Natural hybridization is known to play a vital role in speciation;however,the mechanisms underlying the early stages of natural hybridization remain unclear.Where two plant species come into contact,two driving forces...Natural hybridization is known to play a vital role in speciation;however,the mechanisms underlying the early stages of natural hybridization remain unclear.Where two plant species come into contact,two driving forces may balance the dynamic consequences of hybridization:fusion by hybridization-mediated gene flow,and separation by reproductive isolation(RI)(Ma et al.,2010a,b;Chang et al.,2022).展开更多
As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome （BAC） by BAC strategy. The current physical contigs are expec...As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome （BAC） by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa.展开更多
Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1%of azoospermia or severe oligospermia.However,the underlying mechanisms of pathogenesis and...Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1%of azoospermia or severe oligospermia.However,the underlying mechanisms of pathogenesis and etiologies are still largely unknown.Herein,we investigated apparently balanced interchromosomal structural rearrangements in six cases with azoospermia/severe oligospermia to comprehensively identify and delineate cryptic structural rearrangements and the related copy number variants.In addition,high read-depth genome sequencing(GS)(30-fold)was performed to investigate point mutations causative of male infertility.Mate-pair GS(4-fold)revealed additional structural rearrangements and/or copy number changes in 5 of 6 cases and detected a total of 48 rearrangements.Overall,the breakpoints caused truncations of 30 RefSeq genes,five of which were associated with spermatogenesis.Furthermore,the breakpoints disrupted 43 topological-associated domains.Direct disruptions or potential dysregulations of genes,which play potential roles in male germ cell development,apoptosis,and spermatogenesis,were found in all cases(n=6).In addition,high read-depth GS detected dual molecular findings in case MI6,involving a complex rearrangement and two point mutations in the gene DNAH1.Overall,our study provided the molecular characteristics of apparently balanced interchromosomal structural rearrangements in patients with male infertility.We demonstrated the complexity of chromosomal structural rearrangements,potential gene disruptions/dysregulation and single-gene mutations could be the contributing mechanisms underlie male infertility.展开更多
Medicinal plants are renowned for their abundant production of secondary metabolites,which exhibit notable pharmacological activities and great potential for drug development.The biosynthesis of secondary metabolites ...Medicinal plants are renowned for their abundant production of secondary metabolites,which exhibit notable pharmacological activities and great potential for drug development.The biosynthesis of secondary metabolites is highly intricate and influenced by various intrinsic and extrinsic factors,resulting in substantial species diversity and content variation.Consequently,precise regulation of secondary metabolite synthesis is of utmost importance.In recent years,genome sequencing has emerged as a valuable tool for investigating the synthesis and regulation of secondary metabolites in medicinal plants,facilitated by the widespread use of high-throughput sequencing technologies.This review highlights the latest advancements in genome sequencing within this field and presents several strategies for studying secondary metabolites.Specifically,the article elucidates how genome sequencing can unravel the pathways for secondary metabolite synthesis in medicinal plants,offering insights into the functions and regulatory mechanisms of participating enzymes.Comparative analyses of plant genomes allow identification of shared pathways of metabolite synthesis among species,thereby providing novel avenues for obtaining cost-effective biosynthetic intermediates.By examining individual genomic variations,genes or gene clusters associated with the synthesis of specific compounds can be discovered,indicating potential targets and directions for drug development and the exploration of alternative compound sources.Moreover,the advent of gene-editing technology has enabled the precise modifications of medicinal plant genomes.Optimization of specific secondary metabolite synthesis pathways becomes thus feasible,enabling the precise editing of target genes to regulate secondary metabolite production within cells.These findings serve as valuable references and lessons for future drug development endeavors,conservation of rare resources,and the exploration of new resources.展开更多
Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be a...Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be associated with many physiological and pathological conditions（Bai and Wong,2005）.展开更多
The microbial potential of Penicillium has received critical attention.The present research aimed to elucidate the efficacy of crude enzyme secreted from Penicillium oxalicum WX-209 in degrading citrus segments and ev...The microbial potential of Penicillium has received critical attention.The present research aimed to elucidate the efficacy of crude enzyme secreted from Penicillium oxalicum WX-209 in degrading citrus segments and evaluate the safety of the process.Results showed that citrus segment membranes gradually dissolved after treatment with the crude enzyme solution,indicating good degradation capability.No significant differences in body weight,food ingestion rate,hematology,blood biochemistry,and weight changes of different organs were found between the enzyme intake and control groups.Serial experiments showed that the crude enzyme had high biological safety.Moreover,the whole genome of P.oxalicum WX-209 was sequenced by PacBio and Illumina platforms.Twenty-five scaffolds were assembled to generate 36 Mbp size of genome sequence comprising 11369 predicted genes modeled with a GC content of 48.33%.A total of 592 genes were annotated to encode enzymes related to carbohydrates,and some degradation enzyme genes were identified in strain P.oxalicum WX-209.展开更多
Objective:To surveill emerging variants by nanopore technology-based genome sequencing in different COVID-19 waves in Sri Lanka and to examine the association with the sample characteristics,and vaccination status.Met...Objective:To surveill emerging variants by nanopore technology-based genome sequencing in different COVID-19 waves in Sri Lanka and to examine the association with the sample characteristics,and vaccination status.Methods:The study analyzed 207 RNA positive swab samples received to sequence laboratory during different waves.The N gene cut-off threshold of less than 30 was considered as the major inclusion criteria.Viral RNA was extracted,and elutes were subjected to nanopore sequencing.All the sequencing data were uploaded in the publicly accessible database,GISAID.Results:The Omicron,Delta and Alpha variants accounted for 58%,22%and 4%of the variants throughout the period.Less than 1%were Kappa variant and 16%of the study samples remained unassigned.Omicron variant was circulated among all age groups and in all the provinces.Ct value and variants assigned percentage was 100%in Ct values of 10-15 while only 45%assigned Ct value over 25.Conclusions:The present study examined the emergence,prevalence,and distribution of SARS-CoV-2 variants locally and has shown that nanopore technology-based genome sequencing enables whole genome sequencing in a low resource setting country.展开更多
Objective To evaluate a single-reaction genome amplification method, the multisegment reverse transcription-PCR （M-RTPCR）, for its sensitivity to full genome sequencing of influenza A virus, and the ability to diffe...Objective To evaluate a single-reaction genome amplification method, the multisegment reverse transcription-PCR （M-RTPCR）, for its sensitivity to full genome sequencing of influenza A virus, and the ability to differentiate mix-subtype virus, using the next generation sequencing （NGS） platform. Methods Virus genome copy was quantified and seria（iy diluted to different titers, followed by amplification with the M-RTPCR method and sequencing on the NGS platform. Furthermore, we manually mixed two subtype viruses to different titer rate and amplified the mixed virus with the M-RTPCR protocol, followed by whole genome sequencing on the NGS platform. We also used clinical samples to test the method performance. Results The M-RTPCR method obtained complete genome of testing virus at 125 copies/reaction and determined the virus subtype at titer of 25 copies/reaction. Moreover, the two subtypes in the mixed virus could be discriminated, even though these two virus copies differed by 200-fold using this amplification protocol. The sensitivity of this protocol we detected using virus RNA was also confirmed with clinical samples containing Iow-titer virus. Conclusion The M-RTPCR is a robust and sensitive amplification method for whole genome sequencing of influenza A virus using NGS platform.展开更多
Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the...Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the community by immune evasion mechanisms. Due to mutation within S gene, most Omicron variants have reported S gene target failure (SGTF) with some commercially available PCR kits. Such diagnostic features can be used as markers to screen Omicron. However, Whole Genome Sequencing (WGS) is the only gold standard approach to confirm novel microorganisms at genetically level as similar mutations can also be found in other variants that are circulating at low frequencies worldwide. This Retrospective study is aimed to assess RT-PCR sensitivity in the detection of S gene target failure in comparison with whole genome sequencing to detect variants of Omicron. Methods: We have analysed retrospective data of SARS-CoV-2 positive RT-PCR samples for S gene target failure (SGTF) with TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) and combined with sequencing technologies to study the emerged pattern of SARS-CoV-2 variants during third wave at the tertiary care centre, Surat. Results: From the first day of December 2021 till the end of February 2022, a total of 321,803 diagnostic RT-PCR tests for SARS-CoV-2 were performed, of which 20,566 positive cases were reported at our tertiary care centre with an average cumulative positivity of 6.39% over a period of three months. In the month of December 21 samples characterized by the SGTF (70/129) were suggestive of being infected by the Omicron variant and identified as Omicron (B.1.1.529 lineage) when sequence. In the month of January, we analysed a subset of samples (n = 618) with SGTF (24%) and without SGTF (76%) with Ct values Conclusions: During the COVID-19 pandemic, it took almost more than 15 days to diagnose infection and identify pathogen by sequencing technology. In contrast to that molecular assay provided quick identification with the help of SGTF phenomenon within 5 hours of duration. This strategy helps scientists and health policymakers for the quick isolation and identification of clusters. That ultimately results in a decreased transmission of pathogen among the community.展开更多
This study demonstrates that sequential UV,pulse,and laser treatments are effective for inducing mutations in membrane proteins and enhancing the protease activity of Bacillus licheniformis.Of the six different treatm...This study demonstrates that sequential UV,pulse,and laser treatments are effective for inducing mutations in membrane proteins and enhancing the protease activity of Bacillus licheniformis.Of the six different treatment combinations tested,the sequential application of Laser,Pulse,and UV(LPU-2)provided the highest lethality rate(96.44±1.97%)and was selected as the optimal combination for subsequent mutagenesis.Through highthroughput screening of the mutant library,25 strains exhibiting more than 30%relative enzyme activity were selected for second-step screening.Among the strains,LPU-2.1 exhibited the highest protease activity(57.90±0.45 U/mL)in shaking flask fermentation and maximum hydrolysis zone(3.24 cm).Finally,the whole genome resequencing of LPU-2.1 revealed significant genetic alterations,including 20.3 bp insertions in gene ctg_04128,which encodes a membrane protein(MprF).Compared to the wild strain,LPU-2.1 demonstrated a significant increase in protease activity,which was 68%.The genome of LPU-2.1 encoded a total of 4470 proteins,with 3174 sequences(70.91%)being annotated in the GO database.Further analysis in the KEGG platform indicated the active biosynthesis of lysine via L-Lysyl-tRNA in LPU-2.1 produced by enzyme 6.1.16 involved in the aminoacyl-tRNA biosynthesis pathway.These results disclose that the combinatorial irradiation of B.licheniformis caused a modification in the ABC transporter and the two-component systems,which might have impacted the protease production of the mutant.展开更多
This study aimed to isolate and characterize cellulase-producing yeasts from six traditional fermented foods and evaluate their potential for modifying wheat bran through solid-state fermentation.A total of 28 isolate...This study aimed to isolate and characterize cellulase-producing yeasts from six traditional fermented foods and evaluate their potential for modifying wheat bran through solid-state fermentation.A total of 28 isolates were obtained,from which five strains(SD-ZZ-3,HQ-CC-7,MQ-GZ-4,FT-XJ-1,and MQ-GZ-3)with high enzymatic index values were identified.Among the selected isolates,FT-XJ-1 strain displayed robust growth,the widest carbon utilization capacity and the highest cellulase activity in liquid culture.Moreover,the solid-state fermentation using each of the isolate inoculum induced significant changes in composition and structure of wheat bran,with noted reductions in insoluble dietary fiber and cellulose content.In particular,the bran sample fermented by FT-XJ-1 strain achieved the greatest cellulose reduction(28.57%)and decreased crystallinity of cellulose,illustrating the outperformed modification effect on wheat bran.With whole genome sequencing for FT-XJ-1,genes encoding cellulolytic enzymes were annotated,further validating the cellulase degradation capacities.Collectively,strain FT-XJ-1 could effectively degrade cellulose and improve wheat bran structure,which can be potentially used as promising starter for whole wheat product processing.展开更多
Lacticaseibacillus paracasei is a facultative anaerobic bacterium,which is classified as a Generally Recognized as Safe(GRAS)microorganism by the Food and Drug Administration(FDA).In this study,we reported the whole g...Lacticaseibacillus paracasei is a facultative anaerobic bacterium,which is classified as a Generally Recognized as Safe(GRAS)microorganism by the Food and Drug Administration(FDA).In this study,we reported the whole genome sequence of Lacticaseibacillus paracasei 36(L.paracasei 36),which consisted of a circular chromosome and three circular plasmids,with a total length of 3,166,237 bp and an average G+C content of 46.21%.Based on genetic analyses of production of harmful metabolites,virulence factors,and antibiotic resistance,as well as in vivo safety tests conducted with L.paracasei 36,we postulated that L.paracasei 36 was safe.The stress-response genes of L.paracasei 36 indicated that it exhibited robust tolerance to the gastrointestinal tract,temperature,and osmotic pressure.Additionally,it demonstrated high capacities for colonization and adhesion,as well as notable antioxidant activity.The metabolomic results of the L.paracasei 36 fermentation supernatant demonstrated that metabolites were mainly concentrated in amino acid metabolism and biosynthesis of other secondary metabolites,and there was a notable increase in proclavaminic acid and lactic acid.In conclusion,L.paracasei 36 possessed favorable probiotic characteristics and safety,thereby establishing it as a probiotic candidate with considerable potential.展开更多
Rice bran is nutrient-dense milling by-product,but the high content of insoluble dietary fiber(IDF)restricts processing suitability and application in foods.To address this,cellulolytic fungi were isolated from tradit...Rice bran is nutrient-dense milling by-product,but the high content of insoluble dietary fiber(IDF)restricts processing suitability and application in foods.To address this,cellulolytic fungi were isolated from traditional fermented foods.A total of seven fungal strains with clear hydrolysis zones were obtained and identified based on morphology and internal transcribed spacer sequencing.Their growth behavior,carbon and nitrogen utilization,and enzyme activities were further assessed to compare their metabolic capacities.Solid-state fermentation using each isolate induced distinct changes in dietary fiber composition of rice bran.Among the isolates,HTDQt-JL2 showed the most pronounced effect during SSF,yielding the highest conversion of IDF to soluble dietary fiber along with substantial reductions in cellulose and hemicellulose content.Genomic analysis of HTDQt-JL2 revealed an extensive set of genes encoding carbohydrate-active enzymes,particularly those involved in plant cell wall degradation,consistent with its observed fermentation efficiency.These findings indicate that HTDQt-JL2 is an effective microbial candidate for rice bran modification,enhancing the physicochemical properties and expanding the potential as a functional food ingredient.展开更多
Dear Editor,Neurodevelopmental disorders(NDD)are a group of diseases with high phenotypic heterogeneity characterized by inability in cognition,communication,psychological skills,and motor development.The common types...Dear Editor,Neurodevelopmental disorders(NDD)are a group of diseases with high phenotypic heterogeneity characterized by inability in cognition,communication,psychological skills,and motor development.The common types of NDDs include autism spectrum disorder(ASD),attention-deficit/hyperactivity disorder(ADHD),epilepsy,schizophrenia,etc.(Parenti et al.,2020).展开更多
Non-O1/non-O139 Vibrio(V.)cholerae(NOVC)has emerged as a potential pathogen in patients with compromised health conditions[1].We report the whole genome sequencing(WGS)of a rare NOVC sepsis isolate(GenBank Accession:G...Non-O1/non-O139 Vibrio(V.)cholerae(NOVC)has emerged as a potential pathogen in patients with compromised health conditions[1].We report the whole genome sequencing(WGS)of a rare NOVC sepsis isolate(GenBank Accession:GCF_051906115.1)from an 89-year-old male admitted to the Intensive Care Unit(ICU)with septic shock(lactate 6.61 mmol/L)digestive illness.展开更多
Background Whole blood samples are often used to generate whole genome sequences,which provide valuable insights into the genetic make-up of viruses.However,the collection and management present significant challenges...Background Whole blood samples are often used to generate whole genome sequences,which provide valuable insights into the genetic make-up of viruses.However,the collection and management present significant challenges,particularly in remote and resource-limited communities,where maintaining a cold chain is often difficult and costly.The use of dry blood spots(DBS)is gradually increasing to overcome these logistical barriers with reduced biosafety constraints.We propose an alternative approach using native DBS Lassa virus(LASV)-positive samples as a substitute for whole blood.Findings Next-generation sequencing(NGS)was performed on RNA extracted from whole blood and DBS samples using Illumina technology.RNA concentration,cycle threshold(Ct)values and sequence read counts were statistically compared.A total of 78 samples from 39 LASV-positive Mastomys atalensis were analysed.Whole blood had significantly higher mean RNA concentration(26.5±1.9)than DBS(3.4±0.3),P<0.05.Mean Ct values in whole blood were significantly lower than in DBS(P=0.0001).Log mean sequence reads and NGS coverage for both S and L segments were significantly higher in whole blood(P=0.0001).RNA concentration showed no association with sequence coverage(P=0.382),while Ct values showed a strong association(P=0.0001).Conclusions Our study demonstrates that DBS is a viable alternative for whole genome sequencing of LASV,although whole blood samples consistently outperform DBS in terms of RNA concentration,Ct values and NGS coverage.展开更多
Orchid origin and evolution are common topics in evolutionary biology. Orchidaceae have approximately 30 000 orchid species distributed in diverse habitats and account for approximately 10% of the flowering plant spec...Orchid origin and evolution are common topics in evolutionary biology. Orchidaceae have approximately 30 000 orchid species distributed in diverse habitats and account for approximately 10% of the flowering plant species worldwide. Orchids provide us with materials to explore coevolution and organic evolution. In this review, we highlighted the genome study progress of orchids. In addition, we revealed the role of MADS-box gene families in the floral morphology and evolution of orchids. Genomics studies confirmed that all five subfamilies of existing orchids evolved from a common ancestor. Loss of Mβ MADS-box genes resulted in the endosperm from the seed of all existing orchids being absent. Perianth reversion to the ancestral state occurred because Apostasia and Apostasioideae lost B-AP3 and E class paralogous genes. Loss of P-subclade members of MIKC*-Type in Phalaenopsis equestris, Dendrobium catenatum, and Epidendroideae caused the formation of pollinium.In addition, the combined loss of AGL12 and contraction of ANR1 gave orchids the ability to be successfully epiphytic on trees or rocks and to develop a unique root system. Both pollinium and epiphytic production on trees are beneficial for orchid adaptations, and Epidendroideae evolved more species(~ 20 000) than Apostasioideae(16 species). Genome studies shed new light on determining the evolutionary history of orchids and understanding the genetic mechanisms of orchid morphological evolution.展开更多
The bacterial pathogen Xanthomonas oryzae pv.oryzae(Xoo),belonging to Xanthomonas sp.,causes one of the most destructive vascular diseases in rice worldwide,particularly in Asia and Africa.To better understand Xoo pat...The bacterial pathogen Xanthomonas oryzae pv.oryzae(Xoo),belonging to Xanthomonas sp.,causes one of the most destructive vascular diseases in rice worldwide,particularly in Asia and Africa.To better understand Xoo pathogenesis,we performed genome sequencing of the Korea race 1 strain DY89031(J18)and analyzed the phylogenetic tree of 63 Xoo strains.We found that the rich diversity of evolutionary features is likely associated with the rice cultivation regions.Further,virulence effector proteins secreted by the type III secretion system(T3SS)of Xoo showed pathogenesis divergence.The genome of DY89031 shows a remarkable difference from that of the widely prevailed Philippines race 6 strain PXO99A,which is avirulent to rice Xa21,a well-known disease resistance(R)gene that can be broken down by DY89031.Interestingly,plant inoculation experiments with the PXO99A transformants expressing the DY89031 genes enabled us to identify additional TAL(transcription activator-like)and non-TAL effectors that may support DY89031-specific virulence.Characterization of DY89031 genome and identification of new effectors will facilitate the investigation of the rice-Xoo interaction and new mechanisms involved.展开更多
Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly ...Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. Methods In this proof-of-concept study using Enterovirus 71 （EV71） and Coxsackievirus A16 （CA16） strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Results Within the first minute （min） of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min （on average）, 99% identity was achieved for 10 CA16 strains in a single run. Conclusion MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use.展开更多
基金supported by the National Natural Science Foundation of China(U23A20160,32360336)Guizhou Provincial Key Technology R&D Program(Qian KeHe ZhiCheng[2023]YiBan035).
文摘Natural hybridization is known to play a vital role in speciation;however,the mechanisms underlying the early stages of natural hybridization remain unclear.Where two plant species come into contact,two driving forces may balance the dynamic consequences of hybridization:fusion by hybridization-mediated gene flow,and separation by reproductive isolation(RI)(Ma et al.,2010a,b;Chang et al.,2022).
基金This work was supported by grants from the National Academy of Agricultural Science(Code #200901FHT020508369)the BioGreen21 Program(Code #20050301034438 and Code #20070301034037),Rural Development Administration, Republic of Korea
文摘As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome （BAC） by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa.
基金supported by the National Natural Science Foundation of China(No.31801042)the Health and Medical Research Fund(No.04152666 and No.07180576)General Research Fund(No.14115418),and Direct Grant(No.2020.052).
文摘Apparently balanced chromosomal structural rearrangements are known to cause male infertility and account for approximately 1%of azoospermia or severe oligospermia.However,the underlying mechanisms of pathogenesis and etiologies are still largely unknown.Herein,we investigated apparently balanced interchromosomal structural rearrangements in six cases with azoospermia/severe oligospermia to comprehensively identify and delineate cryptic structural rearrangements and the related copy number variants.In addition,high read-depth genome sequencing(GS)(30-fold)was performed to investigate point mutations causative of male infertility.Mate-pair GS(4-fold)revealed additional structural rearrangements and/or copy number changes in 5 of 6 cases and detected a total of 48 rearrangements.Overall,the breakpoints caused truncations of 30 RefSeq genes,five of which were associated with spermatogenesis.Furthermore,the breakpoints disrupted 43 topological-associated domains.Direct disruptions or potential dysregulations of genes,which play potential roles in male germ cell development,apoptosis,and spermatogenesis,were found in all cases(n=6).In addition,high read-depth GS detected dual molecular findings in case MI6,involving a complex rearrangement and two point mutations in the gene DNAH1.Overall,our study provided the molecular characteristics of apparently balanced interchromosomal structural rearrangements in patients with male infertility.We demonstrated the complexity of chromosomal structural rearrangements,potential gene disruptions/dysregulation and single-gene mutations could be the contributing mechanisms underlie male infertility.
基金funded by the National Natural Science Foundation of China,grant number 81603221.
文摘Medicinal plants are renowned for their abundant production of secondary metabolites,which exhibit notable pharmacological activities and great potential for drug development.The biosynthesis of secondary metabolites is highly intricate and influenced by various intrinsic and extrinsic factors,resulting in substantial species diversity and content variation.Consequently,precise regulation of secondary metabolite synthesis is of utmost importance.In recent years,genome sequencing has emerged as a valuable tool for investigating the synthesis and regulation of secondary metabolites in medicinal plants,facilitated by the widespread use of high-throughput sequencing technologies.This review highlights the latest advancements in genome sequencing within this field and presents several strategies for studying secondary metabolites.Specifically,the article elucidates how genome sequencing can unravel the pathways for secondary metabolite synthesis in medicinal plants,offering insights into the functions and regulatory mechanisms of participating enzymes.Comparative analyses of plant genomes allow identification of shared pathways of metabolite synthesis among species,thereby providing novel avenues for obtaining cost-effective biosynthetic intermediates.By examining individual genomic variations,genes or gene clusters associated with the synthesis of specific compounds can be discovered,indicating potential targets and directions for drug development and the exploration of alternative compound sources.Moreover,the advent of gene-editing technology has enabled the precise modifications of medicinal plant genomes.Optimization of specific secondary metabolite synthesis pathways becomes thus feasible,enabling the precise editing of target genes to regulate secondary metabolite production within cells.These findings serve as valuable references and lessons for future drug development endeavors,conservation of rare resources,and the exploration of new resources.
文摘Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be associated with many physiological and pathological conditions（Bai and Wong,2005）.
基金the financial support of the National Natural Science Foundation of China[32201960,32073020]Science and Technology Innovation Program of Hunan Province[2022RC1150]+2 种基金Changsha Municipal Natural Science Foundation[kq2202332]Hunan innovative province construction project[2019NK2041]Agricultural Science and Technology Innovation Project of Hunan Province[2021CX05].
文摘The microbial potential of Penicillium has received critical attention.The present research aimed to elucidate the efficacy of crude enzyme secreted from Penicillium oxalicum WX-209 in degrading citrus segments and evaluate the safety of the process.Results showed that citrus segment membranes gradually dissolved after treatment with the crude enzyme solution,indicating good degradation capability.No significant differences in body weight,food ingestion rate,hematology,blood biochemistry,and weight changes of different organs were found between the enzyme intake and control groups.Serial experiments showed that the crude enzyme had high biological safety.Moreover,the whole genome of P.oxalicum WX-209 was sequenced by PacBio and Illumina platforms.Twenty-five scaffolds were assembled to generate 36 Mbp size of genome sequence comprising 11369 predicted genes modeled with a GC content of 48.33%.A total of 592 genes were annotated to encode enzymes related to carbohydrates,and some degradation enzyme genes were identified in strain P.oxalicum WX-209.
文摘Objective:To surveill emerging variants by nanopore technology-based genome sequencing in different COVID-19 waves in Sri Lanka and to examine the association with the sample characteristics,and vaccination status.Methods:The study analyzed 207 RNA positive swab samples received to sequence laboratory during different waves.The N gene cut-off threshold of less than 30 was considered as the major inclusion criteria.Viral RNA was extracted,and elutes were subjected to nanopore sequencing.All the sequencing data were uploaded in the publicly accessible database,GISAID.Results:The Omicron,Delta and Alpha variants accounted for 58%,22%and 4%of the variants throughout the period.Less than 1%were Kappa variant and 16%of the study samples remained unassigned.Omicron variant was circulated among all age groups and in all the provinces.Ct value and variants assigned percentage was 100%in Ct values of 10-15 while only 45%assigned Ct value over 25.Conclusions:The present study examined the emergence,prevalence,and distribution of SARS-CoV-2 variants locally and has shown that nanopore technology-based genome sequencing enables whole genome sequencing in a low resource setting country.
基金funded by a project(2014ZX10004002)of the Chinese National Key Program of Mega Infectious Disease of the National 12th Five-Year Plan
文摘Objective To evaluate a single-reaction genome amplification method, the multisegment reverse transcription-PCR （M-RTPCR）, for its sensitivity to full genome sequencing of influenza A virus, and the ability to differentiate mix-subtype virus, using the next generation sequencing （NGS） platform. Methods Virus genome copy was quantified and seria（iy diluted to different titers, followed by amplification with the M-RTPCR method and sequencing on the NGS platform. Furthermore, we manually mixed two subtype viruses to different titer rate and amplified the mixed virus with the M-RTPCR protocol, followed by whole genome sequencing on the NGS platform. We also used clinical samples to test the method performance. Results The M-RTPCR method obtained complete genome of testing virus at 125 copies/reaction and determined the virus subtype at titer of 25 copies/reaction. Moreover, the two subtypes in the mixed virus could be discriminated, even though these two virus copies differed by 200-fold using this amplification protocol. The sensitivity of this protocol we detected using virus RNA was also confirmed with clinical samples containing Iow-titer virus. Conclusion The M-RTPCR is a robust and sensitive amplification method for whole genome sequencing of influenza A virus using NGS platform.
文摘Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the community by immune evasion mechanisms. Due to mutation within S gene, most Omicron variants have reported S gene target failure (SGTF) with some commercially available PCR kits. Such diagnostic features can be used as markers to screen Omicron. However, Whole Genome Sequencing (WGS) is the only gold standard approach to confirm novel microorganisms at genetically level as similar mutations can also be found in other variants that are circulating at low frequencies worldwide. This Retrospective study is aimed to assess RT-PCR sensitivity in the detection of S gene target failure in comparison with whole genome sequencing to detect variants of Omicron. Methods: We have analysed retrospective data of SARS-CoV-2 positive RT-PCR samples for S gene target failure (SGTF) with TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) and combined with sequencing technologies to study the emerged pattern of SARS-CoV-2 variants during third wave at the tertiary care centre, Surat. Results: From the first day of December 2021 till the end of February 2022, a total of 321,803 diagnostic RT-PCR tests for SARS-CoV-2 were performed, of which 20,566 positive cases were reported at our tertiary care centre with an average cumulative positivity of 6.39% over a period of three months. In the month of December 21 samples characterized by the SGTF (70/129) were suggestive of being infected by the Omicron variant and identified as Omicron (B.1.1.529 lineage) when sequence. In the month of January, we analysed a subset of samples (n = 618) with SGTF (24%) and without SGTF (76%) with Ct values Conclusions: During the COVID-19 pandemic, it took almost more than 15 days to diagnose infection and identify pathogen by sequencing technology. In contrast to that molecular assay provided quick identification with the help of SGTF phenomenon within 5 hours of duration. This strategy helps scientists and health policymakers for the quick isolation and identification of clusters. That ultimately results in a decreased transmission of pathogen among the community.
基金the Key Research and Development Program of Zhenjiang City(Grant No.:NY2023001)Zhenjiang City Innovation Capacity Building Program for Key Laboratories of Enter-prises(Grant No.:SS2024003)Jiangsu Funding Program for Excellent Postdoctoral Talent(Grant No.:2022ZB668)for the financial support.
文摘This study demonstrates that sequential UV,pulse,and laser treatments are effective for inducing mutations in membrane proteins and enhancing the protease activity of Bacillus licheniformis.Of the six different treatment combinations tested,the sequential application of Laser,Pulse,and UV(LPU-2)provided the highest lethality rate(96.44±1.97%)and was selected as the optimal combination for subsequent mutagenesis.Through highthroughput screening of the mutant library,25 strains exhibiting more than 30%relative enzyme activity were selected for second-step screening.Among the strains,LPU-2.1 exhibited the highest protease activity(57.90±0.45 U/mL)in shaking flask fermentation and maximum hydrolysis zone(3.24 cm).Finally,the whole genome resequencing of LPU-2.1 revealed significant genetic alterations,including 20.3 bp insertions in gene ctg_04128,which encodes a membrane protein(MprF).Compared to the wild strain,LPU-2.1 demonstrated a significant increase in protease activity,which was 68%.The genome of LPU-2.1 encoded a total of 4470 proteins,with 3174 sequences(70.91%)being annotated in the GO database.Further analysis in the KEGG platform indicated the active biosynthesis of lysine via L-Lysyl-tRNA in LPU-2.1 produced by enzyme 6.1.16 involved in the aminoacyl-tRNA biosynthesis pathway.These results disclose that the combinatorial irradiation of B.licheniformis caused a modification in the ABC transporter and the two-component systems,which might have impacted the protease production of the mutant.
基金financial support by National Natural Science Foundation of China(32330081,32302136)additionally funded by R&D Program of Beijing Municipal Education Commission(KM202310011011).
文摘This study aimed to isolate and characterize cellulase-producing yeasts from six traditional fermented foods and evaluate their potential for modifying wheat bran through solid-state fermentation.A total of 28 isolates were obtained,from which five strains(SD-ZZ-3,HQ-CC-7,MQ-GZ-4,FT-XJ-1,and MQ-GZ-3)with high enzymatic index values were identified.Among the selected isolates,FT-XJ-1 strain displayed robust growth,the widest carbon utilization capacity and the highest cellulase activity in liquid culture.Moreover,the solid-state fermentation using each of the isolate inoculum induced significant changes in composition and structure of wheat bran,with noted reductions in insoluble dietary fiber and cellulose content.In particular,the bran sample fermented by FT-XJ-1 strain achieved the greatest cellulose reduction(28.57%)and decreased crystallinity of cellulose,illustrating the outperformed modification effect on wheat bran.With whole genome sequencing for FT-XJ-1,genes encoding cellulolytic enzymes were annotated,further validating the cellulase degradation capacities.Collectively,strain FT-XJ-1 could effectively degrade cellulose and improve wheat bran structure,which can be potentially used as promising starter for whole wheat product processing.
基金financially supported by the National Natural Science Foundation of China(No.32072766)the Natural Science Foundation of Zhejiang province(No.LZ20C170002).
文摘Lacticaseibacillus paracasei is a facultative anaerobic bacterium,which is classified as a Generally Recognized as Safe(GRAS)microorganism by the Food and Drug Administration(FDA).In this study,we reported the whole genome sequence of Lacticaseibacillus paracasei 36(L.paracasei 36),which consisted of a circular chromosome and three circular plasmids,with a total length of 3,166,237 bp and an average G+C content of 46.21%.Based on genetic analyses of production of harmful metabolites,virulence factors,and antibiotic resistance,as well as in vivo safety tests conducted with L.paracasei 36,we postulated that L.paracasei 36 was safe.The stress-response genes of L.paracasei 36 indicated that it exhibited robust tolerance to the gastrointestinal tract,temperature,and osmotic pressure.Additionally,it demonstrated high capacities for colonization and adhesion,as well as notable antioxidant activity.The metabolomic results of the L.paracasei 36 fermentation supernatant demonstrated that metabolites were mainly concentrated in amino acid metabolism and biosynthesis of other secondary metabolites,and there was a notable increase in proclavaminic acid and lactic acid.In conclusion,L.paracasei 36 possessed favorable probiotic characteristics and safety,thereby establishing it as a probiotic candidate with considerable potential.
基金funded by National Natural Science Foundation of China(32330081,32302136)support R&D Program of Beijing Municipal Education Commission(KM202310011011).
文摘Rice bran is nutrient-dense milling by-product,but the high content of insoluble dietary fiber(IDF)restricts processing suitability and application in foods.To address this,cellulolytic fungi were isolated from traditional fermented foods.A total of seven fungal strains with clear hydrolysis zones were obtained and identified based on morphology and internal transcribed spacer sequencing.Their growth behavior,carbon and nitrogen utilization,and enzyme activities were further assessed to compare their metabolic capacities.Solid-state fermentation using each isolate induced distinct changes in dietary fiber composition of rice bran.Among the isolates,HTDQt-JL2 showed the most pronounced effect during SSF,yielding the highest conversion of IDF to soluble dietary fiber along with substantial reductions in cellulose and hemicellulose content.Genomic analysis of HTDQt-JL2 revealed an extensive set of genes encoding carbohydrate-active enzymes,particularly those involved in plant cell wall degradation,consistent with its observed fermentation efficiency.These findings indicate that HTDQt-JL2 is an effective microbial candidate for rice bran modification,enhancing the physicochemical properties and expanding the potential as a functional food ingredient.
基金supported by the National Key Research and Development Program of China(2022YFC2703900)the CAMS Innovation Fund for Medical Sciences(2021-I2M-1018)+1 种基金the National Natural Science Foundation of China(82394420 and 82394423)the Theranostics and Translational Research Facility of National Infrastructures for Translational Medicine,Institute of Clinical Medicine,Peking Union Medical College Hospital,Chinese Academy of Medical Sciences&Peking Union Medical College for the support。
文摘Dear Editor,Neurodevelopmental disorders(NDD)are a group of diseases with high phenotypic heterogeneity characterized by inability in cognition,communication,psychological skills,and motor development.The common types of NDDs include autism spectrum disorder(ASD),attention-deficit/hyperactivity disorder(ADHD),epilepsy,schizophrenia,etc.(Parenti et al.,2020).
文摘Non-O1/non-O139 Vibrio(V.)cholerae(NOVC)has emerged as a potential pathogen in patients with compromised health conditions[1].We report the whole genome sequencing(WGS)of a rare NOVC sepsis isolate(GenBank Accession:GCF_051906115.1)from an 89-year-old male admitted to the Intensive Care Unit(ICU)with septic shock(lactate 6.61 mmol/L)digestive illness.
基金Open Access funding enabled and organized by Projekt DEAL.Funding for this study was provided by the Deutsche Forschungsgemainschaft(DFG-German Research Foundation)through the LAROCS project(ref BO 3790/1&2-1,FI 1781/1&2-1)the LASSEVO project(ref FI 1781/6-1)+2 种基金the DFG Research Infrastructure NGS_CC(INST 269/768-1,project 407482635,DRESDENconcept Genome Center)the Next Generation Sequencing Competence Network(project 423957469)the Medical Research Council(MC_UU_00034/6).
文摘Background Whole blood samples are often used to generate whole genome sequences,which provide valuable insights into the genetic make-up of viruses.However,the collection and management present significant challenges,particularly in remote and resource-limited communities,where maintaining a cold chain is often difficult and costly.The use of dry blood spots(DBS)is gradually increasing to overcome these logistical barriers with reduced biosafety constraints.We propose an alternative approach using native DBS Lassa virus(LASV)-positive samples as a substitute for whole blood.Findings Next-generation sequencing(NGS)was performed on RNA extracted from whole blood and DBS samples using Illumina technology.RNA concentration,cycle threshold(Ct)values and sequence read counts were statistically compared.A total of 78 samples from 39 LASV-positive Mastomys atalensis were analysed.Whole blood had significantly higher mean RNA concentration(26.5±1.9)than DBS(3.4±0.3),P<0.05.Mean Ct values in whole blood were significantly lower than in DBS(P=0.0001).Log mean sequence reads and NGS coverage for both S and L segments were significantly higher in whole blood(P=0.0001).RNA concentration showed no association with sequence coverage(P=0.382),while Ct values showed a strong association(P=0.0001).Conclusions Our study demonstrates that DBS is a viable alternative for whole genome sequencing of LASV,although whole blood samples consistently outperform DBS in terms of RNA concentration,Ct values and NGS coverage.
基金supported by the Teamwork Projects Funded by Guangdong Natural Science Foundation,China(Grant No.2017A030312004)The National Natural Science Foundation of China(Grant No.31870199)+2 种基金The National Key Research and Development Program of China(Grant No.2018YFD1000401)Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization Construction Funds(Grant No.115/118990050115/KJG18016A)。
文摘Orchid origin and evolution are common topics in evolutionary biology. Orchidaceae have approximately 30 000 orchid species distributed in diverse habitats and account for approximately 10% of the flowering plant species worldwide. Orchids provide us with materials to explore coevolution and organic evolution. In this review, we highlighted the genome study progress of orchids. In addition, we revealed the role of MADS-box gene families in the floral morphology and evolution of orchids. Genomics studies confirmed that all five subfamilies of existing orchids evolved from a common ancestor. Loss of Mβ MADS-box genes resulted in the endosperm from the seed of all existing orchids being absent. Perianth reversion to the ancestral state occurred because Apostasia and Apostasioideae lost B-AP3 and E class paralogous genes. Loss of P-subclade members of MIKC*-Type in Phalaenopsis equestris, Dendrobium catenatum, and Epidendroideae caused the formation of pollinium.In addition, the combined loss of AGL12 and contraction of ANR1 gave orchids the ability to be successfully epiphytic on trees or rocks and to develop a unique root system. Both pollinium and epiphytic production on trees are beneficial for orchid adaptations, and Epidendroideae evolved more species(~ 20 000) than Apostasioideae(16 species). Genome studies shed new light on determining the evolutionary history of orchids and understanding the genetic mechanisms of orchid morphological evolution.
基金supported by Chinese Academy of Sciences(XDB27040201)the National Natural Science Foundation of China(3181101746)。
文摘The bacterial pathogen Xanthomonas oryzae pv.oryzae(Xoo),belonging to Xanthomonas sp.,causes one of the most destructive vascular diseases in rice worldwide,particularly in Asia and Africa.To better understand Xoo pathogenesis,we performed genome sequencing of the Korea race 1 strain DY89031(J18)and analyzed the phylogenetic tree of 63 Xoo strains.We found that the rich diversity of evolutionary features is likely associated with the rice cultivation regions.Further,virulence effector proteins secreted by the type III secretion system(T3SS)of Xoo showed pathogenesis divergence.The genome of DY89031 shows a remarkable difference from that of the widely prevailed Philippines race 6 strain PXO99A,which is avirulent to rice Xa21,a well-known disease resistance(R)gene that can be broken down by DY89031.Interestingly,plant inoculation experiments with the PXO99A transformants expressing the DY89031 genes enabled us to identify additional TAL(transcription activator-like)and non-TAL effectors that may support DY89031-specific virulence.Characterization of DY89031 genome and identification of new effectors will facilitate the investigation of the rice-Xoo interaction and new mechanisms involved.
基金supported by the National key research and development plan(2016TFC1202700,2016YFC1200900)Beijing Municipal Science&Technology Commission project(grant numbers D151100002115003)Guangzhou Municipal Science&Technology Commission project(grant numbers 2015B2150820)
文摘Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. Methods In this proof-of-concept study using Enterovirus 71 （EV71） and Coxsackievirus A16 （CA16） strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Results Within the first minute （min） of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min （on average）, 99% identity was achieved for 10 CA16 strains in a single run. Conclusion MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use.
