Objective China is among the 30 countries with a high burden of tuberculosis(TB)worldwide,and TB remains a public health concern.Kashgar Prefecture in the southern Xinjiang Autonomous Region is considered as one of th...Objective China is among the 30 countries with a high burden of tuberculosis(TB)worldwide,and TB remains a public health concern.Kashgar Prefecture in the southern Xinjiang Autonomous Region is considered as one of the highest TB burden regions in China.However,molecular epidemiological studies of Kashgar are lacking.Methods A population-based retrospective study was conducted using whole-genome sequencing(WGS)to determine the characteristics of drug resistance and the transmission patterns.Results A total of 1,668 isolates collected in 2020 were classified into lineages 2(46.0%),3(27.5%),and 4(26.5%).The drug resistance rates revealed by WGS showed that the top three drugs in terms of the resistance rate were isoniazid(7.4%,124/1,668),streptomycin(6.0%,100/1,668),and rifampicin(3.3%,55/1,668).The rate of rifampicin resistance was 1.8%(23/1,290)in the new cases and 9.4%(32/340)in the previously treated cases.Known resistance mutations were detected more frequently in lineage 2 strains than in lineage 3 or 4 strains,respectively:18.6%vs.8.7 or 9%,P<0.001.The estimated proportion of recent transmissions was 25.9%(432/1,668).Multivariate logistic analyses indicated that sex,age,occupation,lineage,and drug resistance were the risk factors for recent transmission.Despite the low rate of drug resistance,drug-resistant strains had a higher risk of recent transmission than the susceptible strains(adjusted odds ratio,1.414;95%CI,1.023–1.954;P=0.036).Among all patients with drug-resistant tuberculosis(DR-TB),78.4%(171/218)were attributed to the transmission of DR-TB strains.Conclusion Our results suggest that drug-resistant strains are more transmissible than susceptible strains and that transmission is the major driving force of the current DR-TB epidemic in Kashgar.展开更多
The common marmoset(Callithrix jacchus)has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies.Epileptic marmosets have been independ...The common marmoset(Callithrix jacchus)has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies.Epileptic marmosets have been independently reported in two Asian primate research centers.Nevertheless,the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated.Here,we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing.We identified 14558184 single nucleotide polymorphisms(SNPs)from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples.Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers.In addition,SNP and copy number variation(CNV)analyses suggested that the WW domain-containing oxidoreductase(WWOX)and Tyrosine-protein phosphatase nonreceptor type 21(PTPN21)genes may be associated with epilepsy in marmosets.Notably,KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets.This study provides valuable population genomic resources for marmosets in two Asian primate centers.Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers,while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.展开更多
BACKGROUND Gastric cancer(GC), a multifactorial disease, is caused by pathogens, such as Helicobacter pylori(H. pylori) and Epstein-Barr virus(EBV), and genetic components.AIM To investigate microbiomes and host genom...BACKGROUND Gastric cancer(GC), a multifactorial disease, is caused by pathogens, such as Helicobacter pylori(H. pylori) and Epstein-Barr virus(EBV), and genetic components.AIM To investigate microbiomes and host genome instability by cost-effective,low-coverage wholegenome sequencing,as biomarkers for GC subtyping.METHODS Samples from 40 GC patients were collected from Taizhou Hospital,Zhejiang Province,affiliated with Wenzhou Medical University.DNA from the samples was subjected to low-coverage wholegenome sequencing with a median genome coverage of 1.86×(range:1.03×to 3.17×) by Illumina×10,followed by copy number analyses using a customized bioinformatics workflow ultrasensitive chromosomal aneuploidy detector.RESULTS Of the 40 GC samples,20 (50%) were found to be enriched with microbiomes.EBV DNA was detected in 5 GC patients (12.5%).H.pylori DNA was found in 15 (37.5%) patients.The other 20(50%) patients were found to have relatively higher genomic instability.Copy number amplifications of the oncogenes,ERBB2 and KRAS,were found in 9 (22.5%) and 7 (17.5%) of the GC samples,respectively.EBV enrichment was found to be associated with tumors in the gastric cardia and fundus.H.pylori enrichment was found to be associated with tumors in the pylorus and antrum.Tumors with elevated genomic instability showed no localization and could be observed in any location.Additionally,H.pylori-enriched GC was found to be associated with the Borrmann type Ⅱ/Ⅲ and gastritis history.EBV-enriched GC was not associated with gastritis.No statistically significant correlation was observed between genomic instability and gastritis.Furthermore,these three different molecular subtypes showed distinct survival outcomes (P=0.019).EBV-positive tumors had the best prognosis,whereas patients with high genomic instability (CIN+) showed the worst survival.Patients with H.pylori infection showed intermediate prognosis compared with the other two subtypes.CONCLUSION Thus,using low-coverage whole-genome sequencing,GC can be classified into three categories based on disease etiology;this classification may prove useful for GC diagnosis and precision medicine.展开更多
Primary central nervous system lymphoma(PCNSL)is an uncommon non-Hodgkin’s lymphoma with poor prognosis.This study aimed to depict the genetic landscape of Chinese PCNSLs.Whole-genome sequencing was performed on 68 n...Primary central nervous system lymphoma(PCNSL)is an uncommon non-Hodgkin’s lymphoma with poor prognosis.This study aimed to depict the genetic landscape of Chinese PCNSLs.Whole-genome sequencing was performed on 68 newly diagnosed Chinese PCNSL samples,whose genomic characteristics and clinicopathologic features were also analyzed.Structural variations were identified in all patients with a mean of 349,which did not significantly influence prognosis.Copy loss occurred in all samples,while gains were detected in 77.9%of the samples.The high level of copy number variations was significantly associated with poor progression-free survival(PFS)and overall survival(OS).A total of 263 genes mutated in coding regions were identified,including 6 newly discovered genes(ROBO2,KMT2C,CXCR4,MYOM2,BCLAF1,and NRXN3)detected in≥10%of the cases.CD79B mutation was significantly associated with lower PFS,TMSB4X mutation and high expression of TMSB4X protein was associated with lower OS.A prognostic risk scoring system was also established for PCNSL,which included Karnofsky performance status and six mutated genes(BRD4,EBF1,BTG1,CCND3,STAG2,and TMSB4X).Collectively,this study comprehensively reveals the genomic landscape of newly diagnosed Chinese PCNSLs,thereby enriching the present understanding of the genetic mechanisms of PCNSL.展开更多
Objective: The increase in the development of resistance to multiple drugs in mycobacterium tuberculosis(MTB) poses a substantial obstacle to the prevention and management of tuberculosis(TB). A thorough investigation...Objective: The increase in the development of resistance to multiple drugs in mycobacterium tuberculosis(MTB) poses a substantial obstacle to the prevention and management of tuberculosis(TB). A thorough investigation of the genotypes linked to multidrug resistance is crucial for comprehending the mechanisms underlying drug resistance. The objective of this research was to assess the attributes of gene mutations associated with multidrug resistance in clinical isolates of mycobacterium tuberculosis through the utilization of whole-genome sequencing. Methods: A total of 124 strains of drug-resistant mycobacterium tuberculosis were collected, and the genomic DNA of both multidrug-resistant and rifampin-resistant strains were extracted and sequenced. Bioinformatics was used to analyze and compare multidrug resistance-related gene sequences in order to detect the variation of multidrug resistance genes. Results: The results revealed that the resistance spectrum of XDR-TB group was much wider than that of the other three groups, with the RR-TB group having the most limited resistance spectrum.Within the MDR-TB strains, fabG1 exhibited the highest frequency of mutations, while RRS, gyrA, and rpoB were identified as the predominant mutation bases in XDR-TB strains. Additionally, rpoB emerged as the primary mutation base in MDR-TB and RR-TB strains. Notably, the fabG1 mutation was found to be closely associated with PDR-TB. Furthermore, the correlation between the mutation rate of rpoB and multidrug resistance was deemed to be of secondary importance. Conclusion: Various strains of MTB exhibited distinct mechanisms of drug resistance, with the gene mutations of fabG1,RRS, gyrA, and rpoB potentially playing a pivotal role in the development of drug resistance. However, the primary genes responsible for drug resistance mutations varied among different strains of TB.展开更多
The fall armyworm(FAW),Spodoptera frugiperda,is a major pest native to the Americas that has recently invaded the Old World.Point mutations in the target-site proteins acetylcholinesterase-1(ace-1),voltage-gated sodiu...The fall armyworm(FAW),Spodoptera frugiperda,is a major pest native to the Americas that has recently invaded the Old World.Point mutations in the target-site proteins acetylcholinesterase-1(ace-1),voltage-gated sodium channel(VGSC)and ryanodine receptor(RyR)have been identified in S.frugiperda as major resistance mechanisms to organophosphate,pyrethroid and diamide insecticides respectively.Mutations in the adenosine triphosphate-binding cassette transporter C2 gene(ABCC2)have also been identified to confer resistance to Cry IF protein.In this study,we applied a whole-genome sequencing(WGS)approach to identify point mutations in the target-site genes in 150 FAW individuals collected from China,Malawi,Uganda and Brazil.This approach revealed three amino acid substitutions(A201S,G227A and F290V)of S.frugiperda ace-1,which are known to be associated with organophosphate resistance.The Brazilian population had all three ace-1 point mutations and the 227A allele(mean frequency=0.54)was the most common.Populations from China,Malawi and Uganda harbored two of the three ace-1 point mutations(A201S and F290V)with the 290V allele(0.47-0.58)as the dominant allele.Point mutations in VGSC(T929I,L932F and L1014F)and RyR(I4790M and G4946E)were not detected in any of the 150 individuals.A novel 12-bp insertion mutation in exon 15 of the ABCC2 gene was identified in some of the Brazilian individuals but absent in the invasive populations.Our results not only demonstrate robustness of the WGS-based genomic approach for detection of resistance mutations,but also provide insights for improvement of resistance management tactics in S.frugiperda.展开更多
We aimed to develop a whole-genome sequencing(WGS)-based copy number variant(CNV)calling algorithm with the potential of replacing chromosomal microarray assay(CMA)for clinical diagnosis.JAX-CNV is thus developed for ...We aimed to develop a whole-genome sequencing(WGS)-based copy number variant(CNV)calling algorithm with the potential of replacing chromosomal microarray assay(CMA)for clinical diagnosis.JAX-CNV is thus developed for CNV detection from WGS data.The performance of this CNV calling algorithm was evaluated in a blinded manner on 31 samples and compared to the 112 CNVs reported by clinically validated CMAs for these 31 samples.The result showed that JAX-CNV recalled 100%of these CNVs.Besides,JAX-CNV identified an average of 30 CNVs per individual,representing an approximately seven-fold increase compared to calls of clinically validated CMAs.Experimental validation of 24 randomly selected CNVs showed one false positive,i.e.,a false discovery rate(FDR)of 4.17%.A robustness test on lowercoverage data revealed a 100%sensitivity for CNVs larger than 300 kb(the current threshold for College of American Pathologists)down to 10×coverage.For CNVs larger than 50 kb,sensitivities were 100%for coverages deeper than 20×,97%for 15×,and 95%for 10×.We developed a WGS-based CNV pipeline,including this newly developed CNV caller JAX-CNV,and found it capable of detecting CMA-reported CNVs at a sensitivity of 100%with about a FDR of 4%.We propose that JAX-CNV could be further examined in a multi-institutional study to justify the transition of first-tier genetic testing from CMAs to WGS.JAX-CNV is available at https://github.com/TheJacksonLaboratory/JAX-CNV.展开更多
We performed a genome-wide scan to detect selection signatures that showed evidence of positive selection in the domestication process by re-sequencing the whole genomes of Landrace and Yorkshire pigs.Fifteen annotate...We performed a genome-wide scan to detect selection signatures that showed evidence of positive selection in the domestication process by re-sequencing the whole genomes of Landrace and Yorkshire pigs.Fifteen annotated elements with 13 associated genes were identified using the Z-transformed FST(Z(FST))method,and 208 annotated elements with 140 associated genes were identified using the Z-transformed heterozygosity(ZHp)method.The functional analysis and the results of previous studies showed that most of the candidate genes were associated with basic metabolism,disease resistance,cellular processes,and biochemical signals,and several were related to body morphology and organs.They included PPP3CA,which plays an essential role in the transduction of intracellular Ca2+-mediated signals,and WWTR1,which plays a pivotal role in organ size control and tumor suppression.These results suggest that genes associated with body morphology were subject to selection pressure during domestication,whereas genes involved in basic metabolism and disease resistance were subject to selection during artificial breeding.Our findings provide new insights into the potential genetic variation of phenotypic diversity in different pig breeds and will help to better understand the selection effects of modern breeding in Landrace and Yorkshire pigs.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
The application of microorganisms as probiotics is limited due to lack of safety evaluation.Here,a novel multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 with aroma-producing properties was identified from ...The application of microorganisms as probiotics is limited due to lack of safety evaluation.Here,a novel multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 with aroma-producing properties was identified from marine mangrove microorganisms.Its safety and probiotic properties were assessed in accordance with phenotype and whole-genome sequencing analysis.Results showed that the genes and phenotypic expression of related virulence,antibiotic resistance and retroelement were rarely found.Hyphal morphogenesis genes(SIT4,HOG1,SPA2,ERK1,ICL1,CST20,HSP104,TPS1,and RHO1)and phospholipase secretion gene(VPS4)were annotated.True hyphae and phospholipase were absent.Only one retroelement(Tad1-65_BG)was found.Major biogenic amines(BAs)encoding genes were absent,except for spermidine synthase(JA9_002594),spermine synthase(JA9_004690),and tyrosine decarboxylase(inx).The production of single BAs and total BAs was far below the food-defined thresholds.GXDK6 had no resistance to common antifungal drugs.Virulence enzymes,such as gelatinase,DNase,hemolytic,lecithinase,and thrombin were absent.Acute toxicity test with mice demonstrated that GXDK6 is safe.GXDK6 has a good reproduction ability in the simulation gastrointestinal tract.GXDK6 also has a strong antioxidant ability,β-glucosidase,and inulinase activity.To sum up,GXDK6 is considered as a safe probiotic for human consumption and food fermentation.展开更多
Germplasm resource innovation is a crucial factor for cultivar development,particularly within the context of hybrid rice breeding based on the three-line system.Quan 9311A,a cytoplasmic male sterile(CMS)line,has been...Germplasm resource innovation is a crucial factor for cultivar development,particularly within the context of hybrid rice breeding based on the three-line system.Quan 9311A,a cytoplasmic male sterile(CMS)line,has been successfully cultivated using rice restoration materials and extensively employed as a female parent in hybrid breeding program in China.This line was developed by crossing the CMS line Zhong 9A with a two-line restorer line 93-11,with the intention of eliminating the restoring ability of 93-11 while retaining the sterility gene WA352c from Zhong 9A.Quan 9311A effectively amalgamates the most favorable agronomic traits from both parental lines.In this study,the relationship between phenotypic characteristics and the known functional genes of Quan 9311A were analyzed using the rice genome navigation technology based on whole-genome sequencing.The findings revealed that Quan 9311A harbors multiple superior alleles from both 93-11 and Zhong 9A,providing exceptional agronomic traits that are unavailable in earlier CMS lines.Despite the removal of the fertility restorer gene Rf3 from 93-11,numerous chromosomal segments from 93-11 persist in the Quan 9311A genome.Furthermore,the hybrid rice Quanyousimiao(QYSM)and the restorer line Wushansimiao(WSSM)were used as examples to illustrate the important role of Quan 9311A as the female parent in heterosis.It was found that QYSM carries a great number of superior alleles,which accounts for its high grain yield and wide adaptability.These insights not only advanced the utilization of hybrid rice pairing groups but also provided guidance for future breeding endeavors.The study introduced innovative concepts to further integrate genomics with traditional breeding techniques.Ultimately,Quan 9311A signified a significant milestone in rice breeding technology,opening up novel avenues for hybrid rice development.展开更多
Objective To explore the genotyping characteristics of human fecal Escherichia coli(E. coli) and the relationships between antibiotic resistance genes(ARGs) and multidrug resistance(MDR) of E. coli in Miyun District, ...Objective To explore the genotyping characteristics of human fecal Escherichia coli(E. coli) and the relationships between antibiotic resistance genes(ARGs) and multidrug resistance(MDR) of E. coli in Miyun District, Beijing, an area with high incidence of infectious diarrheal cases but no related data.Methods Over a period of 3 years, 94 E. coli strains were isolated from fecal samples collected from Miyun District Hospital, a surveillance hospital of the National Pathogen Identification Network. The antibiotic susceptibility of the isolates was determined by the broth microdilution method. ARGs,multilocus sequence typing(MLST), and polymorphism trees were analyzed using whole-genome sequencing data(WGS).Results This study revealed that 68.09% of the isolates had MDR, prevalent and distributed in different clades, with a relatively high rate and low pathogenicity. There was no difference in MDR between the diarrheal(49/70) and healthy groups(15/24).Conclusion We developed a random forest(RF) prediction model of TEM.1 + baeR + mphA + mphB +QnrS1 + AAC.3-IId to identify MDR status, highlighting its potential for early resistance identification. The causes of MDR are likely mobile units transmitting the ARGs. In the future, we will continue to strengthen the monitoring of ARGs and MDR, and increase the number of strains to further verify the accuracy of the MDR markers.展开更多
Objective Mutations in 23 S rRNA gene are known to be associated with macrolide resistance in Mycoplasma pneumoniae(M. pneumoniae). However, these mutations alone do not fully explain the high resistance rates in Asia...Objective Mutations in 23 S rRNA gene are known to be associated with macrolide resistance in Mycoplasma pneumoniae(M. pneumoniae). However, these mutations alone do not fully explain the high resistance rates in Asia. The aim of this study was to investigate other possible mutations involved in macrolide resistance in M. pneumoniae. Methods The whole genomes of 10 clinical isolates of M. pneumoniae with macrolide resistance were sequenced by Illumina Hi Seq2000 platform. The role of the macrolide-specific efflux transporter was assessed by efflux-pump inhibition assays with reserpine and carbonyl cyanide m-chlorophenyl-hydrazone(CCCP). Results A total of 56 single nucleotide polymorphisms(SNPs) were identified in 10 clinical isolates in comparison to the reference strains M129 and FH. Strikingly, 4 of 30 SNPs causing non-synonymous mutations were clustered in macrolide-specific efflux system gene mac B encoding macrolide-specific efflux pump protein of the ATP-binding cassette transporter family. In assays of the minimal inhibitory concentrations(MIC) of macrolide antibiotics in the presence of the efflux pump inhibitors caused a significant decrease of MICs, even under detectable levels in some strains. Conclusion Our study suggests that macrolide efflux pump may contribute to macrolide resistance in M. pneumoniae in addition to the common point mutations in 23 S r RNA gene.展开更多
Gonorrhea is one of the most common sexually transmitted diseases worldwide. To cure infection and prevent transmission,timely and appropriate antimicrobial therapy is necessary. Unfortunately, Neisseria gonorrhoeae, ...Gonorrhea is one of the most common sexually transmitted diseases worldwide. To cure infection and prevent transmission,timely and appropriate antimicrobial therapy is necessary. Unfortunately, Neisseria gonorrhoeae, the etiological agent of gonorrhea, has acquired nearly all known mechanisms of antimicrobial resistance(AMR), thereby compromising the efficacy of antimicrobial therapy. Treatment failure resulting from AMR has become a global public health concern. Whole-genome sequencing is an effective method to determine the AMR characteristics of N. gonorrhoeae. Compared with next-generation sequencing, the MinION sequencer(Oxford Nanopore Technologies(ONT)) has the advantages of long read length and portability. Based on a pilot study using MinION to sequence the genome of N. gonorrhoeae, we optimized the workflow of sequencing and data analysis in the current study. Here we sequenced nine isolates within one flow cell using a multiplexed sequencing strategy. After hybrid assembly with Illumina reads, nine integral circular chromosomes were obtained. By using the online tool Pathogenwatch and a BLAST-based workflow, we acquired complete AMR profiles related to seven classes of antibiotics. We also evaluated the performance of ONT-only assemblies. Most AMR determinants identified by ONT-only assemblies were the same as those identified by hybrid assemblies. Moreover, one of the nine assemblies indicated a potentially novel antimicrobial-related mutation located in mtrR which results in a frame-shift, premature stop codon, and truncated peptide.In addition, this is the first study using the MinION sequencer to obtain complete genome sequences of N. gonorrhoeae strains which are epidemic in China. This study shows that complete genome sequences and antimicrobial characteristics of N.gonorrhoeae can be obtained using the MinION sequencer in a simple and cost-effective manner, with hardly any knowledge of bioinformatics required. More importantly, this strategy provides us with a potential approach to discover new AMR determinants.展开更多
The three-dimensional(3D)conformation of chromatin is integral to the precise regulation of gene expression.The 3D genome and genomic variations in non-alcoholic fatty liver disease(NAFLD)are largely unknown,despite t...The three-dimensional(3D)conformation of chromatin is integral to the precise regulation of gene expression.The 3D genome and genomic variations in non-alcoholic fatty liver disease(NAFLD)are largely unknown,despite their key roles in cellular function and physiological processes.Highthroughput chromosome conformation capture(Hi-C),Nanopore sequencing,and RNA-sequencing(RNA-seq)assays were performed on the liver of normal and NAFLD mice.A high-resolution 3D chromatin interaction map was generated to examine different 3D genome hierarchies including A/B compartments,topologically associated domains(TADs),and chromatin loops by Hi-C,and whole genome sequencing identifying structural variations(SVs)and copy number variations(CNVs)by Nanopore sequencing.We identified variations in thousands of regions across the genome with respect to 3D chromatin organization and genomic rearrangements,between normal and NAFLD mice,and revealed gene dysregulation frequently accompanied by these variations.Candidate target genes were identified in NAFLD,impacted by genetic rearrangements and spatial organization disruption.Our data provide a high-resolution 3D genome interaction resource for NAFLD investigations,revealed the relationship among genetic rearrangements,spatial organization disruption,and gene regulation,and identified candidate genes associated with these variations implicated in the pathogenesis of NAFLD.The newly findings offer insights into novel mechanisms of NAFLD pathogenesis and can provide a new conceptual framework for NAFLD therapy.展开更多
BACKGROUND Interleukin 10 receptor alpha subunit(IL10RA)dysfunction is the main cause of very early-onset inflammatory bowel disease(VEO-IBD)in East Asians.AIM To identify disease-causing gene mutations in four patien...BACKGROUND Interleukin 10 receptor alpha subunit(IL10RA)dysfunction is the main cause of very early-onset inflammatory bowel disease(VEO-IBD)in East Asians.AIM To identify disease-causing gene mutations in four patients with VEO-IBD and verify functional changes related to the disease-causing mutations.METHODS From May 2016 to September 2020,four young patients with clinically diagnosed VEO-IBD were recruited.Before hospitalization,using targeted gene panel sequencing and trio-whole-exome sequencing(WES),three patients were found to harbor a IL10RA mutation(c.301C>T,p.R101W in one patient;c.537G>A,p.T179T in two patients),but WES results of the fourth patient were not conclusive.We performed whole-genome sequencing(WGS)on patients A and B and reanalyzed the data from patients C and D.Peripheral blood mononuclear cells(PBMCs)from patient D were isolated and stimulated with lipopolysaccharide(LPS),interleukin 10(IL-10),and LPS+IL-10.Serum IL-10 levels in four patients and tumor necrosis factor-α(TNF-α)in the cell supernatant were determined by enzyme-linked immunosorbent assay.Phosphorylation of signal transducer and activator of transcription 3(STAT3)at Tyr705 and Ser727 in PBMCs was determined by western blot analysis.RESULTS The four children in our study consisted of two males and two females.The age at disease onset ranged from 18 d to 9 mo.After hospitalization,a novel 333-bp deletion encompassing exon 1 of IL10RA was found in patients A and B using WGS and was found in patients C and D after reanalysis of their WES data.Patient D was homozygous for the 333 bp deletion.All four patients had elevated serum IL-10 levels.In vitro,IL-10-stimulated PBMCs from patient D failed to induce STAT3 phosphorylation at Tyr705 and only minimally suppressed TNF-αproduction induced by LPS.Phosphorylation at Ser727 in PBMCs was not affected by LPS or LPS+IL-10 in both healthy subjects and in patient D.CONCLUSION WGS revealed a novel 333-bp deletion of IL10RA in four patients with VEO-IBD,whereas the WES results were inconclusive.展开更多
Objectives:The wide use of antibiotics for acne is the main cause of drug-resistant Cutibacterium acnes.However,the complete genetic sequence reference of C.acnes has not yet been reported.Herein,we report the complet...Objectives:The wide use of antibiotics for acne is the main cause of drug-resistant Cutibacterium acnes.However,the complete genetic sequence reference of C.acnes has not yet been reported.Herein,we report the complete genetic sequence of Cutibacterium acnes type strain ATCC6919.Methods:Whole-genome sequencing of Cutibacterium acnes ATCC6919 was performed using both the Illumina Hiseq4000 and PacBio RSII single-molecule real-time sequencing platforms.The generated sequence reads were de novo assembled using the HGAP3 protocol of single-molecule real-time analysis v.2.3.0 software.The draft genome was annotated and further analyzed by various bioinformatics tools.Results:The total genome length of Cutibacterium acnes ATCC6919 was 2,495,001 bp(60.02%G+C content),with 2,450 coding sequences including 2,358 proteins,45 tRNAs,9 rRNAs,and 1 sRNA.The Comprehensive Antibiotic Resistance Database showed that the gene(thy A)found in ATCC6919 was associated with resistance to aminosalicylic acid.Antimicrobial susceptibility testing showed that this isolate was not sensitive to metronidazole and sulfamethoxazole,but was sensitive to all other tested antimicrobials(erythromycin,azithromycin,clarithromycin,tetracycline,minocycline,trimethoprim,levofloxacin,ceftriaxone,and doxycycline).Conclusion:This study reports the complete genome sequence of Cutibacterium acnes ATCC6919,which provides a valuable reference for comparative analysis based on the genomic characteristics and resistance gene diversity of Cutibacterium acnes.展开更多
The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study.In the past decade,a large number of phylogenetic studies adopti...The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study.In the past decade,a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era.In the meantime,a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent.This review focuses on the utility of genomic data(from organelle genomes,to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations,describes the baseline methodology of experimental and analytical procedures,and summarizes recent progress in flowering plant phylogenomics at the ordinal,familial,tribal,and lower levels.We also discuss the challenges,such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors,and underlying biological factors,such as whole-genome duplication,hybridization/introgression,and incomplete lineage sorting,together suggesting that a bifurcating tree may not be the best model for the tree of life.Finally,we discuss promising avenues for future plant phylogenomic studies.展开更多
Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identif...Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identifying the mechanism responsible for the tolerance of a highly toxic diet,we have made a major advancement by explaining the genome of sika deer.We generated the first high-quality,chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food,especially the expansion of the UGT family 2 subfamily B of UGT genes.The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation.Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.展开更多
High myopia has long been highly prevalent worldwide with a largely yet unexplained genetic contribution.To identify novel susceptibility genes for axial length(AL)in highly myopic eyes,a genome-wide association study...High myopia has long been highly prevalent worldwide with a largely yet unexplained genetic contribution.To identify novel susceptibility genes for axial length(AL)in highly myopic eyes,a genome-wide association study(GWAS)was performed using the genomic dataset of 350 deep whole-genome sequencing data from highly myopic patients.Top single nucleotide polymorphisms(SNPs)were functionally annotated.Immunofluorescence staining,quantitative polymerase chain reaction,and western blot were performed using neural retina of form-deprived myopic mice.Enrichment analyses were further performed.We identified the four top SNPs and found that ADAM Metallopeptidase With Thrombospondin Type 1 Motif 16(ADAMTS16)and Phosphatidylinositol Glycan Anchor Biosynthesis Class Z(PIGZ)had the potential of clinical signifi-cance.Animal experiments confirmed that PIGZ expression could be observed and showed higher expression level in form-deprived mice,especially in the ganglion cell layer.The messenger RNA(mRNA)levels of both ADAMTS16 and PIGZ were significantly higher in the neural retina of form-deprived eyes(p=0.005 and 0.007 respectively),and both proteins showed significantly upregulated expression in the neural retina of deprived eyes(p=0.004 and 0.042,respectively).Enrichment analysis revealed a significant role of cellular adhesion and signal transduction in AL,and also several AL-related pathways including circadian entrainment and inflammatory mediator regulation of transient receptor potential channels were proposed.In conclusion,the current study identified four novel SNPs associated with AL in highly myopic eyes and confirmed that the expression of ADAMTS16 and PIGZ was significantly upregulated in neural retina of deprived eyes.Enrichment analyses provided novel insight into the etiology of high myopia and opened avenues for future research interest.展开更多
基金funded by the National Key R&D Program of China [2022YFC2305200]Natural Science Foundation of Xinjiang Uygur Autonomous Region [2021A01D145 and 2022D01A115]Applied Technology Research and Development Programing Project of Kashgar Prefecture [KS2021031 and KS2021034]。
文摘Objective China is among the 30 countries with a high burden of tuberculosis(TB)worldwide,and TB remains a public health concern.Kashgar Prefecture in the southern Xinjiang Autonomous Region is considered as one of the highest TB burden regions in China.However,molecular epidemiological studies of Kashgar are lacking.Methods A population-based retrospective study was conducted using whole-genome sequencing(WGS)to determine the characteristics of drug resistance and the transmission patterns.Results A total of 1,668 isolates collected in 2020 were classified into lineages 2(46.0%),3(27.5%),and 4(26.5%).The drug resistance rates revealed by WGS showed that the top three drugs in terms of the resistance rate were isoniazid(7.4%,124/1,668),streptomycin(6.0%,100/1,668),and rifampicin(3.3%,55/1,668).The rate of rifampicin resistance was 1.8%(23/1,290)in the new cases and 9.4%(32/340)in the previously treated cases.Known resistance mutations were detected more frequently in lineage 2 strains than in lineage 3 or 4 strains,respectively:18.6%vs.8.7 or 9%,P<0.001.The estimated proportion of recent transmissions was 25.9%(432/1,668).Multivariate logistic analyses indicated that sex,age,occupation,lineage,and drug resistance were the risk factors for recent transmission.Despite the low rate of drug resistance,drug-resistant strains had a higher risk of recent transmission than the susceptible strains(adjusted odds ratio,1.414;95%CI,1.023–1.954;P=0.036).Among all patients with drug-resistant tuberculosis(DR-TB),78.4%(171/218)were attributed to the transmission of DR-TB strains.Conclusion Our results suggest that drug-resistant strains are more transmissible than susceptible strains and that transmission is the major driving force of the current DR-TB epidemic in Kashgar.
基金supported by the National Natural Science Foundation of China (82001372)National Key Research and Development Program of China (2018YFE0126700)+3 种基金Shanghai Jiao Tong University 2030 Initiative (WH510363001-7)Shanghai Municipal Commission of Science and Technology Program (21dz2210100)Shanghai Education Commission Research and Innovation Program (2019-01-07-00-02-E00037)a National Institutes of Health (NIH)grant (5R01HG002385)to E.E.E。
文摘The common marmoset(Callithrix jacchus)has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies.Epileptic marmosets have been independently reported in two Asian primate research centers.Nevertheless,the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated.Here,we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing.We identified 14558184 single nucleotide polymorphisms(SNPs)from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples.Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers.In addition,SNP and copy number variation(CNV)analyses suggested that the WW domain-containing oxidoreductase(WWOX)and Tyrosine-protein phosphatase nonreceptor type 21(PTPN21)genes may be associated with epilepsy in marmosets.Notably,KCTD18-like gene deletion was more common in epileptic marmosets than control marmosets.This study provides valuable population genomic resources for marmosets in two Asian primate centers.Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers,while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.
基金Supported by Program of Taizhou Science and Technology Grant,No.20ywb29Medical Health Science and Technology Project of Zhejiang Province,No.2021PY083+2 种基金Key Technology Research and Development Program of Zhejiang Province,No.2019C03040Open Project Program of Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province,No.21SZDSYS01 and 21SZDSYS09Major Research Program of Taizhou Enze Medical Center Grant,No.19EZZDA2
文摘BACKGROUND Gastric cancer(GC), a multifactorial disease, is caused by pathogens, such as Helicobacter pylori(H. pylori) and Epstein-Barr virus(EBV), and genetic components.AIM To investigate microbiomes and host genome instability by cost-effective,low-coverage wholegenome sequencing,as biomarkers for GC subtyping.METHODS Samples from 40 GC patients were collected from Taizhou Hospital,Zhejiang Province,affiliated with Wenzhou Medical University.DNA from the samples was subjected to low-coverage wholegenome sequencing with a median genome coverage of 1.86×(range:1.03×to 3.17×) by Illumina×10,followed by copy number analyses using a customized bioinformatics workflow ultrasensitive chromosomal aneuploidy detector.RESULTS Of the 40 GC samples,20 (50%) were found to be enriched with microbiomes.EBV DNA was detected in 5 GC patients (12.5%).H.pylori DNA was found in 15 (37.5%) patients.The other 20(50%) patients were found to have relatively higher genomic instability.Copy number amplifications of the oncogenes,ERBB2 and KRAS,were found in 9 (22.5%) and 7 (17.5%) of the GC samples,respectively.EBV enrichment was found to be associated with tumors in the gastric cardia and fundus.H.pylori enrichment was found to be associated with tumors in the pylorus and antrum.Tumors with elevated genomic instability showed no localization and could be observed in any location.Additionally,H.pylori-enriched GC was found to be associated with the Borrmann type Ⅱ/Ⅲ and gastritis history.EBV-enriched GC was not associated with gastritis.No statistically significant correlation was observed between genomic instability and gastritis.Furthermore,these three different molecular subtypes showed distinct survival outcomes (P=0.019).EBV-positive tumors had the best prognosis,whereas patients with high genomic instability (CIN+) showed the worst survival.Patients with H.pylori infection showed intermediate prognosis compared with the other two subtypes.CONCLUSION Thus,using low-coverage whole-genome sequencing,GC can be classified into three categories based on disease etiology;this classification may prove useful for GC diagnosis and precision medicine.
基金supported by funds from the Translational Research Grant of National Clinical Research Center for Hematologic Disease (No.2020ZKZC01)the National Natural Science Foundation of China (Nos.81830006,82170219,and 81800188)the Lymphoma Research Fund of China Anti-Cancer Association.
文摘Primary central nervous system lymphoma(PCNSL)is an uncommon non-Hodgkin’s lymphoma with poor prognosis.This study aimed to depict the genetic landscape of Chinese PCNSLs.Whole-genome sequencing was performed on 68 newly diagnosed Chinese PCNSL samples,whose genomic characteristics and clinicopathologic features were also analyzed.Structural variations were identified in all patients with a mean of 349,which did not significantly influence prognosis.Copy loss occurred in all samples,while gains were detected in 77.9%of the samples.The high level of copy number variations was significantly associated with poor progression-free survival(PFS)and overall survival(OS).A total of 263 genes mutated in coding regions were identified,including 6 newly discovered genes(ROBO2,KMT2C,CXCR4,MYOM2,BCLAF1,and NRXN3)detected in≥10%of the cases.CD79B mutation was significantly associated with lower PFS,TMSB4X mutation and high expression of TMSB4X protein was associated with lower OS.A prognostic risk scoring system was also established for PCNSL,which included Karnofsky performance status and six mutated genes(BRD4,EBF1,BTG1,CCND3,STAG2,and TMSB4X).Collectively,this study comprehensively reveals the genomic landscape of newly diagnosed Chinese PCNSLs,thereby enriching the present understanding of the genetic mechanisms of PCNSL.
文摘Objective: The increase in the development of resistance to multiple drugs in mycobacterium tuberculosis(MTB) poses a substantial obstacle to the prevention and management of tuberculosis(TB). A thorough investigation of the genotypes linked to multidrug resistance is crucial for comprehending the mechanisms underlying drug resistance. The objective of this research was to assess the attributes of gene mutations associated with multidrug resistance in clinical isolates of mycobacterium tuberculosis through the utilization of whole-genome sequencing. Methods: A total of 124 strains of drug-resistant mycobacterium tuberculosis were collected, and the genomic DNA of both multidrug-resistant and rifampin-resistant strains were extracted and sequenced. Bioinformatics was used to analyze and compare multidrug resistance-related gene sequences in order to detect the variation of multidrug resistance genes. Results: The results revealed that the resistance spectrum of XDR-TB group was much wider than that of the other three groups, with the RR-TB group having the most limited resistance spectrum.Within the MDR-TB strains, fabG1 exhibited the highest frequency of mutations, while RRS, gyrA, and rpoB were identified as the predominant mutation bases in XDR-TB strains. Additionally, rpoB emerged as the primary mutation base in MDR-TB and RR-TB strains. Notably, the fabG1 mutation was found to be closely associated with PDR-TB. Furthermore, the correlation between the mutation rate of rpoB and multidrug resistance was deemed to be of secondary importance. Conclusion: Various strains of MTB exhibited distinct mechanisms of drug resistance, with the gene mutations of fabG1,RRS, gyrA, and rpoB potentially playing a pivotal role in the development of drug resistance. However, the primary genes responsible for drug resistance mutations varied among different strains of TB.
基金National Key Research Development Program of China(No.2019YFD0300103 to YW)the Fundamental Research Funds for the Central Universities of China(KYZ201920 to YW).
文摘The fall armyworm(FAW),Spodoptera frugiperda,is a major pest native to the Americas that has recently invaded the Old World.Point mutations in the target-site proteins acetylcholinesterase-1(ace-1),voltage-gated sodium channel(VGSC)and ryanodine receptor(RyR)have been identified in S.frugiperda as major resistance mechanisms to organophosphate,pyrethroid and diamide insecticides respectively.Mutations in the adenosine triphosphate-binding cassette transporter C2 gene(ABCC2)have also been identified to confer resistance to Cry IF protein.In this study,we applied a whole-genome sequencing(WGS)approach to identify point mutations in the target-site genes in 150 FAW individuals collected from China,Malawi,Uganda and Brazil.This approach revealed three amino acid substitutions(A201S,G227A and F290V)of S.frugiperda ace-1,which are known to be associated with organophosphate resistance.The Brazilian population had all three ace-1 point mutations and the 227A allele(mean frequency=0.54)was the most common.Populations from China,Malawi and Uganda harbored two of the three ace-1 point mutations(A201S and F290V)with the 290V allele(0.47-0.58)as the dominant allele.Point mutations in VGSC(T929I,L932F and L1014F)and RyR(I4790M and G4946E)were not detected in any of the 150 individuals.A novel 12-bp insertion mutation in exon 15 of the ABCC2 gene was identified in some of the Brazilian individuals but absent in the invasive populations.Our results not only demonstrate robustness of the WGS-based genomic approach for detection of resistance mutations,but also provide insights for improvement of resistance management tactics in S.frugiperda.
基金supported in part by the operational funds from The First Affiliated Hospital of Xi’an Jiaotong University, Chinasupported by the National Institutes of Health, USA (Grant Nos. U24AG041689 and U54AG052427)+5 种基金supported by the National Natural Science Foundation of China (Grant Nos. 61702406 and 31671372)the National Science and Technology Major Project of China (Grant No. 2018ZX10302205)the National Key R&D Program of China (Grant Nos. 2018YFC0910400 and 2017YFC0907500)the General Financial Grant from the China Postdoctoral Science Foundation (Grant No. 2017M623178)supported in part by the Ewha Womans University Research, South Korea (Grant No. 2018-2019)supported in part by the Connecticut Bio-Innovative Fund, USA
文摘We aimed to develop a whole-genome sequencing(WGS)-based copy number variant(CNV)calling algorithm with the potential of replacing chromosomal microarray assay(CMA)for clinical diagnosis.JAX-CNV is thus developed for CNV detection from WGS data.The performance of this CNV calling algorithm was evaluated in a blinded manner on 31 samples and compared to the 112 CNVs reported by clinically validated CMAs for these 31 samples.The result showed that JAX-CNV recalled 100%of these CNVs.Besides,JAX-CNV identified an average of 30 CNVs per individual,representing an approximately seven-fold increase compared to calls of clinically validated CMAs.Experimental validation of 24 randomly selected CNVs showed one false positive,i.e.,a false discovery rate(FDR)of 4.17%.A robustness test on lowercoverage data revealed a 100%sensitivity for CNVs larger than 300 kb(the current threshold for College of American Pathologists)down to 10×coverage.For CNVs larger than 50 kb,sensitivities were 100%for coverages deeper than 20×,97%for 15×,and 95%for 10×.We developed a WGS-based CNV pipeline,including this newly developed CNV caller JAX-CNV,and found it capable of detecting CMA-reported CNVs at a sensitivity of 100%with about a FDR of 4%.We propose that JAX-CNV could be further examined in a multi-institutional study to justify the transition of first-tier genetic testing from CMAs to WGS.JAX-CNV is available at https://github.com/TheJacksonLaboratory/JAX-CNV.
基金supported by the grants from the Sichuan Science and Technology Program,China(2020YFN0024)the earmarked fund for the China Agriculture Research System(CARS-35-01A)+2 种基金the National Key R&D Program of China(2018YFD0501204)the National Natural Science Foundation of China(C170102)the Sichuan Innovation Team of Pig,China(sccxtd-2021-08)。
文摘We performed a genome-wide scan to detect selection signatures that showed evidence of positive selection in the domestication process by re-sequencing the whole genomes of Landrace and Yorkshire pigs.Fifteen annotated elements with 13 associated genes were identified using the Z-transformed FST(Z(FST))method,and 208 annotated elements with 140 associated genes were identified using the Z-transformed heterozygosity(ZHp)method.The functional analysis and the results of previous studies showed that most of the candidate genes were associated with basic metabolism,disease resistance,cellular processes,and biochemical signals,and several were related to body morphology and organs.They included PPP3CA,which plays an essential role in the transduction of intracellular Ca2+-mediated signals,and WWTR1,which plays a pivotal role in organ size control and tumor suppression.These results suggest that genes associated with body morphology were subject to selection pressure during domestication,whereas genes involved in basic metabolism and disease resistance were subject to selection during artificial breeding.Our findings provide new insights into the potential genetic variation of phenotypic diversity in different pig breeds and will help to better understand the selection effects of modern breeding in Landrace and Yorkshire pigs.
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This research was supported by the Funding Project of Chinese Central Government Guiding to the Guangxi Local Science and Technology Development(GUIKEZY21195021)the Natural Science Fund for Distinguished Young Scholars of Guangxi Zhuang Autonomous Region of China(2019GXNSFFA245011)+3 种基金the Funding Project of Chinese Central Government Guiding to the Nanning Local Science and Technology Development(20231012)the Funding Projects of Guangxi Key Research and Development Plan(GUIKE AB23075173)the Funding Project of Technological Development from Angel Yeast(Chongzuo)Co.,Ltd.(JS1006020230722019)the Innovation Project of Guangxi Graduate Education(YCBZ2021012).
文摘The application of microorganisms as probiotics is limited due to lack of safety evaluation.Here,a novel multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 with aroma-producing properties was identified from marine mangrove microorganisms.Its safety and probiotic properties were assessed in accordance with phenotype and whole-genome sequencing analysis.Results showed that the genes and phenotypic expression of related virulence,antibiotic resistance and retroelement were rarely found.Hyphal morphogenesis genes(SIT4,HOG1,SPA2,ERK1,ICL1,CST20,HSP104,TPS1,and RHO1)and phospholipase secretion gene(VPS4)were annotated.True hyphae and phospholipase were absent.Only one retroelement(Tad1-65_BG)was found.Major biogenic amines(BAs)encoding genes were absent,except for spermidine synthase(JA9_002594),spermine synthase(JA9_004690),and tyrosine decarboxylase(inx).The production of single BAs and total BAs was far below the food-defined thresholds.GXDK6 had no resistance to common antifungal drugs.Virulence enzymes,such as gelatinase,DNase,hemolytic,lecithinase,and thrombin were absent.Acute toxicity test with mice demonstrated that GXDK6 is safe.GXDK6 has a good reproduction ability in the simulation gastrointestinal tract.GXDK6 also has a strong antioxidant ability,β-glucosidase,and inulinase activity.To sum up,GXDK6 is considered as a safe probiotic for human consumption and food fermentation.
基金This study was funded by the National Natural Science Foundation of China(Grant No.32001516)Shanghai Agriculture Applied Technology Development Program,China(Grant No.X20190103)Rice Industry of China Agriculture Research System(Grant No.CARS-01-03).
文摘Germplasm resource innovation is a crucial factor for cultivar development,particularly within the context of hybrid rice breeding based on the three-line system.Quan 9311A,a cytoplasmic male sterile(CMS)line,has been successfully cultivated using rice restoration materials and extensively employed as a female parent in hybrid breeding program in China.This line was developed by crossing the CMS line Zhong 9A with a two-line restorer line 93-11,with the intention of eliminating the restoring ability of 93-11 while retaining the sterility gene WA352c from Zhong 9A.Quan 9311A effectively amalgamates the most favorable agronomic traits from both parental lines.In this study,the relationship between phenotypic characteristics and the known functional genes of Quan 9311A were analyzed using the rice genome navigation technology based on whole-genome sequencing.The findings revealed that Quan 9311A harbors multiple superior alleles from both 93-11 and Zhong 9A,providing exceptional agronomic traits that are unavailable in earlier CMS lines.Despite the removal of the fertility restorer gene Rf3 from 93-11,numerous chromosomal segments from 93-11 persist in the Quan 9311A genome.Furthermore,the hybrid rice Quanyousimiao(QYSM)and the restorer line Wushansimiao(WSSM)were used as examples to illustrate the important role of Quan 9311A as the female parent in heterosis.It was found that QYSM carries a great number of superior alleles,which accounts for its high grain yield and wide adaptability.These insights not only advanced the utilization of hybrid rice pairing groups but also provided guidance for future breeding endeavors.The study introduced innovative concepts to further integrate genomics with traditional breeding techniques.Ultimately,Quan 9311A signified a significant milestone in rice breeding technology,opening up novel avenues for hybrid rice development.
基金funded by the National Pathogen Identification Network project and Research on Key Technologies of Intelligent Monitoring,Early Warning and Tracing of Infectious Diseases in Miyun。
文摘Objective To explore the genotyping characteristics of human fecal Escherichia coli(E. coli) and the relationships between antibiotic resistance genes(ARGs) and multidrug resistance(MDR) of E. coli in Miyun District, Beijing, an area with high incidence of infectious diarrheal cases but no related data.Methods Over a period of 3 years, 94 E. coli strains were isolated from fecal samples collected from Miyun District Hospital, a surveillance hospital of the National Pathogen Identification Network. The antibiotic susceptibility of the isolates was determined by the broth microdilution method. ARGs,multilocus sequence typing(MLST), and polymorphism trees were analyzed using whole-genome sequencing data(WGS).Results This study revealed that 68.09% of the isolates had MDR, prevalent and distributed in different clades, with a relatively high rate and low pathogenicity. There was no difference in MDR between the diarrheal(49/70) and healthy groups(15/24).Conclusion We developed a random forest(RF) prediction model of TEM.1 + baeR + mphA + mphB +QnrS1 + AAC.3-IId to identify MDR status, highlighting its potential for early resistance identification. The causes of MDR are likely mobile units transmitting the ARGs. In the future, we will continue to strengthen the monitoring of ARGs and MDR, and increase the number of strains to further verify the accuracy of the MDR markers.
基金supported by the grants from National Nature Science Foundation of China(81601778 and 81672062)the Beijing Natural Science Foundation(7152025)Beijing Talents Fund(2015000021469G192)
文摘Objective Mutations in 23 S rRNA gene are known to be associated with macrolide resistance in Mycoplasma pneumoniae(M. pneumoniae). However, these mutations alone do not fully explain the high resistance rates in Asia. The aim of this study was to investigate other possible mutations involved in macrolide resistance in M. pneumoniae. Methods The whole genomes of 10 clinical isolates of M. pneumoniae with macrolide resistance were sequenced by Illumina Hi Seq2000 platform. The role of the macrolide-specific efflux transporter was assessed by efflux-pump inhibition assays with reserpine and carbonyl cyanide m-chlorophenyl-hydrazone(CCCP). Results A total of 56 single nucleotide polymorphisms(SNPs) were identified in 10 clinical isolates in comparison to the reference strains M129 and FH. Strikingly, 4 of 30 SNPs causing non-synonymous mutations were clustered in macrolide-specific efflux system gene mac B encoding macrolide-specific efflux pump protein of the ATP-binding cassette transporter family. In assays of the minimal inhibitory concentrations(MIC) of macrolide antibiotics in the presence of the efflux pump inhibitors caused a significant decrease of MICs, even under detectable levels in some strains. Conclusion Our study suggests that macrolide efflux pump may contribute to macrolide resistance in M. pneumoniae in addition to the common point mutations in 23 S r RNA gene.
基金supported by the Chinese Academy of Medical Sciences Innovation Fund for Medical Science (2016-I2M-3-021)。
文摘Gonorrhea is one of the most common sexually transmitted diseases worldwide. To cure infection and prevent transmission,timely and appropriate antimicrobial therapy is necessary. Unfortunately, Neisseria gonorrhoeae, the etiological agent of gonorrhea, has acquired nearly all known mechanisms of antimicrobial resistance(AMR), thereby compromising the efficacy of antimicrobial therapy. Treatment failure resulting from AMR has become a global public health concern. Whole-genome sequencing is an effective method to determine the AMR characteristics of N. gonorrhoeae. Compared with next-generation sequencing, the MinION sequencer(Oxford Nanopore Technologies(ONT)) has the advantages of long read length and portability. Based on a pilot study using MinION to sequence the genome of N. gonorrhoeae, we optimized the workflow of sequencing and data analysis in the current study. Here we sequenced nine isolates within one flow cell using a multiplexed sequencing strategy. After hybrid assembly with Illumina reads, nine integral circular chromosomes were obtained. By using the online tool Pathogenwatch and a BLAST-based workflow, we acquired complete AMR profiles related to seven classes of antibiotics. We also evaluated the performance of ONT-only assemblies. Most AMR determinants identified by ONT-only assemblies were the same as those identified by hybrid assemblies. Moreover, one of the nine assemblies indicated a potentially novel antimicrobial-related mutation located in mtrR which results in a frame-shift, premature stop codon, and truncated peptide.In addition, this is the first study using the MinION sequencer to obtain complete genome sequences of N. gonorrhoeae strains which are epidemic in China. This study shows that complete genome sequences and antimicrobial characteristics of N.gonorrhoeae can be obtained using the MinION sequencer in a simple and cost-effective manner, with hardly any knowledge of bioinformatics required. More importantly, this strategy provides us with a potential approach to discover new AMR determinants.
基金financially supported by Liao Ning Revitalization Talents Program(XLYC1802121,China)。
文摘The three-dimensional(3D)conformation of chromatin is integral to the precise regulation of gene expression.The 3D genome and genomic variations in non-alcoholic fatty liver disease(NAFLD)are largely unknown,despite their key roles in cellular function and physiological processes.Highthroughput chromosome conformation capture(Hi-C),Nanopore sequencing,and RNA-sequencing(RNA-seq)assays were performed on the liver of normal and NAFLD mice.A high-resolution 3D chromatin interaction map was generated to examine different 3D genome hierarchies including A/B compartments,topologically associated domains(TADs),and chromatin loops by Hi-C,and whole genome sequencing identifying structural variations(SVs)and copy number variations(CNVs)by Nanopore sequencing.We identified variations in thousands of regions across the genome with respect to 3D chromatin organization and genomic rearrangements,between normal and NAFLD mice,and revealed gene dysregulation frequently accompanied by these variations.Candidate target genes were identified in NAFLD,impacted by genetic rearrangements and spatial organization disruption.Our data provide a high-resolution 3D genome interaction resource for NAFLD investigations,revealed the relationship among genetic rearrangements,spatial organization disruption,and gene regulation,and identified candidate genes associated with these variations implicated in the pathogenesis of NAFLD.The newly findings offer insights into novel mechanisms of NAFLD pathogenesis and can provide a new conceptual framework for NAFLD therapy.
基金the National Natural Science Foundation of China,No.81741103.
文摘BACKGROUND Interleukin 10 receptor alpha subunit(IL10RA)dysfunction is the main cause of very early-onset inflammatory bowel disease(VEO-IBD)in East Asians.AIM To identify disease-causing gene mutations in four patients with VEO-IBD and verify functional changes related to the disease-causing mutations.METHODS From May 2016 to September 2020,four young patients with clinically diagnosed VEO-IBD were recruited.Before hospitalization,using targeted gene panel sequencing and trio-whole-exome sequencing(WES),three patients were found to harbor a IL10RA mutation(c.301C>T,p.R101W in one patient;c.537G>A,p.T179T in two patients),but WES results of the fourth patient were not conclusive.We performed whole-genome sequencing(WGS)on patients A and B and reanalyzed the data from patients C and D.Peripheral blood mononuclear cells(PBMCs)from patient D were isolated and stimulated with lipopolysaccharide(LPS),interleukin 10(IL-10),and LPS+IL-10.Serum IL-10 levels in four patients and tumor necrosis factor-α(TNF-α)in the cell supernatant were determined by enzyme-linked immunosorbent assay.Phosphorylation of signal transducer and activator of transcription 3(STAT3)at Tyr705 and Ser727 in PBMCs was determined by western blot analysis.RESULTS The four children in our study consisted of two males and two females.The age at disease onset ranged from 18 d to 9 mo.After hospitalization,a novel 333-bp deletion encompassing exon 1 of IL10RA was found in patients A and B using WGS and was found in patients C and D after reanalysis of their WES data.Patient D was homozygous for the 333 bp deletion.All four patients had elevated serum IL-10 levels.In vitro,IL-10-stimulated PBMCs from patient D failed to induce STAT3 phosphorylation at Tyr705 and only minimally suppressed TNF-αproduction induced by LPS.Phosphorylation at Ser727 in PBMCs was not affected by LPS or LPS+IL-10 in both healthy subjects and in patient D.CONCLUSION WGS revealed a novel 333-bp deletion of IL10RA in four patients with VEO-IBD,whereas the WES results were inconclusive.
文摘Objectives:The wide use of antibiotics for acne is the main cause of drug-resistant Cutibacterium acnes.However,the complete genetic sequence reference of C.acnes has not yet been reported.Herein,we report the complete genetic sequence of Cutibacterium acnes type strain ATCC6919.Methods:Whole-genome sequencing of Cutibacterium acnes ATCC6919 was performed using both the Illumina Hiseq4000 and PacBio RSII single-molecule real-time sequencing platforms.The generated sequence reads were de novo assembled using the HGAP3 protocol of single-molecule real-time analysis v.2.3.0 software.The draft genome was annotated and further analyzed by various bioinformatics tools.Results:The total genome length of Cutibacterium acnes ATCC6919 was 2,495,001 bp(60.02%G+C content),with 2,450 coding sequences including 2,358 proteins,45 tRNAs,9 rRNAs,and 1 sRNA.The Comprehensive Antibiotic Resistance Database showed that the gene(thy A)found in ATCC6919 was associated with resistance to aminosalicylic acid.Antimicrobial susceptibility testing showed that this isolate was not sensitive to metronidazole and sulfamethoxazole,but was sensitive to all other tested antimicrobials(erythromycin,azithromycin,clarithromycin,tetracycline,minocycline,trimethoprim,levofloxacin,ceftriaxone,and doxycycline).Conclusion:This study reports the complete genome sequence of Cutibacterium acnes ATCC6919,which provides a valuable reference for comparative analysis based on the genomic characteristics and resistance gene diversity of Cutibacterium acnes.
基金supported by the Priority Research Program of the Chinese Academy of Sciences (CAS) (Grant No.XDB31000000)Large-scale Scientific Facilities of the CAS (Grant No.2017LSF-GBOWS-2)。
文摘The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study.In the past decade,a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era.In the meantime,a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent.This review focuses on the utility of genomic data(from organelle genomes,to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations,describes the baseline methodology of experimental and analytical procedures,and summarizes recent progress in flowering plant phylogenomics at the ordinal,familial,tribal,and lower levels.We also discuss the challenges,such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors,and underlying biological factors,such as whole-genome duplication,hybridization/introgression,and incomplete lineage sorting,together suggesting that a bifurcating tree may not be the best model for the tree of life.Finally,we discuss promising avenues for future plant phylogenomic studies.
基金This work was supported by the National Key R&D Program of China(Grant No.2018YFD0502204)the Agricultural Science and Technology Innovation Program of China(Grant No.CAAS-ASTIP-2019-ISAPS)+1 种基金the Special Animal Genetic Resources Platform of National Scientific and Technical Infrastructure Center(Grant No.NSTIC TZDWZYK2019)the Sika deer Genome Project of China(Grant No.20140309016YY).
文摘Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identifying the mechanism responsible for the tolerance of a highly toxic diet,we have made a major advancement by explaining the genome of sika deer.We generated the first high-quality,chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food,especially the expansion of the UGT family 2 subfamily B of UGT genes.The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation.Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.
基金Funding was provided by the National Natural Science Foundation of China,82122017:Xiangjia Zhu,81970780:Yi Lu,81870642:Xiangjia Zhu,81670835:Yi LuScience and Technology Innovation Plan of Shanghai Science and Technology Commission,19441900700:Xiangjia Zhu,21S31904900:Xiangjia Zhu+3 种基金Shanghai Hospital Development Center,SHDC12019X08:Xiangjia ZhuShanghai Shenkang Hospital Development Center,SHDC2020CR4078:Xiangjia ZhuDouble-E Plan of Eye&ENT Hospital,SYA202006:Xiangjia ZhuShanghai Municipal Key Clinical Specialty Program,shslczdzk01901:Xiangjia Zhu.
文摘High myopia has long been highly prevalent worldwide with a largely yet unexplained genetic contribution.To identify novel susceptibility genes for axial length(AL)in highly myopic eyes,a genome-wide association study(GWAS)was performed using the genomic dataset of 350 deep whole-genome sequencing data from highly myopic patients.Top single nucleotide polymorphisms(SNPs)were functionally annotated.Immunofluorescence staining,quantitative polymerase chain reaction,and western blot were performed using neural retina of form-deprived myopic mice.Enrichment analyses were further performed.We identified the four top SNPs and found that ADAM Metallopeptidase With Thrombospondin Type 1 Motif 16(ADAMTS16)and Phosphatidylinositol Glycan Anchor Biosynthesis Class Z(PIGZ)had the potential of clinical signifi-cance.Animal experiments confirmed that PIGZ expression could be observed and showed higher expression level in form-deprived mice,especially in the ganglion cell layer.The messenger RNA(mRNA)levels of both ADAMTS16 and PIGZ were significantly higher in the neural retina of form-deprived eyes(p=0.005 and 0.007 respectively),and both proteins showed significantly upregulated expression in the neural retina of deprived eyes(p=0.004 and 0.042,respectively).Enrichment analysis revealed a significant role of cellular adhesion and signal transduction in AL,and also several AL-related pathways including circadian entrainment and inflammatory mediator regulation of transient receptor potential channels were proposed.In conclusion,the current study identified four novel SNPs associated with AL in highly myopic eyes and confirmed that the expression of ADAMTS16 and PIGZ was significantly upregulated in neural retina of deprived eyes.Enrichment analyses provided novel insight into the etiology of high myopia and opened avenues for future research interest.
