The replacement of winter wheat varieties has contributed significantly to yield improvement worldwide,with remarkable progress in China.Drawing on two sets of data,production yield from the National Bureau of Statist...The replacement of winter wheat varieties has contributed significantly to yield improvement worldwide,with remarkable progress in China.Drawing on two sets of data,production yield from the National Bureau of Statistics of China and experimental yield from literature,this study aims to(1)illustrate the increasing patterns of production yield among different provinces from 1978 to 2018 in China,(2)explore the genetic gain in yield and yield relevant traits through the variety replacement based on experimental yield from 1937 to 2016 in China,and(3)compare the yield gap between experimental yield and production yield.The results show that both the production and experimental yields significantly increased along with the variety replacement.The national annual yield increase ratio for the production yield was 1.67%from 1978 to 2018,varying from 0.96%in Sichuan Province to 2.78%in Hebei Province;such ratio for the experimental yield was 1.13%from 1937 to 2016.The yield gap between experimental and production yields decreased from the 1970s to the 2010s.This study reveals significant increases in some yield components consequent to variety replacement,including thousand-grain weight,kernel number per spike,and grain number per square meter;however,no change is shown in spike number per square meter.The biomass and harvest index consistently and significantly increased,whereas the plant height decreased significantly.展开更多
Traditional transgenic detection methods require high test conditions and struggle to be both sensitive and efficient.In this study,a one-tube dual recombinase polymerase amplification(RPA)reaction system for CP4-EPSP...Traditional transgenic detection methods require high test conditions and struggle to be both sensitive and efficient.In this study,a one-tube dual recombinase polymerase amplification(RPA)reaction system for CP4-EPSPS and Cry1Ab/Ac was proposed and combined with a lateral flow immunochromatographic assay,named“Dual-RPA-LFD”,to visualize the dual detection of genetically modified(GM)crops.In which,the herbicide tolerance gene CP4-EPSPS and the insect resistance gene Cry1Ab/Ac were selected as targets taking into account the current status of the most widespread application of insect resistance and herbicide tolerance traits and their stacked traits.Gradient diluted plasmids,transgenic standards,and actual samples were used as templates to conduct sensitivity,specificity,and practicality assays,respectively.The constructed method achieved the visual detection of plasmid at levels as low as 100 copies,demonstrating its high sensitivity.In addition,good applicability to transgenic samples was observed,with no cross-interference between two test lines and no influence from other genes.In conclusion,this strategy achieved the expected purpose of simultaneous detection of the two popular targets in GM crops within 20 min at 37°C in a rapid,equipmentfree field manner,providing a new alternative for rapid screening for transgenic assays in the field.展开更多
Ce rebral palsy is a diagnostic term utilized to describe a group of permanent disorders affecting movement and posture.Patients with cerebral palsy are often only capable of limited activity,resulting from non-progre...Ce rebral palsy is a diagnostic term utilized to describe a group of permanent disorders affecting movement and posture.Patients with cerebral palsy are often only capable of limited activity,resulting from non-progressive disturbances in the fetal or neonatal brain.These disturbances severely impact the child’s daily life and impose a substantial economic burden on the family.Although cerebral palsy encompasses various brain injuries leading to similar clinical outcomes,the unde rstanding of its etiological pathways remains incomplete owing to its complexity and heterogeneity.This review aims to summarize the current knowledge on the genetic factors influencing cerebral palsy development.It is now widely acknowledged that genetic mutations and alterations play a pivotal role in cerebral palsy development,which can be further influenced by environmental fa ctors.Des pite continuous research endeavors,the underlying fa ctors contributing to cerebral palsy remain are still elusive.However,significant progress has been made in genetic research that has markedly enhanced our comprehension of the genetic factors underlying cerebral palsy development.Moreove r,these genetic factors have been categorized based on the identified gene mutations in patients through clinical genotyping,including thrombosis,angiogenesis,mitochondrial and oxidative phosphorylation function,neuronal migration,and cellular autophagy.Furthermore,exploring targeted genotypes holds potential for precision treatment.In conclusion,advancements in genetic research have substantially improved our understanding of the genetic causes underlying cerebral palsy.These breakthroughs have the potential to pave the way for new treatments and therapies,consequently shaping the future of cerebral palsy research and its clinical management.The investigation of cerebral palsy genetics holds the potential to significantly advance treatments and management strategies.By elucidating the underlying cellular mechanisms,we can develop to rgeted interventions to optimize outcomes.A continued collaboration between researchers and clinicians is imperative to comprehensively unravel the intricate genetic etiology of cerebral palsy.展开更多
Insertional mutation,phenotypic evaluation,and mutated gene cloning are widely used to clone genes from scratch.Exogenous genes can be integrated into the genome during non-homologous end joining(NHEJ)of the double-st...Insertional mutation,phenotypic evaluation,and mutated gene cloning are widely used to clone genes from scratch.Exogenous genes can be integrated into the genome during non-homologous end joining(NHEJ)of the double-strand breaks of DNA,causing insertional mutation.The random insertional mutant library constructed using this method has become a method of forward genetics for gene cloning.However,the establishment of a random insertional mutant library requires a high transformation efficiency of exogenous genes.Many microalgal species show a low transformation efficiency,making constructing random insertional mutant libraries difficult.In this study,we established a highly efficient transformation method for constructing a random insertional mutant library of Nannochloropsis oceanica,and tentatively tried to isolate its genes to prove the feasibility of the method.A gene that may control the growth rate and cell size was identified.This method will facilitate the genetic studies of N.oceanica,which should also be a reference for other microalgal species.展开更多
To reduce the cost and increase the efficiency of plant genetic marker fingerprinting for variety discrimination,it is desirable to identify the optimal marker combinations.We describe a marker combination screening m...To reduce the cost and increase the efficiency of plant genetic marker fingerprinting for variety discrimination,it is desirable to identify the optimal marker combinations.We describe a marker combination screening model based on the genetic algorithm(GA)and implemented in a software tool,Loci Scan.Ratio-based variety discrimination power provided the largest optimization space among multiple fitness functions.Among GA parameters,an increase in population size and generation number enlarged optimization depth but also calculation workload.Exhaustive algorithm afforded the same optimization depth as GA but vastly increased calculation time.In comparison with two other software tools,Loci Scan accommodated missing data,reduced calculation time,and offered more fitness functions.In large datasets,the sample size of training data exerted the strongest influence on calculation time,whereas the marker size of training data showed no effect,and target marker number had limited effect on analysis speed.展开更多
This study evaluated the genetic and agronomic parameter estimates of maize under different nitrogen rates. The trial was established at the Njala Agricultural Research Centre experimental site during 2021 and 2022 in...This study evaluated the genetic and agronomic parameter estimates of maize under different nitrogen rates. The trial was established at the Njala Agricultural Research Centre experimental site during 2021 and 2022 in a split block design with three maize varieties (IWCD2, 2009EVDT, and DMR-ESR-Yellow) and seven nitrogen (0, 30, 60, 90, 120, 150 and 180 kg∙N∙ha<sup>−</sup><sup>1</sup>) rates. Findings showed that cob diameter and anthesis silking time (ASI) had intermediate heritability, ASI had high genetic advance, ASI and grain yield had high genotypic coefficient of variation (GCV), while traits with high phenotypic coefficient of variation (PCV) were plant height, ASI, grain yield, number of kernel per cob, number of kernel rows, ear length, and ear height. The PCV values were higher than GCV, indicating the influence of the environment in the studied traits. Nitrogen rates and variety significantly (p < 0.05) influenced grain yield production. Mean grain yields and economic parameter estimates increased with increasing nitrogen rates, with the 30 and 180 kg∙N∙ha<sup>−</sup><sup>1</sup> plots exhibiting the lowest and highest grain yields of 1238 kg∙ha<sup>−</sup><sup>1</sup> and 2098 kg∙ha<sup>−</sup><sup>1</sup>, respectively. Variety and nitrogen effects on partial factor productivity (PFP<sub>N</sub>), agronomic efficiency (AEN), net returns (NR), value cost ratio (VCR) and marginal return (MR) indicated that these parameters were significantly affected (p < 0.05) by these factors. The highest PFP<sub>N</sub> (41.3 kg grain kg<sup>−</sup><sup>1</sup>∙N) and AEN (29.4 kg grain kg<sup>−</sup><sup>1</sup>∙N) were obtained in the 30 kg∙N∙ha<sup>−</sup><sup>1</sup> plots, while the highest VCR (2.8) and MR (SLL 1.8 SLL<sup>−</sup><sup>1</sup> spent on N) were obtained in the 180 kg∙N∙ha<sup>−</sup><sup>1</sup>. The significant influence of variety and nitrogen on traits suggests that increasing yields and maximizing profits require use of appropriate nitrogen fertilization and improved farming practices that could be exploited for increased productivity of maize.展开更多
Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened pheasants.Reeves’s Pheasant(Syrmaticus r...Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened pheasants.Reeves’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat loss.There is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened bird.Here,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic divergence.Furthermore,we identified candidate genes linked with adaptation across the current distribution of Reeves’s Pheasant.The present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 genes.We also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those populations.By comparing with other threatened species,we found that Reeves’s Pheasants have low genetic diversity.Runs of homozygosity suggest that the Shennongjia population has experienced serious inbreeding.The demographic history results indicated that three populations experienced several declines during the glacial period.Local adaptative analysis among the populations identified 241 candidate genes under directional selection.They are involved in a large variety of processes,including the immune response and pigmentation.Our results suggest that the three populations should be considered as three different conservation units.The current study provides genetic evidence for conserving the threatened Reeves’s Pheasant and provides genomic resources for global biodiversity management.展开更多
This study proposes a hybridization of two efficient algorithm’s Multi-objective Ant Lion Optimizer Algorithm(MOALO)which is a multi-objective enhanced version of the Ant Lion Optimizer Algorithm(ALO)and the Genetic ...This study proposes a hybridization of two efficient algorithm’s Multi-objective Ant Lion Optimizer Algorithm(MOALO)which is a multi-objective enhanced version of the Ant Lion Optimizer Algorithm(ALO)and the Genetic Algorithm(GA).MOALO version has been employed to address those problems containing many objectives and an archive has been employed for retaining the non-dominated solutions.The uniqueness of the hybrid is that the operators like mutation and crossover of GA are employed in the archive to update the solutions and later those solutions go through the process of MOALO.A first-time hybrid of these algorithms is employed to solve multi-objective problems.The hybrid algorithm overcomes the limitation of ALO of getting caught in the local optimum and the requirement of more computational effort to converge GA.To evaluate the hybridized algorithm’s performance,a set of constrained,unconstrained test problems and engineering design problems were employed and compared with five well-known computational algorithms-MOALO,Multi-objective Crystal Structure Algorithm(MOCryStAl),Multi-objective Particle Swarm Optimization(MOPSO),Multi-objective Multiverse Optimization Algorithm(MOMVO),Multi-objective Salp Swarm Algorithm(MSSA).The outcomes of five performance metrics are statistically analyzed and the most efficient Pareto fronts comparison has been obtained.The proposed hybrid surpasses MOALO based on the results of hypervolume(HV),Spread,and Spacing.So primary objective of developing this hybrid approach has been achieved successfully.The proposed approach demonstrates superior performance on the test functions,showcasing robust convergence and comprehensive coverage that surpasses other existing algorithms.展开更多
The utilisation of polygenic scoring models may enhance the clinician’s ability to risk stratify an inflammatory bowel disease patient’s individual risk for venous thromboembolism(VTE)and guide the appropriate usage...The utilisation of polygenic scoring models may enhance the clinician’s ability to risk stratify an inflammatory bowel disease patient’s individual risk for venous thromboembolism(VTE)and guide the appropriate usage of VTE thromboprophylaxis,yet there is a need to validate such models in ethnically diverse populations.展开更多
Hereditary hearing loss(HHL),a genetic disorder that impairs auditory function,significantly affects quality of life and incurs substantial economic losses for society.To investigate the underlying causes of HHL and e...Hereditary hearing loss(HHL),a genetic disorder that impairs auditory function,significantly affects quality of life and incurs substantial economic losses for society.To investigate the underlying causes of HHL and evaluate therapeutic outcomes,appropriate animal models are necessary.Pigs have been extensively used as valuable large animal models in biomedical research.In this review,we highlight the advantages of pig models in terms of ear anatomy,inner ear morphology,and electrophysiological characteristics,as well as recent advancements in the development of distinct genetically modified porcine models of hearing loss.Additionally,we discuss the prospects,challenges,and recommendations regarding the use pig models in HHL research.Overall,this review provides insights and perspectives for future studies on HHL using porcine models.展开更多
Fluoride and nitrate enriched groundwater are potential threats to the safety of the groundwater supply that may cause significant effects on human health and public safety,especially in aggregated population areas an...Fluoride and nitrate enriched groundwater are potential threats to the safety of the groundwater supply that may cause significant effects on human health and public safety,especially in aggregated population areas and economic hubs.This study focuses on the high F^(−)and NO_(3)^(−)concentration groundwater in Tongzhou District,Beijing,North China.A total of 36 groundwater samples were collected to analyze the hydrochemical characteristics,elucidate genetic mechanisms and evaluate the potential human health risks.The results of the analysis indicate:Firstly,most of the groundwater samples are characterized by Mg-HCO_(3) and Na-HCO_(3) with the pH ranging from 7.19 to 8.28 and TDS with a large variation across the range 471-2337 mg/L.The NO_(3)^(−)concentration in 38.89%groundwater samples and the F^(−)concentration in 66.67%groundwater samples exceed the permissible limited value.Secondly,F^(−)in groundwater originates predominantly from water-rock interactions and the fluorite dissolution,which is also regulated by cation exchange,competitive adsorption of HCO_(3)−and an alkaline environment.Thirdly,the effect of sewage disposal and agricultural activities have a significant effect on high NO3-concentration,while the high F^(−)concentration is less influenced by anthropogenic activity.The alkaline environment favors nitrification,thus being conducive to the production of NO_(3)^(−).Finally,the health risk assessment is evaluated for different population groups.The results indicate that high NO_(3)^(−)and F^(−)concentration in groundwater would have the largest threat to children’s health.The findings of this study could contribute to the provision of a scientific basis for groundwater supply policy formulation relating to public health in Tongzhou District.展开更多
Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the w...Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the wild,but in 1999 was rediscovered.However,little is known about its genetic load.We collected 67 individuals from five wild,isolated T.sutchuenensis populations,and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T.sutchuenensis to delineate the conservation units of T.sutchuenensis,based on whole transcriptome sequencing data,as well as target capture sequencing data.We found that populations of T.sutchuenensis could be divided into three groups.These groups had low levels genetic diversity and were moderately genetically differentiated.Our findings also indicate that T.sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum.Among Thuja species,T.sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection.However,distribution of fitness effects analysis indicated a high extinction risk for T.sutchuenensis.Multiple lines of evidence identified three management units for T.sutchuenensis.Although T.sutchuenensis possesses a low genetic load,low genetic diversity,suboptimal fitness,and anthropogenic pressures all present an extinction risk for this rare conifer.This might also hold true for many endangered plant species in the mountains all over the world.展开更多
Studying on the genetic diversity and genetic relationship of flowering cherry cultivars is extremely important for germplasm conservation, cultivar identification and breeding. Flowering cherry is widely cultivated a...Studying on the genetic diversity and genetic relationship of flowering cherry cultivars is extremely important for germplasm conservation, cultivar identification and breeding. Flowering cherry is widely cultivated as an important woody ornamental plant in worldwide, especially Japan, China. However, owning to the morphological similarity, many cultivars are distinguished hardly in non-flowering season. Here, we evaluated the genetic diversity and genetic relationship of 40 flowering cherry cultivars, which are mainly cultivated in China. We selected 13 polymorphicprimers to amplify to allele fragments with fluorescent-labeled capillary electrophoresis technology. The population structure analysis results show that these cultivars could be divided into 4 subpopulations. At the population level, N<sub>a</sub> and N<sub>e</sub> were 6.062, 4.326, respectively. H<sub>o</sub> and H<sub>e</sub> were 0.458 and 0.670, respectively. The Shannon’s information index (I) was 1.417. The Pop3, which originated from P. serrulata, had the highest H<sub>o</sub>, H<sub>e</sub>, and I among the 4 subpopulations. AMOVA showed that only 4% of genetic variation came from populations, the 39% variation came from individuals and 57% (p < 0.05) came from intra-individuals. 5 polymorphic SSR primers were selected to construct molecular ID code system of these cultivars. This analysis on the genetic diversity and relationship of the 40 flowering cherry cultivars will help to insight into the genetic background, relationship of these flowering cherry cultivars and promote to identify similar cultivars.展开更多
Multidrug-resistant(MDR)Enterobacteriaceae critically threaten duck farming and public health.The phenotypes,genotypes,and associated mobile genetic elements(MGEs)of MDR Enterobacteriaceae isolated from 6 duck farms i...Multidrug-resistant(MDR)Enterobacteriaceae critically threaten duck farming and public health.The phenotypes,genotypes,and associated mobile genetic elements(MGEs)of MDR Enterobacteriaceae isolated from 6 duck farms in Zhejiang Province,China,were investigated.A total of 215 isolates were identified as Escherichia coli(64.65%),Klebsiella pneumoniae(12.09%),Proteus mirabilis(10.23%),Salmonella(8.84%),and Enterobacter cloacae(4.19%).Meanwhile,all isolates were resistant to at least two antibiotics.Most isolates carried tet(A)(85.12%),blaTEM(78.60%)and sul1(67.44%)resistance genes.Gene co-occurrence analysis showed that the resistance genes were associated with IS26 and integrons.A conjugative IncFII plasmid pSDM004 containing all the above MGEs was detected in Proteus mirabilis isolate SDM004.This isolate was resistant to 18 antibiotics and carried the blaNDM-5 gene.MGEs,especially plasmids,are the primary antibiotic resistance gene transmission route in duck farms.These findings provide a theoretical basis for the rational use of antibiotics in farms which are substantial for evaluating public health and food safety.展开更多
Surface wave inversion is a key step in the application of surface waves to soil velocity profiling.Currently,a common practice for the process of inversion is that the number of soil layers is assumed to be known bef...Surface wave inversion is a key step in the application of surface waves to soil velocity profiling.Currently,a common practice for the process of inversion is that the number of soil layers is assumed to be known before using heuristic search algorithms to compute the shear wave velocity profile or the number of soil layers is considered as an optimization variable.However,an improper selection of the number of layers may lead to an incorrect shear wave velocity profile.In this study,a deep learning and genetic algorithm hybrid learning procedure is proposed to perform the surface wave inversion without the need to assume the number of soil layers.First,a deep neural network is adapted to learn from a large number of synthetic dispersion curves for inferring the layer number.Then,the shear-wave velocity profile is determined by a genetic algorithm with the known layer number.By applying this procedure to both simulated and real-world cases,the results indicate that the proposed method is reliable and efficient for surface wave inversion.展开更多
Global climate change has increased concerns regarding biodiversity loss.However,many key conservation issues still required further research,including demographic history,deleterious mutation load,adaptive evolution,...Global climate change has increased concerns regarding biodiversity loss.However,many key conservation issues still required further research,including demographic history,deleterious mutation load,adaptive evolution,and putative introgression.Here we generated the first chromosome-level genome of the endangered Chinese hazelnut,Corylus chinensis,and compared the genomic signatures with its sympatric widespread C.kwechowensiseC.yunnanensis complex.We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation.Population genomics revealed that both C.chinensis and the C.kwechowensis eC.yunnanensis complex had diverged into two genetic lineages,forming a consistent pattern of southwestern-northern differentiation.Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene,whereas the widespread northern lineages have remained stable(C.chinensis)or have even recovered from population bottlenecks(C.kwechowensis eC.yunnanensis complex)during the Quaternary.Compared with C.kwechowensiseC.yunnanensis complex,C.chinensis showed significantly lower genomic diversity and higher inbreeding level.However,C.chinensis carried significantly fewer deleterious mutations than C.kwechowensiseC.yunnanensis complex,as more effective purging selection reduced the accumulation of homozygous variants.We also detected signals of positive selection and adaptive introgression in different lineages,which facilitated the accumulation of favorable variants and formation of local adaptation.Hence,both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C.chinensis.Overall,our study provides critical insights into lineage differentiation,local adaptation,and the potential for future recovery of endangered trees.展开更多
Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals ...Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals aged 28 days–85 years.A total of 706 stool samples from patients with acute gastroenteritis collected between January 2019 and January 2020 were analyzed for 17 causative pathogens,including RVA,using a Gastrointestinal Pathogen Panel,followed by genotyping,virus isolation,and complete sequencing to assess the genetic diversity of RVA.Results The overall RVA infection rate was 14.59%(103/706),with an irregular epidemiological pattern.The proportion of co-infection with RVA and other pathogens was 39.81%(41/103).Acute gastroenteritis is highly prevalent in young children aged 0–1 year,and RVA is the key pathogen circulating in patients 6–10 months of age with diarrhea.G9P[8](58.25%,60/103)was found to be the predominant genotype in the RVA strains,and the 41 RVA-positive strains that were successfully sequenced belonged to three different RVA genotypes in the phylogenetic analysis.Recombination analysis showed that gene reassortment events,selection pressure,codon usage bias,gene polymorphism,and post-translational modifications(PTMs)occurred in the G9P[8]and G3P[8]strains.Conclusion This study provides molecular evidence of RVA prevalence in the Pearl River Delta region of China,further enriching the existing information on its genetics and evolutionary characteristics and suggesting the emergence of genetic diversity.Strengthening the surveillance of genotypic changes and gene reassortment in RVA strains is essential for further research and a better understanding of strain variations for further vaccine development.展开更多
In this editorial,we comment on the article by Marangoni et al,published in the recent issue of the World Journal of Gastroenterology 2023;29:5618-5629,about“Diet as an epigenetic factor in inflammatory bowel disease...In this editorial,we comment on the article by Marangoni et al,published in the recent issue of the World Journal of Gastroenterology 2023;29:5618-5629,about“Diet as an epigenetic factor in inflammatory bowel disease”.The authors emphasized the role of diet,especially the interaction with genetics,in promoting the inflam-matory process in inflammatory bowel disease(IBD)patients,focusing on DNA methylation,histone modifications,and the influence of microRNAs.In this editorial,we explore the interaction between genetics,gut microbiota,and diet,in an only way.Furthermore,we provided dietary recommendations for patients with IBD.The Western diet,characterized by a low fiber content and deficiency the micronutrients,impacts short-chain fatty acids production and may be related to the pathogenesis of IBD.On the other hand,the consumption of the Mediter-ranean diet and dietary fibers are associated with reduced risk of IBD flares,particularly in Crohn’s disease(CD)patients.According to the dietary guidance from the International Organization for the Study of Inflammatory Bowel Diseases(IOIBD),the regular consumption of fruits and vegetables while reducing the consumption of saturated,trans,dairy fat,additives,processed foods rich in maltodextrins,and artificial sweeteners containing sucralose or saccharine is recommended to CD patients.For patients with ulcerative colitis,the IOIBD recommends the increased intake of natural sources of omega-3 fatty acids and follows the same restrictive recommendations aimed at CD patients,with the possible inclusion of red meats.In conclusion,IBD is a complex and hetero-geneous disease,and future studies are needed to elucidate the influence of epigenetics on diet and microbiota in IBD patients.展开更多
Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is...Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is,33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship,genetic diversity,and genetic structure between them by specific length amplified fragment sequencing(SLAF-seq).Finally,470725 polymorphic SLAF tags and 58622 valid SNP markers were obtained.Phylogenetic analysis showed that 61 samples were classified into 2 clusters:wild populations and cultivated populations,and some wild yews were categorized into the cultivated populations;the genetic diversity analysis showed that the Nei diversity index of wild populations(0.4068)was smaller than that of cultivated populations(0.4414),and the polymorphic information content(PIC)of wild populations(0.2861)was smaller than that of cultivated populations(0.3309).The genetic differentiation analysis showed that the total populations of gene diversity(H_(t))of cultivated and wild populations were respectively 0.8159 and 0.5685,the coefficient of gene differentiation(G_(st))of cultivated and wild populations was respectively 0.3021 and 0.1068,and the gene flow(N_(m))(2.4967)of wild populations was larger than cultivated populations(0.8199).The molecular variance(AMOVA)revealed that inter-population variation accounted for 29.57%of the total genetic variation,while intra-population variation accounted for 70.42% of the total genetic variation(p<0.001),this suggested that the genetic variation in the T.cuspidata is mainly attributed to within-population factors.In conclusion,the genetic distance between geographical ecological groups of wild populations was generally smaller than that of cultivated populations,and the degree of genetic diversity and genetic differentiation was smaller than that of cultivated populations.As evident,the utilization of SLAF-seq technology enables efficient and accurate development of SNP markers suitable for genetic analysis of T.cuspidata species.These developed SNP markers can provide a molecular foundation for T.cuspidata breeding,construction of genetic maps,variety identification,and association analysis of agronomic traits.展开更多
Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and hap...Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and haplotype.Methods:Thirty-nine blood samples infected with P.knowlesi were collected in Sabah,Malaysian Borneo and Peninsular Malaysia.The S-type SSU rRNA gene was amplified using polymerase chain reaction,cloned into a vector,and sequenced.The natural selection and haplotype of the S-type SSU rRNA gene sequences were determined using DnaSP v6 and illustrated using NETWORK v10.This study's 39 S-type SSU rRNA sequences and eight sequences from the Genbank database were subjected to phylogenetic analysis using MEGA 11.Results:Overall,the phylogenetic analysis showed no evidence of a geographical cluster of P.knowlesi isolates from different areas in Malaysia based on the S-type SSU rRNA gene sequences.The S-type SSU rRNA gene sequences were relatively conserved and with a purifying effect.Haplotype sharing of the S-type SSU rRNA gene was observed between the P.knowlesi isolates in Sabah,Malaysian Borneo,but not between Sabah,Malaysian Borneo and Peninsular Malaysia.Conclusions:This study suggests that the S-type SSU rRNA gene of P.knowlesi isolates in Sabah,Malaysian Borneo,and Peninsular Malaysia has fewer polymorphic sites,representing the conservation of the gene.These features make the S-type SSU rRNA gene suitable for comparative studies,such as determining the evolutionary relationships and common ancestry among P.knowlesi species.展开更多
基金This research was financially supported by the Natural Science Basic Research Program of Shaanxi,China(2022JM-126)the National Natural Science Foundation of China(52079132).
文摘The replacement of winter wheat varieties has contributed significantly to yield improvement worldwide,with remarkable progress in China.Drawing on two sets of data,production yield from the National Bureau of Statistics of China and experimental yield from literature,this study aims to(1)illustrate the increasing patterns of production yield among different provinces from 1978 to 2018 in China,(2)explore the genetic gain in yield and yield relevant traits through the variety replacement based on experimental yield from 1937 to 2016 in China,and(3)compare the yield gap between experimental yield and production yield.The results show that both the production and experimental yields significantly increased along with the variety replacement.The national annual yield increase ratio for the production yield was 1.67%from 1978 to 2018,varying from 0.96%in Sichuan Province to 2.78%in Hebei Province;such ratio for the experimental yield was 1.13%from 1937 to 2016.The yield gap between experimental and production yields decreased from the 1970s to the 2010s.This study reveals significant increases in some yield components consequent to variety replacement,including thousand-grain weight,kernel number per spike,and grain number per square meter;however,no change is shown in spike number per square meter.The biomass and harvest index consistently and significantly increased,whereas the plant height decreased significantly.
基金supported by the Scientific and Innovative Action Plan of Shanghai(21N31900800)Shanghai Rising-Star Program(23QB1403500)+4 种基金the Shanghai Sailing Program(20YF1443000)Shanghai Science and Technology Commission,the Belt and Road Project(20310750500)Talent Project of SAAS(2023-2025)Runup Plan of SAAS(ZP22211)the SAAS Program for Excellent Research Team(2022(B-16))。
文摘Traditional transgenic detection methods require high test conditions and struggle to be both sensitive and efficient.In this study,a one-tube dual recombinase polymerase amplification(RPA)reaction system for CP4-EPSPS and Cry1Ab/Ac was proposed and combined with a lateral flow immunochromatographic assay,named“Dual-RPA-LFD”,to visualize the dual detection of genetically modified(GM)crops.In which,the herbicide tolerance gene CP4-EPSPS and the insect resistance gene Cry1Ab/Ac were selected as targets taking into account the current status of the most widespread application of insect resistance and herbicide tolerance traits and their stacked traits.Gradient diluted plasmids,transgenic standards,and actual samples were used as templates to conduct sensitivity,specificity,and practicality assays,respectively.The constructed method achieved the visual detection of plasmid at levels as low as 100 copies,demonstrating its high sensitivity.In addition,good applicability to transgenic samples was observed,with no cross-interference between two test lines and no influence from other genes.In conclusion,this strategy achieved the expected purpose of simultaneous detection of the two popular targets in GM crops within 20 min at 37°C in a rapid,equipmentfree field manner,providing a new alternative for rapid screening for transgenic assays in the field.
基金supported by the National Natural Science Foundation of China,No.U21A20347(to CZ)the National Key Research and Development Program of China,No.2022YFC2704801(to CZ)+1 种基金the Henan Key Laboratory of Population Defects Prevention,No.ZD202103(to YX)the Department of Science and Technology of Henan Province of China,No.212102310221(to YX)。
文摘Ce rebral palsy is a diagnostic term utilized to describe a group of permanent disorders affecting movement and posture.Patients with cerebral palsy are often only capable of limited activity,resulting from non-progressive disturbances in the fetal or neonatal brain.These disturbances severely impact the child’s daily life and impose a substantial economic burden on the family.Although cerebral palsy encompasses various brain injuries leading to similar clinical outcomes,the unde rstanding of its etiological pathways remains incomplete owing to its complexity and heterogeneity.This review aims to summarize the current knowledge on the genetic factors influencing cerebral palsy development.It is now widely acknowledged that genetic mutations and alterations play a pivotal role in cerebral palsy development,which can be further influenced by environmental fa ctors.Des pite continuous research endeavors,the underlying fa ctors contributing to cerebral palsy remain are still elusive.However,significant progress has been made in genetic research that has markedly enhanced our comprehension of the genetic factors underlying cerebral palsy development.Moreove r,these genetic factors have been categorized based on the identified gene mutations in patients through clinical genotyping,including thrombosis,angiogenesis,mitochondrial and oxidative phosphorylation function,neuronal migration,and cellular autophagy.Furthermore,exploring targeted genotypes holds potential for precision treatment.In conclusion,advancements in genetic research have substantially improved our understanding of the genetic causes underlying cerebral palsy.These breakthroughs have the potential to pave the way for new treatments and therapies,consequently shaping the future of cerebral palsy research and its clinical management.The investigation of cerebral palsy genetics holds the potential to significantly advance treatments and management strategies.By elucidating the underlying cellular mechanisms,we can develop to rgeted interventions to optimize outcomes.A continued collaboration between researchers and clinicians is imperative to comprehensively unravel the intricate genetic etiology of cerebral palsy.
基金the National Key R&D Program of China(Nos.2018YFD0901506,2018YFD0900305)the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(No.2018 SDKJ0406-3)。
文摘Insertional mutation,phenotypic evaluation,and mutated gene cloning are widely used to clone genes from scratch.Exogenous genes can be integrated into the genome during non-homologous end joining(NHEJ)of the double-strand breaks of DNA,causing insertional mutation.The random insertional mutant library constructed using this method has become a method of forward genetics for gene cloning.However,the establishment of a random insertional mutant library requires a high transformation efficiency of exogenous genes.Many microalgal species show a low transformation efficiency,making constructing random insertional mutant libraries difficult.In this study,we established a highly efficient transformation method for constructing a random insertional mutant library of Nannochloropsis oceanica,and tentatively tried to isolate its genes to prove the feasibility of the method.A gene that may control the growth rate and cell size was identified.This method will facilitate the genetic studies of N.oceanica,which should also be a reference for other microalgal species.
基金supported by the Scientific and Technological Innovation 2030 Major Project(2022ZD04019)the Science and Technology Innovation Capacity Building Project of BAAFS(KJCX20230303)+1 种基金Hainan Province Science and Technology Special Fund(ZDYF2023XDNY077)the Beijing Scholars Program(BSP041)。
文摘To reduce the cost and increase the efficiency of plant genetic marker fingerprinting for variety discrimination,it is desirable to identify the optimal marker combinations.We describe a marker combination screening model based on the genetic algorithm(GA)and implemented in a software tool,Loci Scan.Ratio-based variety discrimination power provided the largest optimization space among multiple fitness functions.Among GA parameters,an increase in population size and generation number enlarged optimization depth but also calculation workload.Exhaustive algorithm afforded the same optimization depth as GA but vastly increased calculation time.In comparison with two other software tools,Loci Scan accommodated missing data,reduced calculation time,and offered more fitness functions.In large datasets,the sample size of training data exerted the strongest influence on calculation time,whereas the marker size of training data showed no effect,and target marker number had limited effect on analysis speed.
文摘This study evaluated the genetic and agronomic parameter estimates of maize under different nitrogen rates. The trial was established at the Njala Agricultural Research Centre experimental site during 2021 and 2022 in a split block design with three maize varieties (IWCD2, 2009EVDT, and DMR-ESR-Yellow) and seven nitrogen (0, 30, 60, 90, 120, 150 and 180 kg∙N∙ha<sup>−</sup><sup>1</sup>) rates. Findings showed that cob diameter and anthesis silking time (ASI) had intermediate heritability, ASI had high genetic advance, ASI and grain yield had high genotypic coefficient of variation (GCV), while traits with high phenotypic coefficient of variation (PCV) were plant height, ASI, grain yield, number of kernel per cob, number of kernel rows, ear length, and ear height. The PCV values were higher than GCV, indicating the influence of the environment in the studied traits. Nitrogen rates and variety significantly (p < 0.05) influenced grain yield production. Mean grain yields and economic parameter estimates increased with increasing nitrogen rates, with the 30 and 180 kg∙N∙ha<sup>−</sup><sup>1</sup> plots exhibiting the lowest and highest grain yields of 1238 kg∙ha<sup>−</sup><sup>1</sup> and 2098 kg∙ha<sup>−</sup><sup>1</sup>, respectively. Variety and nitrogen effects on partial factor productivity (PFP<sub>N</sub>), agronomic efficiency (AEN), net returns (NR), value cost ratio (VCR) and marginal return (MR) indicated that these parameters were significantly affected (p < 0.05) by these factors. The highest PFP<sub>N</sub> (41.3 kg grain kg<sup>−</sup><sup>1</sup>∙N) and AEN (29.4 kg grain kg<sup>−</sup><sup>1</sup>∙N) were obtained in the 30 kg∙N∙ha<sup>−</sup><sup>1</sup> plots, while the highest VCR (2.8) and MR (SLL 1.8 SLL<sup>−</sup><sup>1</sup> spent on N) were obtained in the 180 kg∙N∙ha<sup>−</sup><sup>1</sup>. The significant influence of variety and nitrogen on traits suggests that increasing yields and maximizing profits require use of appropriate nitrogen fertilization and improved farming practices that could be exploited for increased productivity of maize.
基金supported by the Biodiversity Survey,Monitoring and Assessment Project(2019–2023)of the Ministry of Ecology and EnvironmentChina(No.2019HB2096001006 to ZZ)+2 种基金the National Natural Science Foundation of China(31672319)Endangered Species Scientific Commission of China(No.2022–331)supported by the China Scholarship Council,China。
文摘Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened pheasants.Reeves’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat loss.There is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened bird.Here,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic divergence.Furthermore,we identified candidate genes linked with adaptation across the current distribution of Reeves’s Pheasant.The present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 genes.We also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those populations.By comparing with other threatened species,we found that Reeves’s Pheasants have low genetic diversity.Runs of homozygosity suggest that the Shennongjia population has experienced serious inbreeding.The demographic history results indicated that three populations experienced several declines during the glacial period.Local adaptative analysis among the populations identified 241 candidate genes under directional selection.They are involved in a large variety of processes,including the immune response and pigmentation.Our results suggest that the three populations should be considered as three different conservation units.The current study provides genetic evidence for conserving the threatened Reeves’s Pheasant and provides genomic resources for global biodiversity management.
基金supported by the National Research Foundation of Korea(NRF)Grant funded by the Korea government(MSIT)(No.RS-2023-00218176)the Soonchunhyang University Research Fund.
文摘This study proposes a hybridization of two efficient algorithm’s Multi-objective Ant Lion Optimizer Algorithm(MOALO)which is a multi-objective enhanced version of the Ant Lion Optimizer Algorithm(ALO)and the Genetic Algorithm(GA).MOALO version has been employed to address those problems containing many objectives and an archive has been employed for retaining the non-dominated solutions.The uniqueness of the hybrid is that the operators like mutation and crossover of GA are employed in the archive to update the solutions and later those solutions go through the process of MOALO.A first-time hybrid of these algorithms is employed to solve multi-objective problems.The hybrid algorithm overcomes the limitation of ALO of getting caught in the local optimum and the requirement of more computational effort to converge GA.To evaluate the hybridized algorithm’s performance,a set of constrained,unconstrained test problems and engineering design problems were employed and compared with five well-known computational algorithms-MOALO,Multi-objective Crystal Structure Algorithm(MOCryStAl),Multi-objective Particle Swarm Optimization(MOPSO),Multi-objective Multiverse Optimization Algorithm(MOMVO),Multi-objective Salp Swarm Algorithm(MSSA).The outcomes of five performance metrics are statistically analyzed and the most efficient Pareto fronts comparison has been obtained.The proposed hybrid surpasses MOALO based on the results of hypervolume(HV),Spread,and Spacing.So primary objective of developing this hybrid approach has been achieved successfully.The proposed approach demonstrates superior performance on the test functions,showcasing robust convergence and comprehensive coverage that surpasses other existing algorithms.
文摘The utilisation of polygenic scoring models may enhance the clinician’s ability to risk stratify an inflammatory bowel disease patient’s individual risk for venous thromboembolism(VTE)and guide the appropriate usage of VTE thromboprophylaxis,yet there is a need to validate such models in ethnically diverse populations.
基金supported by the National Key Research and Development Program of China (2021YFA0805902,2022YFF0710703)National Natural Science Foundation of China (32201257)+1 种基金Science and Technology Innovation Project of Xiongan New Area (2022XAGG0121)Young Elite Scientists Sponsorship Program by the China Association for Science and Technology (2019QNRC001)。
文摘Hereditary hearing loss(HHL),a genetic disorder that impairs auditory function,significantly affects quality of life and incurs substantial economic losses for society.To investigate the underlying causes of HHL and evaluate therapeutic outcomes,appropriate animal models are necessary.Pigs have been extensively used as valuable large animal models in biomedical research.In this review,we highlight the advantages of pig models in terms of ear anatomy,inner ear morphology,and electrophysiological characteristics,as well as recent advancements in the development of distinct genetically modified porcine models of hearing loss.Additionally,we discuss the prospects,challenges,and recommendations regarding the use pig models in HHL research.Overall,this review provides insights and perspectives for future studies on HHL using porcine models.
基金supported by the project of China Geological Survey(Grant No.DD20221677-2)the fundamental research funds of Chinese Academy of Geological Sciences Basal Research Fund(Grant No.JKYQN202307).
文摘Fluoride and nitrate enriched groundwater are potential threats to the safety of the groundwater supply that may cause significant effects on human health and public safety,especially in aggregated population areas and economic hubs.This study focuses on the high F^(−)and NO_(3)^(−)concentration groundwater in Tongzhou District,Beijing,North China.A total of 36 groundwater samples were collected to analyze the hydrochemical characteristics,elucidate genetic mechanisms and evaluate the potential human health risks.The results of the analysis indicate:Firstly,most of the groundwater samples are characterized by Mg-HCO_(3) and Na-HCO_(3) with the pH ranging from 7.19 to 8.28 and TDS with a large variation across the range 471-2337 mg/L.The NO_(3)^(−)concentration in 38.89%groundwater samples and the F^(−)concentration in 66.67%groundwater samples exceed the permissible limited value.Secondly,F^(−)in groundwater originates predominantly from water-rock interactions and the fluorite dissolution,which is also regulated by cation exchange,competitive adsorption of HCO_(3)−and an alkaline environment.Thirdly,the effect of sewage disposal and agricultural activities have a significant effect on high NO3-concentration,while the high F^(−)concentration is less influenced by anthropogenic activity.The alkaline environment favors nitrification,thus being conducive to the production of NO_(3)^(−).Finally,the health risk assessment is evaluated for different population groups.The results indicate that high NO_(3)^(−)and F^(−)concentration in groundwater would have the largest threat to children’s health.The findings of this study could contribute to the provision of a scientific basis for groundwater supply policy formulation relating to public health in Tongzhou District.
基金This study was financially supported by National Natural Science Foundation of China(grant No.U20A2080,31622015)the Institutional Research Fund from Sichuan University(2021SCUNL102)Fundamental Research Fund for the Central Universities of China(SCU 2021D006,SCU 2022D003).
文摘Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the wild,but in 1999 was rediscovered.However,little is known about its genetic load.We collected 67 individuals from five wild,isolated T.sutchuenensis populations,and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T.sutchuenensis to delineate the conservation units of T.sutchuenensis,based on whole transcriptome sequencing data,as well as target capture sequencing data.We found that populations of T.sutchuenensis could be divided into three groups.These groups had low levels genetic diversity and were moderately genetically differentiated.Our findings also indicate that T.sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum.Among Thuja species,T.sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection.However,distribution of fitness effects analysis indicated a high extinction risk for T.sutchuenensis.Multiple lines of evidence identified three management units for T.sutchuenensis.Although T.sutchuenensis possesses a low genetic load,low genetic diversity,suboptimal fitness,and anthropogenic pressures all present an extinction risk for this rare conifer.This might also hold true for many endangered plant species in the mountains all over the world.
文摘Studying on the genetic diversity and genetic relationship of flowering cherry cultivars is extremely important for germplasm conservation, cultivar identification and breeding. Flowering cherry is widely cultivated as an important woody ornamental plant in worldwide, especially Japan, China. However, owning to the morphological similarity, many cultivars are distinguished hardly in non-flowering season. Here, we evaluated the genetic diversity and genetic relationship of 40 flowering cherry cultivars, which are mainly cultivated in China. We selected 13 polymorphicprimers to amplify to allele fragments with fluorescent-labeled capillary electrophoresis technology. The population structure analysis results show that these cultivars could be divided into 4 subpopulations. At the population level, N<sub>a</sub> and N<sub>e</sub> were 6.062, 4.326, respectively. H<sub>o</sub> and H<sub>e</sub> were 0.458 and 0.670, respectively. The Shannon’s information index (I) was 1.417. The Pop3, which originated from P. serrulata, had the highest H<sub>o</sub>, H<sub>e</sub>, and I among the 4 subpopulations. AMOVA showed that only 4% of genetic variation came from populations, the 39% variation came from individuals and 57% (p < 0.05) came from intra-individuals. 5 polymorphic SSR primers were selected to construct molecular ID code system of these cultivars. This analysis on the genetic diversity and relationship of the 40 flowering cherry cultivars will help to insight into the genetic background, relationship of these flowering cherry cultivars and promote to identify similar cultivars.
基金supported by the National Natural Science Foundation of China(32172188)Science and Technology Cooperation Project of ZheJiang Province(2023SNJF058-3)。
文摘Multidrug-resistant(MDR)Enterobacteriaceae critically threaten duck farming and public health.The phenotypes,genotypes,and associated mobile genetic elements(MGEs)of MDR Enterobacteriaceae isolated from 6 duck farms in Zhejiang Province,China,were investigated.A total of 215 isolates were identified as Escherichia coli(64.65%),Klebsiella pneumoniae(12.09%),Proteus mirabilis(10.23%),Salmonella(8.84%),and Enterobacter cloacae(4.19%).Meanwhile,all isolates were resistant to at least two antibiotics.Most isolates carried tet(A)(85.12%),blaTEM(78.60%)and sul1(67.44%)resistance genes.Gene co-occurrence analysis showed that the resistance genes were associated with IS26 and integrons.A conjugative IncFII plasmid pSDM004 containing all the above MGEs was detected in Proteus mirabilis isolate SDM004.This isolate was resistant to 18 antibiotics and carried the blaNDM-5 gene.MGEs,especially plasmids,are the primary antibiotic resistance gene transmission route in duck farms.These findings provide a theoretical basis for the rational use of antibiotics in farms which are substantial for evaluating public health and food safety.
基金provided through research grant No.0035/2019/A1 from the Science and Technology Development Fund,Macao SARthe assistantship from the Faculty of Science and Technology,University of Macao。
文摘Surface wave inversion is a key step in the application of surface waves to soil velocity profiling.Currently,a common practice for the process of inversion is that the number of soil layers is assumed to be known before using heuristic search algorithms to compute the shear wave velocity profile or the number of soil layers is considered as an optimization variable.However,an improper selection of the number of layers may lead to an incorrect shear wave velocity profile.In this study,a deep learning and genetic algorithm hybrid learning procedure is proposed to perform the surface wave inversion without the need to assume the number of soil layers.First,a deep neural network is adapted to learn from a large number of synthetic dispersion curves for inferring the layer number.Then,the shear-wave velocity profile is determined by a genetic algorithm with the known layer number.By applying this procedure to both simulated and real-world cases,the results indicate that the proposed method is reliable and efficient for surface wave inversion.
基金supported by the National Natural Science Foundation of China(Grant No.32101541)the National Key R&D Program of China(Grant No.2022YFD2200400).
文摘Global climate change has increased concerns regarding biodiversity loss.However,many key conservation issues still required further research,including demographic history,deleterious mutation load,adaptive evolution,and putative introgression.Here we generated the first chromosome-level genome of the endangered Chinese hazelnut,Corylus chinensis,and compared the genomic signatures with its sympatric widespread C.kwechowensiseC.yunnanensis complex.We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation.Population genomics revealed that both C.chinensis and the C.kwechowensis eC.yunnanensis complex had diverged into two genetic lineages,forming a consistent pattern of southwestern-northern differentiation.Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene,whereas the widespread northern lineages have remained stable(C.chinensis)or have even recovered from population bottlenecks(C.kwechowensis eC.yunnanensis complex)during the Quaternary.Compared with C.kwechowensiseC.yunnanensis complex,C.chinensis showed significantly lower genomic diversity and higher inbreeding level.However,C.chinensis carried significantly fewer deleterious mutations than C.kwechowensiseC.yunnanensis complex,as more effective purging selection reduced the accumulation of homozygous variants.We also detected signals of positive selection and adaptive introgression in different lineages,which facilitated the accumulation of favorable variants and formation of local adaptation.Hence,both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C.chinensis.Overall,our study provides critical insights into lineage differentiation,local adaptation,and the potential for future recovery of endangered trees.
基金funded by the grant National Key R&D Program of China(2017ZX10103011-004 and 2018YFC1603804)the Science and Technology Program of Guangdong Province(2018B020207013 and 2019B030316013).
文摘Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals aged 28 days–85 years.A total of 706 stool samples from patients with acute gastroenteritis collected between January 2019 and January 2020 were analyzed for 17 causative pathogens,including RVA,using a Gastrointestinal Pathogen Panel,followed by genotyping,virus isolation,and complete sequencing to assess the genetic diversity of RVA.Results The overall RVA infection rate was 14.59%(103/706),with an irregular epidemiological pattern.The proportion of co-infection with RVA and other pathogens was 39.81%(41/103).Acute gastroenteritis is highly prevalent in young children aged 0–1 year,and RVA is the key pathogen circulating in patients 6–10 months of age with diarrhea.G9P[8](58.25%,60/103)was found to be the predominant genotype in the RVA strains,and the 41 RVA-positive strains that were successfully sequenced belonged to three different RVA genotypes in the phylogenetic analysis.Recombination analysis showed that gene reassortment events,selection pressure,codon usage bias,gene polymorphism,and post-translational modifications(PTMs)occurred in the G9P[8]and G3P[8]strains.Conclusion This study provides molecular evidence of RVA prevalence in the Pearl River Delta region of China,further enriching the existing information on its genetics and evolutionary characteristics and suggesting the emergence of genetic diversity.Strengthening the surveillance of genotypic changes and gene reassortment in RVA strains is essential for further research and a better understanding of strain variations for further vaccine development.
文摘In this editorial,we comment on the article by Marangoni et al,published in the recent issue of the World Journal of Gastroenterology 2023;29:5618-5629,about“Diet as an epigenetic factor in inflammatory bowel disease”.The authors emphasized the role of diet,especially the interaction with genetics,in promoting the inflam-matory process in inflammatory bowel disease(IBD)patients,focusing on DNA methylation,histone modifications,and the influence of microRNAs.In this editorial,we explore the interaction between genetics,gut microbiota,and diet,in an only way.Furthermore,we provided dietary recommendations for patients with IBD.The Western diet,characterized by a low fiber content and deficiency the micronutrients,impacts short-chain fatty acids production and may be related to the pathogenesis of IBD.On the other hand,the consumption of the Mediter-ranean diet and dietary fibers are associated with reduced risk of IBD flares,particularly in Crohn’s disease(CD)patients.According to the dietary guidance from the International Organization for the Study of Inflammatory Bowel Diseases(IOIBD),the regular consumption of fruits and vegetables while reducing the consumption of saturated,trans,dairy fat,additives,processed foods rich in maltodextrins,and artificial sweeteners containing sucralose or saccharine is recommended to CD patients.For patients with ulcerative colitis,the IOIBD recommends the increased intake of natural sources of omega-3 fatty acids and follows the same restrictive recommendations aimed at CD patients,with the possible inclusion of red meats.In conclusion,IBD is a complex and hetero-geneous disease,and future studies are needed to elucidate the influence of epigenetics on diet and microbiota in IBD patients.
基金This work was supported by Grants from the National Science Foundation of China to Yanwen Zhang(32272757,31972363)Grants from the Liaoning Provincial Department of Education Project to Dandan Wang(JYTMS20230698)Grants from the Liaoning Provincial Science and Technology Fund Project:Comparative Multi-Omics Study of Wild and Cultivated Species of Taxus chinensis.
文摘Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is,33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship,genetic diversity,and genetic structure between them by specific length amplified fragment sequencing(SLAF-seq).Finally,470725 polymorphic SLAF tags and 58622 valid SNP markers were obtained.Phylogenetic analysis showed that 61 samples were classified into 2 clusters:wild populations and cultivated populations,and some wild yews were categorized into the cultivated populations;the genetic diversity analysis showed that the Nei diversity index of wild populations(0.4068)was smaller than that of cultivated populations(0.4414),and the polymorphic information content(PIC)of wild populations(0.2861)was smaller than that of cultivated populations(0.3309).The genetic differentiation analysis showed that the total populations of gene diversity(H_(t))of cultivated and wild populations were respectively 0.8159 and 0.5685,the coefficient of gene differentiation(G_(st))of cultivated and wild populations was respectively 0.3021 and 0.1068,and the gene flow(N_(m))(2.4967)of wild populations was larger than cultivated populations(0.8199).The molecular variance(AMOVA)revealed that inter-population variation accounted for 29.57%of the total genetic variation,while intra-population variation accounted for 70.42% of the total genetic variation(p<0.001),this suggested that the genetic variation in the T.cuspidata is mainly attributed to within-population factors.In conclusion,the genetic distance between geographical ecological groups of wild populations was generally smaller than that of cultivated populations,and the degree of genetic diversity and genetic differentiation was smaller than that of cultivated populations.As evident,the utilization of SLAF-seq technology enables efficient and accurate development of SNP markers suitable for genetic analysis of T.cuspidata species.These developed SNP markers can provide a molecular foundation for T.cuspidata breeding,construction of genetic maps,variety identification,and association analysis of agronomic traits.
基金This study was supported by the Ministry of Higher Education,Malaysia(FRGS0322-SG-1/2013)Universiti Malaysia Sabah(GUG0521-2/2020).
文摘Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and haplotype.Methods:Thirty-nine blood samples infected with P.knowlesi were collected in Sabah,Malaysian Borneo and Peninsular Malaysia.The S-type SSU rRNA gene was amplified using polymerase chain reaction,cloned into a vector,and sequenced.The natural selection and haplotype of the S-type SSU rRNA gene sequences were determined using DnaSP v6 and illustrated using NETWORK v10.This study's 39 S-type SSU rRNA sequences and eight sequences from the Genbank database were subjected to phylogenetic analysis using MEGA 11.Results:Overall,the phylogenetic analysis showed no evidence of a geographical cluster of P.knowlesi isolates from different areas in Malaysia based on the S-type SSU rRNA gene sequences.The S-type SSU rRNA gene sequences were relatively conserved and with a purifying effect.Haplotype sharing of the S-type SSU rRNA gene was observed between the P.knowlesi isolates in Sabah,Malaysian Borneo,but not between Sabah,Malaysian Borneo and Peninsular Malaysia.Conclusions:This study suggests that the S-type SSU rRNA gene of P.knowlesi isolates in Sabah,Malaysian Borneo,and Peninsular Malaysia has fewer polymorphic sites,representing the conservation of the gene.These features make the S-type SSU rRNA gene suitable for comparative studies,such as determining the evolutionary relationships and common ancestry among P.knowlesi species.
