projects have more different characteristics than what most biologists have become accustomed to during the capillary-based sequencing er...Due to evolving molecular and informatics technologies,modern genome sequencing projects have more different characteristics than what most biologists have become accustomed to during the capillary-based sequencing era.In this paper,we explore the characteristics that made past insect genome projects successful and place them in the context of next-generation sequencing.By taking into account the intricacies of whitefly biology and the community,we present a roadmap for whitefly-omics,which focuses on the formation of an international consortium,deployment of informatic platforms and realistic generation of reference sequence data.展开更多
Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly ...Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. Methods In this proof-of-concept study using Enterovirus 71 （EV71） and Coxsackievirus A16 （CA16） strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Results Within the first minute （min） of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min （on average）, 99% identity was achieved for 10 CA16 strains in a single run. Conclusion MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use.展开更多
Medicinal plants are renowned for their abundant production of secondary metabolites,which exhibit notable pharmacological activities and great potential for drug development.The biosynthesis of secondary metabolites ...Medicinal plants are renowned for their abundant production of secondary metabolites,which exhibit notable pharmacological activities and great potential for drug development.The biosynthesis of secondary metabolites is highly intricate and influenced by various intrinsic and extrinsic factors,resulting in substantial species diversity and content variation.Consequently,precise regulation of secondary metabolite synthesis is of utmost importance.In recent years,genome sequencing has emerged as a valuable tool for investigating the synthesis and regulation of secondary metabolites in medicinal plants,facilitated by the widespread use of high-throughput sequencing technologies.This review highlights the latest advancements in genome sequencing within this field and presents several strategies for studying secondary metabolites.Specifically,the article elucidates how genome sequencing can unravel the pathways for secondary metabolite synthesis in medicinal plants,offering insights into the functions and regulatory mechanisms of participating enzymes.Comparative analyses of plant genomes allow identification of shared pathways of metabolite synthesis among species,thereby providing novel avenues for obtaining cost-effective biosynthetic intermediates.By examining individual genomic variations,genes or gene clusters associated with the synthesis of specific compounds can be discovered,indicating potential targets and directions for drug development and the exploration of alternative compound sources.Moreover,the advent of gene-editing technology has enabled the precise modifications of medicinal plant genomes.Optimization of specific secondary metabolite synthesis pathways becomes thus feasible,enabling the precise editing of target genes to regulate secondary metabolite production within cells.These findings serve as valuable references and lessons for future drug development endeavors,conservation of rare resources,and the exploration of new resources.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
Apis mellifera filamentous virus(Am FV)is a large DNA virus that is endemic in honeybee colonies.The genome sequence of the Am FV Swiss isolate(Am FV CH–C05)has been reported,but so far very few molecular studies hav...Apis mellifera filamentous virus(Am FV)is a large DNA virus that is endemic in honeybee colonies.The genome sequence of the Am FV Swiss isolate(Am FV CH–C05)has been reported,but so far very few molecular studies have been conducted on this virus.In this study,we isolated and purified Am FV(Am FV CN)from Chinese honeybee(Apis mellifera)colonies and elucidated its genomics and proteomics.Electron microscopy showed ovoid purified virions with dimensions of 300–500×210–285 nm,wrapping a 3165×40 nm filamentous nucleocapsid in three figure-eight loops.Unlike Am FV CH–C05,which was reported to have a circular genome,our data suggest that Am FV CN has a linear genome of approximately 493 kb.A total of 197 ORFs were identified,among which36 putative genes including 18 baculoviral homologs were annotated.The overall nucleotide similarity between the CN and CH–C05 isolates was 96.9%.Several ORFs were newly annotated in Am FV CN,including homologs of per os infectivity factor 4(PIF4)and a putative integrase.Phylogenomic analysis placed Am FVs on a separate branch within the newly proposed virus class Naldaviricetes.Proteomic analysis revealed 47 Am FV virionassociated proteins,of which 14 had over 50%sequence coverage,suggesting that they are likely to be main structural proteins.In addition,all six of the annotated PIFs(PIF-0–5)were identified by proteomics,suggesting that they may function as entry factors in Am FV infection.This study provides fundamental information regarding the molecular biology of Am FV.展开更多
Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be a...Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be associated with many physiological and pathological conditions（Bai and Wong,2005）.展开更多
The microbial potential of Penicillium has received critical attention.The present research aimed to elucidate the efficacy of crude enzyme secreted from Penicillium oxalicum WX-209 in degrading citrus segments and ev...The microbial potential of Penicillium has received critical attention.The present research aimed to elucidate the efficacy of crude enzyme secreted from Penicillium oxalicum WX-209 in degrading citrus segments and evaluate the safety of the process.Results showed that citrus segment membranes gradually dissolved after treatment with the crude enzyme solution,indicating good degradation capability.No significant differences in body weight,food ingestion rate,hematology,blood biochemistry,and weight changes of different organs were found between the enzyme intake and control groups.Serial experiments showed that the crude enzyme had high biological safety.Moreover,the whole genome of P.oxalicum WX-209 was sequenced by PacBio and Illumina platforms.Twenty-five scaffolds were assembled to generate 36 Mbp size of genome sequence comprising 11369 predicted genes modeled with a GC content of 48.33%.A total of 592 genes were annotated to encode enzymes related to carbohydrates,and some degradation enzyme genes were identified in strain P.oxalicum WX-209.展开更多
文摘Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the community by immune evasion mechanisms. Due to mutation within S gene, most Omicron variants have reported S gene target failure (SGTF) with some commercially available PCR kits. Such diagnostic features can be used as markers to screen Omicron. However, Whole Genome Sequencing (WGS) is the only gold standard approach to confirm novel microorganisms at genetically level as similar mutations can also be found in other variants that are circulating at low frequencies worldwide. This Retrospective study is aimed to assess RT-PCR sensitivity in the detection of S gene target failure in comparison with whole genome sequencing to detect variants of Omicron. Methods: We have analysed retrospective data of SARS-CoV-2 positive RT-PCR samples for S gene target failure (SGTF) with TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) and combined with sequencing technologies to study the emerged pattern of SARS-CoV-2 variants during third wave at the tertiary care centre, Surat. Results: From the first day of December 2021 till the end of February 2022, a total of 321,803 diagnostic RT-PCR tests for SARS-CoV-2 were performed, of which 20,566 positive cases were reported at our tertiary care centre with an average cumulative positivity of 6.39% over a period of three months. In the month of December 21 samples characterized by the SGTF (70/129) were suggestive of being infected by the Omicron variant and identified as Omicron (B.1.1.529 lineage) when sequence. In the month of January, we analysed a subset of samples (n = 618) with SGTF (24%) and without SGTF (76%) with Ct values Conclusions: During the COVID-19 pandemic, it took almost more than 15 days to diagnose infection and identify pathogen by sequencing technology. In contrast to that molecular assay provided quick identification with the help of SGTF phenomenon within 5 hours of duration. This strategy helps scientists and health policymakers for the quick isolation and identification of clusters. That ultimately results in a decreased transmission of pathogen among the community.
基金supported by National Institutes of Health R03DE027492 to Shareef Dabdoubsupported by National Institutes of Health,project number 7R01DE027857-06supported by National Institutes of Health R56DE033913 awarded to Purnima Kumar.
文摘Dental implants have restored masticatory function to over 100000000 individuals,yet almost 1000000 implants fail each year due to peri-implantitis,a disease triggered by peri-implant microbial dysbiosis.Our ability to prevent and treat peri-implantitis is hampered by a paucity of knowledge of how these biomes are acquired and the factors that engender normobiosis.Therefore,we combined a 3-month interventional study of 15 systemically and periodontally healthy adults with whole genome sequencing,finescale enumeration and graph theoretics to interrogate colonization dynamics in the pristine peri-implant sulcus.We discovered that colonization trajectories of implants differ substantially from adjoining teeth in acquisition of new members and development of functional synergies.Source-tracking algorithms revealed that this niche is initially seeded by bacteria trapped within the coverscrew chamber during implant placement.These pioneer species stably colonize the microbiome and exert a sustained influence on the ecosystem by serving as anchors of influential hubs and by providing functions that enable cell replication and biofilm maturation.Unlike the periodontal microbiome,recruitment of new members to the peri-implant community occurs on nepotistic principles.Maturation is accompanied by a progressive increase in anaerobiosis,however,the predominant functionalities are oxygen-dependent over the 12-weeks.The peri-implant community is easily perturbed following crown placement,but demonstrates remarkable resilience;returning to pre-perturbation states within three weeks.This study highlights important differences in the development of the periodontal and peri-implant ecosystems,and signposts the importance of placing implants in periodontally healthy individuals or following the successful resolution of periodontal disease.
基金supported by National Natural Science Foundation of China,China(32170102)Natural Science Foundation of Tianjin(21JCYBJC01420)the Fundamental Research Funds for the Central Universities(63233050)。
文摘Objective Pseudomonas aeruginosa(P.aeruginosa)is a prevalent pathogenic bacterium involved in meningitis;however,the virulence factors contributing to this disease remain poorly understood.Methods The virulence of the P.aeruginosa A584,isolated from meningitis samples,was evaluated by constructing in vitro blood-brain barrier and in vivo systemic infection models.qPCR,whole-genome sequencing,and drug efflux assays of A584 were performed to analyze the virulence factors.Results Genomic sequencing showed that A584 formed a phylogenetic cluster with the reference strains NY7610,DDRC3,Pa58,and Pa124.Its genome includes abundant virulence factors,such as hemolysin,the Type IV secretion system,and pyoverdine.A584 is a multidrug-resistant strain,and its wide-spectrum resistance is associated with enhanced drug efflux.Moreover,this strain caused significantly more severe damage to the blood-brain barrier than the standard strain,PAO1.qPCR assays further revealed the downregulation of the blood-brain barrier-associated proteins Claudin-5 and Occludin by A584.During systemic infection,A584 exhibited a higher capacity of brain colonization than PAO1(37.1×10^(6) CFU/g brain versus 2.5×10^(6) CFU/g brain),leading to higher levels of the proinflammatory factors IL-1βand TNF-α.Conclusion This study sheds light on the virulence factors of P.aeruginosa involved in meningitis.
基金supported by grants from the National Natural Science Foundation of China(32002056)the Science and Technology Research Key Project of Henan Province,China(242102111138)。
文摘The potherb mustard Xuecai(XC)cultivar is a cruciferous vegetable that is popular either fresh or pickled.Due to the deep notches in the edges of leaves in mustard XC,this plant can be said to have multipinnately lobed leaves.The net photosynthesis of lobed leaves is significantly greater than that of simple leaves.However,the molecular mechanism of leaf shape variation has not been determined.Here,we used HiFi and Hi-C data to assemble the XC genome.The genome was 961.72 Mb in size,with a contig N50 value of 6.565 Mb.The XC genome was compared with four previously sequenced mustard genomes,and the genomic collinearity regions,SNPs,and indels were identified.Five BjRCO genes were found on chromosome(Chr.)A10 in potherb mustard XC when the BjRCO gene locus was compared against other sequenced B.juncea genomes.Segmental duplication was found to contribute to the BjRCO gene copy number.The transcript expression of BjRCO genes was greater in multipinnately lobed leaves than in sawtooth-like leaves.Together,these findings indicate that both the greater copy number and the expression level of BjRCO genes regulate leaf shape from simple to complex in B.juncea.Gene editing of the BjRCO gene from XC changed the leaf shape from multipinnately lobed to simple.The high-quality XC genome sequence not only provides new insight into B.juncea leaf-type genomics but also helps in deciphering leaf shape variation.Our study provides insights into the variation and evolution of important traits in Brassica plants through a comparative analysis of the sequenced genomes.
基金supported by the Natural Science Foundation of Beijing(7254390)the Youth Science Foundation of Chinese Center for Disease Control and Prevention(2024A103)to W.C.C,the National Key ResearchDevelopment Program of China(2022YFC2304100,2023YFD1800405).
文摘Ectromelia virus(ECTV),a member of the Orthopoxvirus genus,serves as both a causative agent of mousepox and a pivotal surrogate model for studying highly pathogenic orthopoxviruses.Although genomic data on ECTV remains limited,we report the isolation and characterization of a novel strain,ECTV-C-Tan-GD01,obtained from rodents in Guangdong Province,China.Nanopore sequencing yielded a complete genome(199 annotated genes,including one gene truncated at the C-terminus)with inverted terminal repeats(ITRs)harboring a conserved hairpin structure.Notably,a frameshift-inducing“G”deletion in the EV159 gene resulted in the truncation of a semaphorin-like protein.In vitro assays demonstrated cell-associated viral replication kinetics,with maximum titers achieved earlier in Vero/HeLa cells(72 h)than in BHK-21/CEF cells(84 h).Murine challenge experiments revealed extreme virulence(LD50<1 plaque-forming unit(PFU)via intranasal/footpad routes)and hepatosplenic tropism.Furthermore,ECTV-C-Tan-GD01 exhibited utility in evaluating orthopoxvirus countermeasures:a single dose of vaccinia virus Tiantan(VTT)or non-replicating vaccinia virus Tiantan(NTV)conferred cross-protection,while tecovirimat(ST-246),cidofovir(CDV),and brincidofovir(initially CMX001)significantly reduced viral loads and pathology.This study establishes ECTV-C-Tan-GD01 as a dual-purpose resource for probing orthopoxvirus evolution and advancing therapeutic development.
基金supported by the National Key Research and Development Program of China(2021YFD1800402)the National Natural Science Foundation of China(32172856,31972654 and 32302881)+1 种基金the Natural Science Foundation of Shanghai,China(22ZR1476100 and 23ZR1476600)the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(SHVRI-ASTIP-2014-8)。
文摘The inappropriate use of cephalosporins lead to the occurrence and global spread of bacteria resistant to these antimicrobials.In this study,we isolated four Escherichia albertii strains from broilers in eastern China.The antimicrobial susceptibility and genomic characterization of these E.albertii isolates were determined.Our results revealed that these four E.albertii isolates exhibited resistance to tetracyclines,chloramphenicol,β-lactams,aminoglycosides,polymyxin B,sulfonamides,quinolones,and other antimicrobials.Among them,EA04 isolate was multidrug resistant and harbored extended-spectrumβ-lactamases(ESBL)genes blaCTX-Mand blaTEM.Whole genome sequencing and core-genome multilocus sequence typing(cgMLST)based on all ST4638 E.albertii for EA04 inferred highly probable epidemiological links between selected human isolates.Additionally,the ESBL genes blaTEM-141and blaCTX-M-55were coexistent in an approximately 75 kb Inc FII plasmid pEA04.2 in EA04.Comparative analysis indicated that genes blaTEM-141and blaCTX-M-55were located in IS15-blaCTX-M-55-wbu C-blaTEM-141-IS26 region,which similar structures were identified in various bacteria.Furthermore,the plasmid pEA04.2 could be transferable to E.coli EC600 and lead to the resistance to third-generation cephalosporins.These results suggested that chicken potentially serve as a reservoir for multidrug resistant E.albertii,which increases the risk of horizontal transfer of antimicrobial resistance between humans,animals and environment.
基金supported by the Natural Science Foundation of Guangxi,China(2020GXNSFBA297083)the National Natural Science Foundation of China(32072193)。
文摘Lactiplantibacillus plantarum MWFLp-182 was originally isolated from the feces of long-living elderly individuals in Hezhou city,Guangxi,China.L.plantarum MWFLp-182 showed favorable gastric and intestinal tolerance compared with Lactiplantibacillus rhamnosus GG(LGG).L.plantarum MWFLp-182 was further examined for its antioxidant and anti-inflammatory activity in ABAP-treated HT-29 cells.Importantly,it enhanced the expression of anti-inflammatory factor(interleukin-10(IL-10)),antioxidant cytokines(superoxide dismutase(SOD),glutathione peroxidase(GPx),nuclear factor erythroid 2-related factor(Nrf2),and hemeoxygenase 1(HO-1)),B-cell lymphoma-2(Bcl-2),and tight junction(Zonula occludens protein 1(ZO-1),Claudin-1,and Occludin)proteins and genes,and reduced reactive oxygen species(ROS).The complete genome of L.plantarum MWFLp-182 contained a single circular chromosome that was 3257196 bp long,with a G+C content of 44.49%,and a single circular plasmid that was 53560 bp long.The genes tpx,trx A,trx B,npr,nrd H,dps,rec A,gpx,gsh A and ars C in this strain were related to antioxidant function;the key genes involved in antioxidant function were further investigated.In this study,we identified a probiotic candidate with antioxidant properties.
基金Supported by the National Natural Science Foundations of China(3127218631301791)
文摘Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.
基金supported by the National Key Research and Development Program of China(2016YFD0100201 and 2016YFD0100304)the National Science and Technological Innovation Program of China。
文摘Drought stress is an important factor affecting soybean yield.Improving drought tolerance of soybean varieties can increase yield and yield stability when the stress occurs.Identifying QTL related to drought tolerance using molecular marker-assisted selection is able to facilitate the development of drought-tolerant soybean varieties.In this study,we used a high-yielding and drought-sensitive cultivar‘Zhonghuang 35’and a drought-tolerant cultivar‘Jindou 21’to establish F6:9 recombinant inbred lines.We constructed a highdensity genetic map using specific locus amplified fragment sequencing(SLAF-Seq)technology.The genetic map contained 8078 SLAF markers distributing across 20 soybean chromosomes with a total genetic distance of 3780.98 c M and an average genetic distance of0.59 c M between adjacent markers.Two treatments(irrigation and drought)were used in the field tests,the Additive-Inclusive Composite Interval Mapping(ICIM-ADD)was used to call QTL,and plant height and seed weight per plant were used as the indicators of drought tolerance.We identified a total of 23 QTL related to drought tolerance.Among them,seven QTL(q PH2,q PH6,q PH7,q PH17,q PH19-1,q PH19-2,and q PH19-3)on chromosomes 2,6,7,17,and 19 were related to plant height,and five QTL(q SWPP2,q SWPP6,q SWPP13,q SWPP17,and q SWPP19)on chromosomes 2,6,13,17,and 19 were related to seed weight and could be considered as the major QTL.In addition,three common QTL(q PH6/q SWPP6,q PH17/q SWPP17,and q PH19-3/q SWPP19)for both plant height and seed weight per plant were located in the same genomic regions on the same chromosomes.Three(q PH2,q PH17,and q PH19-2)and four novel QTL(q SWPP2,q SWPP13,q SWPP17,and q SWPP19)were identified for plant height and seed weight per plant,respectively.Two pairs of QTL(q PH2/q SWPP2 and q PH17/q SWPP17)were also common for both plant height and seed weight per plant.These QTL and closely linked SLAF markers could be used to accelerate breeding for drought tolerant cultivars via MAS.
基金supported by the grants from the National Natural Science Foundation of China(Grant No.81902401,81972656,31671421,81970107,81600083)the National 135 Major Project of China(Grant No.2018ZX10723204,2018ZX10302205)+3 种基金the Natural Science Foundation of Tianjin(Grant No.19JCQNJC09000)the Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences(2018PT32034)CAMS Innovation Fund for Medical Sciences(Grant No.2016-12M-1-003)supported by the China Scholarship Council(Grant No.201906940003)。
文摘Objective:Epithelial cancers often originate from progenitor cells,while the origin of hepatocellular carcinoma(HCC)is still controversial.HCC,one of the deadliest cancers,is closely linked with liver injuries and chronic inflammation,which trigger massive infiltration of bone marrow-derived cells(BMDCs)during liver repair.Methods:To address the possible roles of BMDCs in HCC origination,we established a diethylnitrosamine(DEN)-induced HCC model in bone marrow transplanted mice.Immunohistochemistry and frozen tissue immunofluorescence were used to verify DENinduced HCC in the pathology of the disease.The cellular origin of DEN-induced HCC was further studied by single cell sequencing,single-cell nested PCR,and immunofluorescence-fluorescence in situ hybridization.Results:Studies by using single cell sequencing and biochemical analysis revealed that HCC cells in these mice were coming from donor mice BMDCs,and not from recipient mice.Furthermore,the copy numbers of mouse orthologs of several HCC-related genes previously reported in human HCC were also altered in our mouse model.DEN-induced HCCs exhibited a similar histological phenotype and genomic profile as human HCCs.Conclusions:These results suggested that BMDCs are an important origin of HCC,which provide important clues to HCC prevention,detection,and treatments.
基金This work was supported by grants from the National Academy of Agricultural Science(Code #200901FHT020508369)the BioGreen21 Program(Code #20050301034438 and Code #20070301034037),Rural Development Administration, Republic of Korea
文摘As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome （BAC） by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa.
基金supported by the National Natural Science Foundation of China(No.31801042)the Health and Medical Research Fund(No.04152666 and No.07180576)General Research Fund(No.14115418),and Direct Grant(No.2020.052).
文摘Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1%of azoospermia or severe oligospermia.However,the underlying mechanisms of pathogenesis and etiologies are still largely unknown.Herein,we investigated apparently balanced interchromosomal structural rearrangements in six cases with azoospermia/severe oligospermia to comprehensively identify and delineate cryptic structural rearrangements and the related copy number variants.In addition,high read-depth genome sequencing(GS)(30-fold)was performed to investigate point mutations causative of male infertility.Mate-pair GS(4-fold)revealed additional structural rearrangements and/or copy number changes in 5 of 6 cases and detected a total of 48 rearrangements.Overall,the breakpoints caused truncations of 30 RefSeq genes,five of which were associated with spermatogenesis.Furthermore,the breakpoints disrupted 43 topological-associated domains.Direct disruptions or potential dysregulations of genes,which play potential roles in male germ cell development,apoptosis,and spermatogenesis,were found in all cases(n=6).In addition,high read-depth GS detected dual molecular findings in case MI6,involving a complex rearrangement and two point mutations in the gene DNAH1.Overall,our study provided the molecular characteristics of apparently balanced interchromosomal structural rearrangements in patients with male infertility.We demonstrated the complexity of chromosomal structural rearrangements,potential gene disruptions/dysregulation and single-gene mutations could be the contributing mechanisms underlie male infertility.
基金supported by the CSIRO Office of the Chief Executive(OCE),Australia
文摘Due to evolving molecular and informatics technologies,modern genome sequencing projects have more different characteristics than what most biologists have become accustomed to during the capillary-based sequencing era.In this paper,we explore the characteristics that made past insect genome projects successful and place them in the context of next-generation sequencing.By taking into account the intricacies of whitefly biology and the community,we present a roadmap for whitefly-omics,which focuses on the formation of an international consortium,deployment of informatic platforms and realistic generation of reference sequence data.
基金supported by the National key research and development plan(2016TFC1202700,2016YFC1200900)Beijing Municipal Science&Technology Commission project(grant numbers D151100002115003)Guangzhou Municipal Science&Technology Commission project(grant numbers 2015B2150820)
文摘Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. Methods In this proof-of-concept study using Enterovirus 71 （EV71） and Coxsackievirus A16 （CA16） strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Results Within the first minute （min） of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min （on average）, 99% identity was achieved for 10 CA16 strains in a single run. Conclusion MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use.
基金funded by the National Natural Science Foundation of China,grant number 81603221.
文摘Medicinal plants are renowned for their abundant production of secondary metabolites,which exhibit notable pharmacological activities and great potential for drug development.The biosynthesis of secondary metabolites is highly intricate and influenced by various intrinsic and extrinsic factors,resulting in substantial species diversity and content variation.Consequently,precise regulation of secondary metabolite synthesis is of utmost importance.In recent years,genome sequencing has emerged as a valuable tool for investigating the synthesis and regulation of secondary metabolites in medicinal plants,facilitated by the widespread use of high-throughput sequencing technologies.This review highlights the latest advancements in genome sequencing within this field and presents several strategies for studying secondary metabolites.Specifically,the article elucidates how genome sequencing can unravel the pathways for secondary metabolite synthesis in medicinal plants,offering insights into the functions and regulatory mechanisms of participating enzymes.Comparative analyses of plant genomes allow identification of shared pathways of metabolite synthesis among species,thereby providing novel avenues for obtaining cost-effective biosynthetic intermediates.By examining individual genomic variations,genes or gene clusters associated with the synthesis of specific compounds can be discovered,indicating potential targets and directions for drug development and the exploration of alternative compound sources.Moreover,the advent of gene-editing technology has enabled the precise modifications of medicinal plant genomes.Optimization of specific secondary metabolite synthesis pathways becomes thus feasible,enabling the precise editing of target genes to regulate secondary metabolite production within cells.These findings serve as valuable references and lessons for future drug development endeavors,conservation of rare resources,and the exploration of new resources.
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the Open Research Fund Program of the State Key Laboratory of Virology of China(Grant No.2019IOV004)the key Research Program of Frontier Sciences of Chinese Academy of Sciences(Grant No.QYZDJ-SSW-SMC021)the National Natural Science Foundation of China(Grant No.31900154 and 31572471)。
文摘Apis mellifera filamentous virus(Am FV)is a large DNA virus that is endemic in honeybee colonies.The genome sequence of the Am FV Swiss isolate(Am FV CH–C05)has been reported,but so far very few molecular studies have been conducted on this virus.In this study,we isolated and purified Am FV(Am FV CN)from Chinese honeybee(Apis mellifera)colonies and elucidated its genomics and proteomics.Electron microscopy showed ovoid purified virions with dimensions of 300–500×210–285 nm,wrapping a 3165×40 nm filamentous nucleocapsid in three figure-eight loops.Unlike Am FV CH–C05,which was reported to have a circular genome,our data suggest that Am FV CN has a linear genome of approximately 493 kb.A total of 197 ORFs were identified,among which36 putative genes including 18 baculoviral homologs were annotated.The overall nucleotide similarity between the CN and CH–C05 isolates was 96.9%.Several ORFs were newly annotated in Am FV CN,including homologs of per os infectivity factor 4(PIF4)and a putative integrase.Phylogenomic analysis placed Am FVs on a separate branch within the newly proposed virus class Naldaviricetes.Proteomic analysis revealed 47 Am FV virionassociated proteins,of which 14 had over 50%sequence coverage,suggesting that they are likely to be main structural proteins.In addition,all six of the annotated PIFs(PIF-0–5)were identified by proteomics,suggesting that they may function as entry factors in Am FV infection.This study provides fundamental information regarding the molecular biology of Am FV.
文摘Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be associated with many physiological and pathological conditions（Bai and Wong,2005）.
基金the financial support of the National Natural Science Foundation of China[32201960,32073020]Science and Technology Innovation Program of Hunan Province[2022RC1150]+2 种基金Changsha Municipal Natural Science Foundation[kq2202332]Hunan innovative province construction project[2019NK2041]Agricultural Science and Technology Innovation Project of Hunan Province[2021CX05].
文摘The microbial potential of Penicillium has received critical attention.The present research aimed to elucidate the efficacy of crude enzyme secreted from Penicillium oxalicum WX-209 in degrading citrus segments and evaluate the safety of the process.Results showed that citrus segment membranes gradually dissolved after treatment with the crude enzyme solution,indicating good degradation capability.No significant differences in body weight,food ingestion rate,hematology,blood biochemistry,and weight changes of different organs were found between the enzyme intake and control groups.Serial experiments showed that the crude enzyme had high biological safety.Moreover,the whole genome of P.oxalicum WX-209 was sequenced by PacBio and Illumina platforms.Twenty-five scaffolds were assembled to generate 36 Mbp size of genome sequence comprising 11369 predicted genes modeled with a GC content of 48.33%.A total of 592 genes were annotated to encode enzymes related to carbohydrates,and some degradation enzyme genes were identified in strain P.oxalicum WX-209.
