Objective To provide a feasible and cost-effective next-generation sequencing （NGS） method for accurate identification of viral pathogens in clinical specimens, because enormous limitations impede the clinical use o...Objective To provide a feasible and cost-effective next-generation sequencing （NGS） method for accurate identification of viral pathogens in clinical specimens, because enormous limitations impede the clinical use of common NGS, such as high cost, complicated procedures, tremendous data analysis, and high background noise in clinical samples. Methods Viruses from cell culture materials or clinical specimens were identified following an improved NGS procedure： reduction of background noise by sample preprocessing, viral enrichment by barcoded oligonucleotide （random hexamer or non-ribosomal hexanucleotide） primer-based amplification, fragmentation-free library construction and sequencing of one-tube mixtures, as well as rapid data analysis using an in-house pipeline. Results NGS data demonstrated that both barcoded primer sets were useful to simultaneously capture multiple viral pathogens in cell culture materials or clinical specimens and verified that hexanucleotide primers captured as many viral sequences as hexamers did. Moreover, direct testing of clinical specimens using this improved hexanucleotide primer-based NGS approach provided further detailed genotypes of enteroviruses causing hand, foot, and mouth disease （HFMD） and identified other potential viruses or differentiated misdiagnosis events. Conclusion The improved barcoded oligonucleotide primer-based NGS approach is simplified, time saving, cost effective, and appropriate for direct identification of viral pathogens in clinical practice.展开更多
Diarrhea,as a global public health problem,causes a large number of infections and deaths every year.Although Escherichia coli(E.coli)is one of the normal flo ra microorganisms in the human intestinal tract,it has fiv...Diarrhea,as a global public health problem,causes a large number of infections and deaths every year.Although Escherichia coli(E.coli)is one of the normal flo ra microorganisms in the human intestinal tract,it has five pathogenic bacteria types that can cause human diarrhea,known as diarrheagenic E.coli.When people are infected,rapid and accurate diagnosis,along with timely treatment,are especially important.Here,we introduce a new method to identify and analyze a large number of pathogenic strains in E.coli by multiplex PCR and barcoded magnetic bead hybridization.Results show that the detection sensitivities of enterohemorrhagic E.coli,enterotoxigenic E.coli,enteropathogenic E.coli,enteroinvasive E.coli and enteroaggregative E.coli were 1.3×10^3 CFU/mL,2×10^4 CFU/mL,4×10^4 CFU/mL,7.2×10^4 CFU/mL and 1.7 CFU/mL respectively.This method has strong specificity and high sensitivity and detects multiple target sequences in one experiment.Compared with other methods,BMB array has great application potential.展开更多
Proteins usually associate with other molecules physically to execute their functions.Identifying these interactions is important for the functional analysis of proteins.Previously,we reported the parallel analysis of...Proteins usually associate with other molecules physically to execute their functions.Identifying these interactions is important for the functional analysis of proteins.Previously,we reported the parallel analysis of translated ORFs(PLATO)to couple ribosome display of full-length ORFs with affinity enrichment of mRNA/protein/ribosome complexes for the “bait”molecules,followed by the deep sequencing analysis of mRNA.However,the sample processing,from extraction of precipitated mRNA to generation of DNA libraries,includes numerous steps,which is tedious and may cause the loss of materials.Barcoded PLATO(PLATO-BC),an improved platform was further developed to test its application for protein interaction discovery.In this report,we tested the antisera-antigen interaction using serum samples from patients with inclusion body myositis(IBM).Tripartite motif containing 21(TRIM21)was identified as a potentially new IBM autoantigen.We also expanded the application of PLATO-BC to identify protein interactions for JQ1,single ubiquitin peptide,and NS5 protein of Zika virus.From PLATO-BC analyses,we identified new protein interactions for these “bait”molecules.We demonstrate that Ewing sarcoma breakpoint region 1(EWSR1)binds to JQ1 and their interactions may interrupt the EWSR1 association with acetylated histone H4.RIO kinase 3(RIOK3),a newly identified ubiquitin-binding protein,is preferentially associated with K63-ubiquitin chain.We also find that Zika NS5 protein interacts with two previously unreported host proteins,par-3 family cell polarity regulator(PARD3)and chromosome 19 open reading frame 53(C19orf53),whose attenuated expression benefits the replication of Zika virus.These results further demonstrate that PLATO-BC is capable of identifying novel protein interactions for various types of “bait”molecules.展开更多
The circadian clock coordinates rhythms in numerous physiological processes to maintain organismal homeostasis. Since the suprachiasmatic nucleus(SCN) is widely accepted as the circadian pacemaker, it is critical to u...The circadian clock coordinates rhythms in numerous physiological processes to maintain organismal homeostasis. Since the suprachiasmatic nucleus(SCN) is widely accepted as the circadian pacemaker, it is critical to understand the neural mechanisms by which rhythmic information is transferred from the SCN to peripheral clocks. Here, we present the first comprehensive map of SCN efferent connections and suggest a molecular logic underlying these projections. The SCN projects broadly to most major regions of the brain, rather than solely to the hypothalamus and thalamus. The efferent projections from different subtypes of SCN neurons vary in distance and intensity, and blocking synaptic transmission of these circuits affects circadian rhythms in locomotion and feeding to different extents. We also developed a barcoding system to integrate retrograde tracing with in-situ sequencing, allowing us to link circuit anatomy and spatial patterns of gene expression. Analyses using this system revealed that brain regions functioning downstream of the SCN receive input from multiple neuropeptidergic cell types within the SCN, and that individual SCN neurons generally project to a single downstream brain region.This map of SCN efferent connections provides a critical foundation for future investigations into the neural circuits underlying SCNmediated rhythms in physiology. Further, our new barcoded tracing method provides a tool for revealing the molecular logic of neuronal circuits within heterogeneous brain regions.展开更多
【目的】应用线粒体DNA条形码技术对尤犀金龟属(Eupatorus Burmeister,1847)昆虫物种界定进行探索,以解决该属物种形态鉴定困难的问题。【方法】基于尤犀金龟属物种线粒体cox1和cox2基因序列数据集,使用Automatic Barcode Gap Discovery...【目的】应用线粒体DNA条形码技术对尤犀金龟属(Eupatorus Burmeister,1847)昆虫物种界定进行探索,以解决该属物种形态鉴定困难的问题。【方法】基于尤犀金龟属物种线粒体cox1和cox2基因序列数据集,使用Automatic Barcode Gap Discovery(ABGD)和Bayesian Poisson Tree Processes(bPTP)对3个形态种进行分子物种界定,并与形态学鉴定结果进行比较。【结果】使用ABGD方法时,cox1数据集的界定结果与形态学鉴定结果一致,cox2数据集的界定结果与形态学鉴定结果存在差异;使用bPTP方法时,2种数据集的界定结果均远高于形态学鉴定结果,且均存在不同程度的过度划分。【结论】cox1是更适合用于鉴定尤犀金龟属昆虫的DNA条形码,使用ABGD方法时,其数据集界定结果与形态学鉴定结果一致。利用分子界定与形态特征鉴定相结合,可极大地提高鉴定效率和准确性。展开更多
Complete plastid genomes have been proposed as potential“super-barcodes”for plant identification and delineation,particularly in cases where standard DNA barcodes may be insufficient.However,few studies have systema...Complete plastid genomes have been proposed as potential“super-barcodes”for plant identification and delineation,particularly in cases where standard DNA barcodes may be insufficient.However,few studies have systematically addressed how taxonomic complexity,especially in rapidly radiating lineages with intricate evolutionary histories,might influencethe efficacyof plastome-scale barcodes.Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains,and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus.Therefore,Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity.In this study,we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes.Our results revealed that the traditional standard barcode combination(nrITS+matK+rbcL+trnH-psbA)achieved the highest discrimination rates(81.25%),closely followed by the plastid large single copy(LSC)region(80.21%),then by full plastome,the supermatrix of proteincoding genes,and hypervariable regions(79.17%).Notably,the matK and ycf1 gene alone could discriminate 78.13%of species.Key determinants of species discrimination by integrating alignment length(AL)and the proportion of parsimony-informative sites(PPIS),as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity.Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes,this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis’specificbiological habits and potentially reflectingunique evolutionary patterns in the plastid genome.展开更多
DNA barcoding has been extensively used for species identification.However,species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods.In this study,we use plant species in Jugl...DNA barcoding has been extensively used for species identification.However,species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods.In this study,we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification(AFRAID)method of species identification,a novel approach for precise species identification in plants.Specifically,we determined(1)the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae,(2)the minimum size of chloroplast dataset for species discrimination,and(3)minimum amount of next generation sequencing(NGS)data required for species identification.We found that species identification rates were highest when whole chloroplast genomes were used,followed by taxon-specific DNA barcodes,and then universal DNA barcodes.Species identification of 100%was achieved when chloroplast genome sequence coverage reached 20%and the original sequencing data reached 500,000 reads.AFRAID accurately identified species for all samples tested after 500,000 clean reads,with far less computing time than common approaches.These results provide a new approach to accurately identify species,overcoming limitations of traditional DNA barcodes.Our method,which uses next generation sequencing to generate partial chloroplast genomes,reveals that DNA barcode regions are not necessarily fixed,accelerating the process of species identification.展开更多
For the classification of the various species of fishes in the genus Spinibarbus,molecular identification and phylogenetic analysis were conducted for five species of fishes in Spinibarbus based on the mitochondrial C...For the classification of the various species of fishes in the genus Spinibarbus,molecular identification and phylogenetic analysis were conducted for five species of fishes in Spinibarbus based on the mitochondrial COI gene.The results showed that the interspecific genetic distances were greater than 0.02,whereas the intraspecific genetic distances were less than 0.02.The phylogenetic tree revealed that the S.caldwelli and the S.hollandi clustered into clade I.The S.yunnanensis and the S.denticulatus clustered in a branch,and then clustered with the S.sinensis to form clade II.Clades I and II together formed the genus Spinibarbus.The S.caldwelli and S.hollandi clustered in two separate subclades,and the genetic distances between them were greater than the genetic distances between each of them and other species within the same subclade.The results of this study indicated that the mitochondrial COI gene sequences were effective for species identification of fishes in the genus Spinibarbus and could be used to explore the phylogeny of this genus.展开更多
The East China Sea(ECS)off the Coast of Zhoushan Archipelago,Zhejiang(ECS-CZA)is home to abundant fishery resources and an important spawning,feeding,and nursing ground for a variety of fish species.Due to long-term o...The East China Sea(ECS)off the Coast of Zhoushan Archipelago,Zhejiang(ECS-CZA)is home to abundant fishery resources and an important spawning,feeding,and nursing ground for a variety of fish species.Due to long-term overfishing,the ichthyoplankton structure has been dramatically altered.Understanding the species composition and distribution of fish eggs and larvae is one of the most essential tasks to accurately regulate fishery resources and formulate effective management policies;however,little is known about the ichthyoplankton in this region.In this study,an integrated strategy of morphology identification(MI)and mitochondrial COI DNA barcoding was used to identify species of fish eggs and larvae collected from the ECSCZA.MI revealed 15 fish egg species belonging to 12 families and 12 fish larva species belonging to 12 families;in contrast,DNA barcoding altogether identified 30 species,including 18 fish egg species and 13 fish larva species.One species was shared between the egg and larva samples.Our study offers useful tools and critical scientific information for further understanding the diversity,distribution,and conservation management of various ichthyoplankton species in the marine environment.展开更多
Sequencing of environmental samples has great potential for biodiversity research,but its application is limited by the lack of reliable DNA barcode databases for species identifications.Such a database has been creat...Sequencing of environmental samples has great potential for biodiversity research,but its application is limited by the lack of reliable DNA barcode databases for species identifications.Such a database has been created for epiphytic lichens of Europe,allowing us to compare the results of environmental sequencing with standard taxonomic surveys.The species undetected by taxonomic surveys(what we term the ghost component)amount to about half of the species actually present in hectare plots of Central European forests.Some of these,which currently occur only as diaspores or weakly developed thalli,are likely to be favoured in the course of global change.The ghost component usually represents a larger fraction in managed forests than in old-growth unmanaged forests.The total species composition of different plots is much more similar than suggested by taxonomic surveys alone.On a regional scale,this supports the well-known statement that“everything is everywhere,but,the environment selects”.展开更多
The real-time screening of biomolecules and single cells in biochips is extremely important for disease prediction and diagnosis,cellular analysis,and life science research.Barcode biochip technology,which is integrat...The real-time screening of biomolecules and single cells in biochips is extremely important for disease prediction and diagnosis,cellular analysis,and life science research.Barcode biochip technology,which is integrated with microfluidics,typically comprises barcode array,sample loading,and reaction unit array chips.Here,we present a review of microfluidics barcode biochip analytical approaches for the high-throughput screening of biomolecules and single cells,including protein biomarkers,microRNA(miRNA),circulating tumor DNA(ctDNA),single-cell secreted proteins,single-cell exosomes,and cell interactions.We begin with an overview of current high-throughput detection and analysis approaches.Following this,we outline recent improvements in microfluidic devices for biomolecule and single-cell detection,highlighting the benefits and limitations of these devices.This paper focuses on the research and development of microfluidic barcode biochips,covering their self-assembly substrate materials and their specific applications with biomolecules and single cells.Looking forward,we explore the prospects and challenges of this technology,with the aim of contributing toward the use of microfluidic barcode detection biochips in medical diagnostics and therapies,and their large-scale commercialization.展开更多
This study introduces a lightweight deep learning model and a novel synthetic dataset designed to restore damaged one-dimensional(1D)barcodes and Quick Response(QR)codes,addressing critical challenges in logistics ope...This study introduces a lightweight deep learning model and a novel synthetic dataset designed to restore damaged one-dimensional(1D)barcodes and Quick Response(QR)codes,addressing critical challenges in logistics operations.The proposed solution leverages an efficient Pix2Pix-based framework,a type of conditional Generative Adversarial Network(GAN)optimized for image-to-image translation tasks,enabling the recovery of degraded barcodes and QR codes with minimal computational overhead.A core contribution of this work is the development of a synthetic dataset that simulates realistic damage scenarios frequently encountered in logistics environments,such as low contrast,misalignment,physical wear,and environmental interference.By training on this diverse and realistic dataset,the model demonstrates exceptional performance in restoring readability and decoding accuracy.The lightweight architecture,featuring a U-Net-based encoder-decoder with separable convolutions,ensures computational efficiency,making the approach suitable for real-time deployment on embedded and resource-constrained devices commonly used in logistics systems.Experimental results reveal significant improvements:QR code decoding ratios increased from 14%to 99%on training data and from 15%to 68%on validation data,while 1D barcode decoding ratios improved from 7%to 73%on training data and from 9%to 44%on validation data.By providing a robust,resource-efficient solution for restoring damaged barcodes and QR codes,this study offers practical advancements for enhancing the reliability of automated scanning systems in logistics operations,particularly under challenging conditions.展开更多
Cell lineage tracing is a key technology for describing the developmental history of individual progenitor cells and assembling them to form a lineage development tree.However,traditional methods have limitations of p...Cell lineage tracing is a key technology for describing the developmental history of individual progenitor cells and assembling them to form a lineage development tree.However,traditional methods have limitations of poor stability and insufficient reso-lution.As an efficient and flexible gene editing tool,CRISPR-Cas9 system has been widely used in biological research.Furthermore,CRISPR-Cas9 gene editing-based tracing methods can introduce fluorescent proteins,reporter genes,or DNA barcodes for high-throughput sequencing,enabling precise lineage analysis,significantly im-proving precision and resolution,and expanding its application range.In this review,we summarize applications of CRISPR-Cas9 system in cell lineage tracing,with special emphasis on its successful applications in traditional model animals(e.g.,zebrafish and mice),large animal models(pigs),and human cells or organoids.We also discussed its potential prospects and challenges in xenotransplantation and regenerative medicine.展开更多
[Objective] A study on the classification of 24 species of Calyptratae entering Ningbo port using DNA barcoding technique was carried out.[Method] The CO I genes of the 24 species of Calyptratae were first sequenced.B...[Objective] A study on the classification of 24 species of Calyptratae entering Ningbo port using DNA barcoding technique was carried out.[Method] The CO I genes of the 24 species of Calyptratae were first sequenced.Based on the comparison and analysis of the obtained sequences,the phylogenetic tree was constructed using MEGA6.0.[Result] The cluster analysis showed the classification of the 24 species of Calyptratae was consistent with the morphological classification at the family and genus levels.However,the cluster analysis could not fully distinguish the closely-related species.[Discussion] The DNA barcoding technique cannot be singly used for classifying and identifying Calyptratae.It should be combined with morphological classification methods,and can be treated as a beneficial supplement for morphological classification methods.展开更多
基金supported by the China Mega-Project for Infectious Disease(2016ZX10004-101,2016ZX10004-215)Beijing Municipal Science&Technology Commission Project(D151100002115003)Guangzhou Municipal Science&Technology Commission Project(2015B2150820)
文摘Objective To provide a feasible and cost-effective next-generation sequencing （NGS） method for accurate identification of viral pathogens in clinical specimens, because enormous limitations impede the clinical use of common NGS, such as high cost, complicated procedures, tremendous data analysis, and high background noise in clinical samples. Methods Viruses from cell culture materials or clinical specimens were identified following an improved NGS procedure： reduction of background noise by sample preprocessing, viral enrichment by barcoded oligonucleotide （random hexamer or non-ribosomal hexanucleotide） primer-based amplification, fragmentation-free library construction and sequencing of one-tube mixtures, as well as rapid data analysis using an in-house pipeline. Results NGS data demonstrated that both barcoded primer sets were useful to simultaneously capture multiple viral pathogens in cell culture materials or clinical specimens and verified that hexanucleotide primers captured as many viral sequences as hexamers did. Moreover, direct testing of clinical specimens using this improved hexanucleotide primer-based NGS approach provided further detailed genotypes of enteroviruses causing hand, foot, and mouth disease （HFMD） and identified other potential viruses or differentiated misdiagnosis events. Conclusion The improved barcoded oligonucleotide primer-based NGS approach is simplified, time saving, cost effective, and appropriate for direct identification of viral pathogens in clinical practice.
基金the National Natural Science Foundation of China(Nos.61971187,61571187,61871180)Education Department Outstanding Young Project of Hunan Province(No.18B299)。
文摘Diarrhea,as a global public health problem,causes a large number of infections and deaths every year.Although Escherichia coli(E.coli)is one of the normal flo ra microorganisms in the human intestinal tract,it has five pathogenic bacteria types that can cause human diarrhea,known as diarrheagenic E.coli.When people are infected,rapid and accurate diagnosis,along with timely treatment,are especially important.Here,we introduce a new method to identify and analyze a large number of pathogenic strains in E.coli by multiplex PCR and barcoded magnetic bead hybridization.Results show that the detection sensitivities of enterohemorrhagic E.coli,enterotoxigenic E.coli,enteropathogenic E.coli,enteroinvasive E.coli and enteroaggregative E.coli were 1.3×10^3 CFU/mL,2×10^4 CFU/mL,4×10^4 CFU/mL,7.2×10^4 CFU/mL and 1.7 CFU/mL respectively.This method has strong specificity and high sensitivity and detects multiple target sequences in one experiment.Compared with other methods,BMB array has great application potential.
基金supported by grants from National Institute of Health(Grant Nos.R33AI116180,R01DE025447,and R01GM117838)
文摘Proteins usually associate with other molecules physically to execute their functions.Identifying these interactions is important for the functional analysis of proteins.Previously,we reported the parallel analysis of translated ORFs(PLATO)to couple ribosome display of full-length ORFs with affinity enrichment of mRNA/protein/ribosome complexes for the “bait”molecules,followed by the deep sequencing analysis of mRNA.However,the sample processing,from extraction of precipitated mRNA to generation of DNA libraries,includes numerous steps,which is tedious and may cause the loss of materials.Barcoded PLATO(PLATO-BC),an improved platform was further developed to test its application for protein interaction discovery.In this report,we tested the antisera-antigen interaction using serum samples from patients with inclusion body myositis(IBM).Tripartite motif containing 21(TRIM21)was identified as a potentially new IBM autoantigen.We also expanded the application of PLATO-BC to identify protein interactions for JQ1,single ubiquitin peptide,and NS5 protein of Zika virus.From PLATO-BC analyses,we identified new protein interactions for these “bait”molecules.We demonstrate that Ewing sarcoma breakpoint region 1(EWSR1)binds to JQ1 and their interactions may interrupt the EWSR1 association with acetylated histone H4.RIO kinase 3(RIOK3),a newly identified ubiquitin-binding protein,is preferentially associated with K63-ubiquitin chain.We also find that Zika NS5 protein interacts with two previously unreported host proteins,par-3 family cell polarity regulator(PARD3)and chromosome 19 open reading frame 53(C19orf53),whose attenuated expression benefits the replication of Zika virus.These results further demonstrate that PLATO-BC is capable of identifying novel protein interactions for various types of “bait”molecules.
基金supported by the National Natural Science Foundation of China(32171157,31971090)Ministry of Science and Technology of the People’s Republic of China(2021ZD0203400)Kuanren Talents’Project of The Second Affiliated Hospital of Chongqing Medical University。
文摘The circadian clock coordinates rhythms in numerous physiological processes to maintain organismal homeostasis. Since the suprachiasmatic nucleus(SCN) is widely accepted as the circadian pacemaker, it is critical to understand the neural mechanisms by which rhythmic information is transferred from the SCN to peripheral clocks. Here, we present the first comprehensive map of SCN efferent connections and suggest a molecular logic underlying these projections. The SCN projects broadly to most major regions of the brain, rather than solely to the hypothalamus and thalamus. The efferent projections from different subtypes of SCN neurons vary in distance and intensity, and blocking synaptic transmission of these circuits affects circadian rhythms in locomotion and feeding to different extents. We also developed a barcoding system to integrate retrograde tracing with in-situ sequencing, allowing us to link circuit anatomy and spatial patterns of gene expression. Analyses using this system revealed that brain regions functioning downstream of the SCN receive input from multiple neuropeptidergic cell types within the SCN, and that individual SCN neurons generally project to a single downstream brain region.This map of SCN efferent connections provides a critical foundation for future investigations into the neural circuits underlying SCNmediated rhythms in physiology. Further, our new barcoded tracing method provides a tool for revealing the molecular logic of neuronal circuits within heterogeneous brain regions.
文摘【目的】应用线粒体DNA条形码技术对尤犀金龟属(Eupatorus Burmeister,1847)昆虫物种界定进行探索,以解决该属物种形态鉴定困难的问题。【方法】基于尤犀金龟属物种线粒体cox1和cox2基因序列数据集,使用Automatic Barcode Gap Discovery(ABGD)和Bayesian Poisson Tree Processes(bPTP)对3个形态种进行分子物种界定,并与形态学鉴定结果进行比较。【结果】使用ABGD方法时,cox1数据集的界定结果与形态学鉴定结果一致,cox2数据集的界定结果与形态学鉴定结果存在差异;使用bPTP方法时,2种数据集的界定结果均远高于形态学鉴定结果,且均存在不同程度的过度划分。【结论】cox1是更适合用于鉴定尤犀金龟属昆虫的DNA条形码,使用ABGD方法时,其数据集界定结果与形态学鉴定结果一致。利用分子界定与形态特征鉴定相结合,可极大地提高鉴定效率和准确性。
基金supported by the National Natural Science Foundation of China(32371700,32071670 and 31870196)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000)+4 种基金the Science and Technology Basic Resources Investigation Program of China(2021FY100200)Yunnan Revitalization Talent Support Program“Young Talent”and“Innovation Team”Projects(202405AS350019)the 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden,Chinese Academy of Science(XTBG-1450101)the Key R&D program of Yunnan Province,China(202103AC100003)the Key Basic Research program of Yunnan Province,China(202101BC070003).
文摘Complete plastid genomes have been proposed as potential“super-barcodes”for plant identification and delineation,particularly in cases where standard DNA barcodes may be insufficient.However,few studies have systematically addressed how taxonomic complexity,especially in rapidly radiating lineages with intricate evolutionary histories,might influencethe efficacyof plastome-scale barcodes.Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains,and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus.Therefore,Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity.In this study,we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes.Our results revealed that the traditional standard barcode combination(nrITS+matK+rbcL+trnH-psbA)achieved the highest discrimination rates(81.25%),closely followed by the plastid large single copy(LSC)region(80.21%),then by full plastome,the supermatrix of proteincoding genes,and hypervariable regions(79.17%).Notably,the matK and ycf1 gene alone could discriminate 78.13%of species.Key determinants of species discrimination by integrating alignment length(AL)and the proportion of parsimony-informative sites(PPIS),as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity.Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes,this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis’specificbiological habits and potentially reflectingunique evolutionary patterns in the plastid genome.
基金supported by the funds from Natural Science Foundation of Hebei Province(C2022402017).
文摘DNA barcoding has been extensively used for species identification.However,species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods.In this study,we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification(AFRAID)method of species identification,a novel approach for precise species identification in plants.Specifically,we determined(1)the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae,(2)the minimum size of chloroplast dataset for species discrimination,and(3)minimum amount of next generation sequencing(NGS)data required for species identification.We found that species identification rates were highest when whole chloroplast genomes were used,followed by taxon-specific DNA barcodes,and then universal DNA barcodes.Species identification of 100%was achieved when chloroplast genome sequence coverage reached 20%and the original sequencing data reached 500,000 reads.AFRAID accurately identified species for all samples tested after 500,000 clean reads,with far less computing time than common approaches.These results provide a new approach to accurately identify species,overcoming limitations of traditional DNA barcodes.Our method,which uses next generation sequencing to generate partial chloroplast genomes,reveals that DNA barcode regions are not necessarily fixed,accelerating the process of species identification.
文摘For the classification of the various species of fishes in the genus Spinibarbus,molecular identification and phylogenetic analysis were conducted for five species of fishes in Spinibarbus based on the mitochondrial COI gene.The results showed that the interspecific genetic distances were greater than 0.02,whereas the intraspecific genetic distances were less than 0.02.The phylogenetic tree revealed that the S.caldwelli and the S.hollandi clustered into clade I.The S.yunnanensis and the S.denticulatus clustered in a branch,and then clustered with the S.sinensis to form clade II.Clades I and II together formed the genus Spinibarbus.The S.caldwelli and S.hollandi clustered in two separate subclades,and the genetic distances between them were greater than the genetic distances between each of them and other species within the same subclade.The results of this study indicated that the mitochondrial COI gene sequences were effective for species identification of fishes in the genus Spinibarbus and could be used to explore the phylogeny of this genus.
文摘The East China Sea(ECS)off the Coast of Zhoushan Archipelago,Zhejiang(ECS-CZA)is home to abundant fishery resources and an important spawning,feeding,and nursing ground for a variety of fish species.Due to long-term overfishing,the ichthyoplankton structure has been dramatically altered.Understanding the species composition and distribution of fish eggs and larvae is one of the most essential tasks to accurately regulate fishery resources and formulate effective management policies;however,little is known about the ichthyoplankton in this region.In this study,an integrated strategy of morphology identification(MI)and mitochondrial COI DNA barcoding was used to identify species of fish eggs and larvae collected from the ECSCZA.MI revealed 15 fish egg species belonging to 12 families and 12 fish larva species belonging to 12 families;in contrast,DNA barcoding altogether identified 30 species,including 18 fish egg species and 13 fish larva species.One species was shared between the egg and larva samples.Our study offers useful tools and critical scientific information for further understanding the diversity,distribution,and conservation management of various ichthyoplankton species in the marine environment.
基金supported by the Technology Agency of the Czech Republic(Grant Nos.SS01010270,SS06010420)by a long-term research development grant RVO(Grant No.67985939)。
文摘Sequencing of environmental samples has great potential for biodiversity research,but its application is limited by the lack of reliable DNA barcode databases for species identifications.Such a database has been created for epiphytic lichens of Europe,allowing us to compare the results of environmental sequencing with standard taxonomic surveys.The species undetected by taxonomic surveys(what we term the ghost component)amount to about half of the species actually present in hectare plots of Central European forests.Some of these,which currently occur only as diaspores or weakly developed thalli,are likely to be favoured in the course of global change.The ghost component usually represents a larger fraction in managed forests than in old-growth unmanaged forests.The total species composition of different plots is much more similar than suggested by taxonomic surveys alone.On a regional scale,this supports the well-known statement that“everything is everywhere,but,the environment selects”.
基金supported by the National Key Research and Development Plan of China(2023YFB3210400)the Natural Science Innovation Group Foundation of China(T2321004)+3 种基金the National Natural Science Foundation of China(62174101)Shandong University Integrated Research and Cultivation Project(2022JC001)Key Research and Development Plan of Shandong Province(Major Science and Technology Innovation Project2022CXGC020501).
文摘The real-time screening of biomolecules and single cells in biochips is extremely important for disease prediction and diagnosis,cellular analysis,and life science research.Barcode biochip technology,which is integrated with microfluidics,typically comprises barcode array,sample loading,and reaction unit array chips.Here,we present a review of microfluidics barcode biochip analytical approaches for the high-throughput screening of biomolecules and single cells,including protein biomarkers,microRNA(miRNA),circulating tumor DNA(ctDNA),single-cell secreted proteins,single-cell exosomes,and cell interactions.We begin with an overview of current high-throughput detection and analysis approaches.Following this,we outline recent improvements in microfluidic devices for biomolecule and single-cell detection,highlighting the benefits and limitations of these devices.This paper focuses on the research and development of microfluidic barcode biochips,covering their self-assembly substrate materials and their specific applications with biomolecules and single cells.Looking forward,we explore the prospects and challenges of this technology,with the aim of contributing toward the use of microfluidic barcode detection biochips in medical diagnostics and therapies,and their large-scale commercialization.
基金supported by the Scientific and Technological Research Council of Turkey(TÜB˙ITAK)through the Industrial R&D Projects Grant Program(TEYDEB)under Project No.3211077(grant recipient:Metin Kahraman)。
文摘This study introduces a lightweight deep learning model and a novel synthetic dataset designed to restore damaged one-dimensional(1D)barcodes and Quick Response(QR)codes,addressing critical challenges in logistics operations.The proposed solution leverages an efficient Pix2Pix-based framework,a type of conditional Generative Adversarial Network(GAN)optimized for image-to-image translation tasks,enabling the recovery of degraded barcodes and QR codes with minimal computational overhead.A core contribution of this work is the development of a synthetic dataset that simulates realistic damage scenarios frequently encountered in logistics environments,such as low contrast,misalignment,physical wear,and environmental interference.By training on this diverse and realistic dataset,the model demonstrates exceptional performance in restoring readability and decoding accuracy.The lightweight architecture,featuring a U-Net-based encoder-decoder with separable convolutions,ensures computational efficiency,making the approach suitable for real-time deployment on embedded and resource-constrained devices commonly used in logistics systems.Experimental results reveal significant improvements:QR code decoding ratios increased from 14%to 99%on training data and from 15%to 68%on validation data,while 1D barcode decoding ratios improved from 7%to 73%on training data and from 9%to 44%on validation data.By providing a robust,resource-efficient solution for restoring damaged barcodes and QR codes,this study offers practical advancements for enhancing the reliability of automated scanning systems in logistics operations,particularly under challenging conditions.
基金supported by Institute of Laboratory Animal Sciences,Chinese Academy of Medical Sciences and Comparative Medicine Center,Peking Union Medical College,Collaborative Innovation Program of the Chinese Academy of Sciences(22SH19)Nonprofit Central Research Institute Fund of Chinese Academy of Medical Sciences(2023-PT180-01).
文摘Cell lineage tracing is a key technology for describing the developmental history of individual progenitor cells and assembling them to form a lineage development tree.However,traditional methods have limitations of poor stability and insufficient reso-lution.As an efficient and flexible gene editing tool,CRISPR-Cas9 system has been widely used in biological research.Furthermore,CRISPR-Cas9 gene editing-based tracing methods can introduce fluorescent proteins,reporter genes,or DNA barcodes for high-throughput sequencing,enabling precise lineage analysis,significantly im-proving precision and resolution,and expanding its application range.In this review,we summarize applications of CRISPR-Cas9 system in cell lineage tracing,with special emphasis on its successful applications in traditional model animals(e.g.,zebrafish and mice),large animal models(pigs),and human cells or organoids.We also discussed its potential prospects and challenges in xenotransplantation and regenerative medicine.
文摘[Objective] A study on the classification of 24 species of Calyptratae entering Ningbo port using DNA barcoding technique was carried out.[Method] The CO I genes of the 24 species of Calyptratae were first sequenced.Based on the comparison and analysis of the obtained sequences,the phylogenetic tree was constructed using MEGA6.0.[Result] The cluster analysis showed the classification of the 24 species of Calyptratae was consistent with the morphological classification at the family and genus levels.However,the cluster analysis could not fully distinguish the closely-related species.[Discussion] The DNA barcoding technique cannot be singly used for classifying and identifying Calyptratae.It should be combined with morphological classification methods,and can be treated as a beneficial supplement for morphological classification methods.
