Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural...Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural variations and other annotation information.B:The second type of visualization map was simple and only showed the synteny relationship between the chromosomes of two or three genomes.C:Multiplatform general GenomeSyn submission page,applicable to Windows,MAC and web platforms;other analysis files can be entered in the"other"option.The publisher would like to apologise for any inconvenience caused.展开更多
Soybean(Glycine max)is a globally important crop that serves as a primary source of edible oil and protein for both humans and animals.Cultivated soybean varieties exhibit considerable genetic diversity depending on t...Soybean(Glycine max)is a globally important crop that serves as a primary source of edible oil and protein for both humans and animals.Cultivated soybean varieties exhibit considerable genetic diversity depending on their geographical origin.Heinong 531(HN531)is an elite cultivar that was released in China in June 2021 with 22.34%seed oil,high resistance to soybean cyst nematode(SCN)race 3,and enhanced yield.However,the genetic basis for these desirable agronomic traits is unclear.In this study,we generated a high-quality genome assembly for HN531 and used it to systematically analyze genes related to agronomic traits such as resistance to SCN.The assembled genome spans 981.20 Mb,featuring a contig N50 of 19.47 Mb,and contains 58,151 predicted gene models.Pan-genomic comparison with 27 previously reported soybean genomes revealed 95,071 structural variants(SVs)of>50 bp,of which 602 were HN531-specific.Furthermore,we identified a copy number variation at rhg1 that underlies resistance to SCN,and we found elite alleles of functional genes underlying important agronomic traits such as seed oil content,adaptability,and yield.This high-quality HN531 genome can be used to explore the genetic basis for the excellent agronomic traits of this cultivar,and is a valuable resource for breeders aiming to improve HN531 and related cultivars.展开更多
Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lac...Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lacking.Here,we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size,gene number,and TE component,which indicates their representativeness of wheat genetic diversity.Pan-gene analyses uncover 140,261 distinct gene families,of which only 23.2%are shared in all accessions.Moreover,we build a∼16.15 Gb graph pangenome containing 695,897 bubbles,intersecting 5132 genes and 230,307 cis-regulatory regions.Pairwise genome comparisons identify∼1,978,221 non-redundant SVs and 497 SV hotspots.Notably,the density of bubbles as well as SVs show remarkable aggregation in centromeres,which probably play an important role in chromosome plasticity and stability.As for functional SVs exploration,we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups.Additionally,several reported functional genes in wheat display complex structural graphs,for example,PPD-A1,VRT-A2,and TaNAAT2-A.These findings deepen our understanding of wheat genetic diversity,providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.展开更多
Hu sheep is an indigenous breed from the Taihu Lake Plain in China,known for its high fertility.Although Hu sheep belong to the Mongolian group,their demographic history and genetic architecture remain inconclusive.He...Hu sheep is an indigenous breed from the Taihu Lake Plain in China,known for its high fertility.Although Hu sheep belong to the Mongolian group,their demographic history and genetic architecture remain inconclusive.Here,we analyze 697 sheep genomes from representatives of Mongolian sheep breeds.Our study suggests that the ancestral Hu sheep first separated from the Mongolian group approximately 3000 years ago.As Hu sheep migrated from the north and flourished in the Taihu Lake Plain around 1000 years ago,they developed a unique genetic foundation and phenotypic characteristics,which are evident in the genomic footprints of selective sweeps and structural variation landscape.Genes associated with reproductive traits(BMPR1B and TDRD10)and horn phenotype(RXFP2)exhibit notable selective sweeps in the genome of Hu sheep.A genome-wide association analysis reveals that structural variations at LOC101110773,MAST2,and ZNF385B may significantly impact polledness,teat number,and early growth in Hu sheep,respectively.Our study offers insights into the evolutionary history of Hu sheep and may serve as a valuable genetic resource to enhance the understanding of complex traits in Hu sheep.展开更多
Avian genomes exhibit compact organization and remarkable chromosomal stability.However,the extent and mechanisms by which structural variation in avian genomes differ from those in other vertebrate lineages are poorl...Avian genomes exhibit compact organization and remarkable chromosomal stability.However,the extent and mechanisms by which structural variation in avian genomes differ from those in other vertebrate lineages are poorly explored.This study generated a diploid genome assembly for the golden pheasant(Chrysolophus pictus),a species distinguished by the vibrant plumage of males.Each haploid genome assembly included complete chromosomalmodels,incorporatingall microchromosomes.Analysis revealed extensive tandem amplification of immune-related genes across the smallest microchromosomes(dot chromosomes),with an average copy number of 54.Structural variation between the haploid genomes was primarily shaped by large insertions and deletions(indels),with minimal contributions from inversions or duplications.Approximately 28%of these large indels were associated with recent insertions of transposable elements,despite their typically low activity in bird genomes.Evidence for significant effects of transposable elements on gene expression was minimal.Evolutionary strata on the sex chromosomes were identified,along with a drastic rearrangement of the W chromosome.These analyses of the high-quality diploid genome of the golden pheasant provide valuable insights into the evolutionary patterns of structural variation in avian genomes.展开更多
"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic s..."Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.展开更多
Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability ...Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.展开更多
Structural variations(SVs),a newly discovered genetic variation,have gained increasing recognition for their importance,yet much about them remains unknown.With the completion of whole-genome sequencing projects in oi...Structural variations(SVs),a newly discovered genetic variation,have gained increasing recognition for their importance,yet much about them remains unknown.With the completion of whole-genome sequencing projects in oil crops,more SVs have been identified,revealing their types,genomic distribution,and characteristics.These findings have demonstrated the crucial roles of SVs in regulating gene expression,driving trait innovation,facilitating domestication,making this an opportune time for a systematic review.We summarized the progress of SV-related studies in oil crops,focusing on the types of SVs and their mechanisms of occurrence,the strategies and methods for SV detection,and the SVs identified in oil crops such as rapeseed,soybean,peanut,and sesame.The various types of SVs,such as presence-absence variations(PAVs),copy number variations(CNVs),and homeologous exchanges(HEs),have been shown.Along with their genomic characterization,their roles in crop domestication and breeding,and regulatory impact on gene expression and agronomic traits have also been demonstrated.This review will provide an overview of the SV research process in oil crops,enabling researchers to quickly understand key information and apply this knowledge in future studies and crop breeding.展开更多
Zeocin can cause double strand breaks of DNA and thus may be employed as a mutagen. In this study, two strains of Nannochloropsis oceanica, the wild and the Zeocin-tolerant strains, were re-sequenced to verify such fu...Zeocin can cause double strand breaks of DNA and thus may be employed as a mutagen. In this study, two strains of Nannochloropsis oceanica, the wild and the Zeocin-tolerant strains, were re-sequenced to verify such function of Zeocin, The results showed that Zeocin can mutate the N. oceanica genome and cause the structural variation. Zeocin either swept away or selected the alleles of genes functioning in ubiquitin-mediated proteolysis, alpha-linolenic acid metabolism, ascorbate and aldarate metabolism, ribosome biogenesis, and circadian rhythm, indicating that N. oceanica may have adjusted its metabolic performances for protein, carbohydrate, and lipid, and changed its ribosome biosynthesis and living rhythm to survive in Zeocin containing medium. In addition, Zeocin caused mutation may have influenced the expression of a set of tanscription factors. It was concluded that Zeocin effectively caused the structural variation of the genome of N. oceanica, and forced the microalgae to select out the alleles of a set of genes around these variations in order to adapt to Zeocin containing medium. Further studies on the genetic basis of the phenotypic adaptation of this haploid and asexual microalga and the application of Zeocin to its genetic improvement are very important.展开更多
In this work,the influence of CO2 on the structural variation and catalytic performance of Na2WO4/Mn/Si O2 for oxidative coupling of methane to ethylene was investigated. The catalyst was prepared by impregnation meth...In this work,the influence of CO2 on the structural variation and catalytic performance of Na2WO4/Mn/Si O2 for oxidative coupling of methane to ethylene was investigated. The catalyst was prepared by impregnation method and characterized by XRD,Raman and XPS techniques. Appropriate amount of CO2 in the reactant gases enhanced the formation of surface tetrahedral Na2WO4 species and promoted the migration of O in MOx,Na,W from the catalyst bulk to surface,which were favorable for oxidative coupling of methane. When the molar ratio of CH4/O2/CO2 was 3/1/2,enriched surface tetrahedral Na2WO4 species and high surface concentration of O in MOx,Na,W were detected,and then high CH4 conversion of 33.1% and high C2H4 selectivity of 56.2% were obtained. With further increase of CO2 in the reagent gases,the content of active surface tetrahedral Na2WO4 species and surface concentration of O in MOx,Na,W decreased,while that of inactive species（Mn WO4 and Mn2O3） increased dramatically,leading to low CH4 conversion and low C2H4 selectivity. It could be speculated that Na2WO4 crystal was transformed into Mn WO4 crystal with excessive CO2 added under the reaction conditions. Pretreatment of Na2WO4/Mn/Si O2 catalyst by moderate amount of CO2 before OCM also promoted the formation of Na2WO4 species.展开更多
Genomic structural variations （SVs）, particularly insertions, deletions and inversions, can contribute to the heterogeneity of millions of nucleotides within a genome, and are likely to make an important contributio...Genomic structural variations （SVs）, particularly insertions, deletions and inversions, can contribute to the heterogeneity of millions of nucleotides within a genome, and are likely to make an important contribution to biological diversity and phenotypic variation （Alkan et al., 2011; Bickhart and Liu, 2014）. With the rapid development of the next-generation sequencing technologies and the new assembly methodolo- gies, the multiple de novo assemblies of genomes within a species allow researchers to explore more detailed SV maps （Li et al., 2011）. Compared with the traditional read depth algorithm using the whole-genome resequencing approach and array-based technologies （Baker, 2012; Wang et al., 2012;展开更多
Chickens are one of the most important domesticated animals,serving as an important protein source.Studying genetic variations in chickens to enhance their production performance is of great potential value.The emerge...Chickens are one of the most important domesticated animals,serving as an important protein source.Studying genetic variations in chickens to enhance their production performance is of great potential value.The emergence of next-generation sequencing has enabled precise analysis of single nucleotide polymorphisms and insertions/deletions in chicken,while third-generation sequencing achieves the accurate structural variant identification.However,the high cost of third-generation sequencing technology limits its application in population studies.The graph-based pan-genome strategy can overcome this challenge by enabling the detection of structural variations using cost-effective next-generation sequencing data.This study constructed a graph-based pangenome for chickens using 12 high-quality genomes.This pan-genome used linear genome GRCg6a as the reference genome,containing variant information from two commercial and nine native chicken breeds.Compared to the linear genome,the pan-genome provided significant improvements in the efficiency of structural variation identification.On the basis of the graph-based pan-genome,high-frequency structural variations related to high egg production in Leghorn chicken were predicted.Additionally,it was discovered that potential structural variations was associated with highland adaptation in Tibetan chickens according to next-generation sequencing and transcriptomics data.Using the pan-genome graph,a new strategy to identify structural variations related to traits of interest in chickens is presented.展开更多
Domestication has shaped the population structure and agronomic traits of tea plants, yet the complexity of tea population structure and genetic variation that determines these traits remains unclear.We here investiga...Domestication has shaped the population structure and agronomic traits of tea plants, yet the complexity of tea population structure and genetic variation that determines these traits remains unclear.We here investigated the resequencing data of 363 diverse tea accessions collected extensively from almost all tea distributions and found that the population structure of tea plants was divided into eight subgroups, which were basically consistent with their geographical distributions. The genetic diversity of tea plants in China decreased from southwest to east as latitude increased. Results also indicated that Camellia sinensis var. assamica(CSA) illustrated divergent selection signatures with Camellia sinensis var. sinensis(CSS). The domesticated genes of CSA were mainly involved in leaf development, flavonoid and alkaloid biosynthesis, while the domesticated genes in CSS mainly participated in amino acid metabolism, aroma compounds biosynthesis,and cold stress. Comparative population genomics further identified ~730 Mb novel sequences, generating 6,058 full-length protein-encoding genes,significantly expanding the gene pool of tea plants.We also discovered 217,376 large-scale structural variations and 56,583 presence and absence variations(PAVs) across diverse tea accessions, some of which were associated with tea quality and stress resistance. Functional experiments demonstrated that two PAV genes(CSS0049975 and CSS0006599)were likely to drive trait diversification in cold tolerance between CSA and CSS tea plants. The overall findings not only revealed the genetic diversity and domestication of tea plants, but also underscored the vital role of structural variations in the diversification of tea plant traits.展开更多
Dissecting the complex regulatory mechanism of seed oil content(SOC)is one of the main research goals in Brassica napus.Increasing evidence suggests that genome architecture is linked to multiple biological functions....Dissecting the complex regulatory mechanism of seed oil content(SOC)is one of the main research goals in Brassica napus.Increasing evidence suggests that genome architecture is linked to multiple biological functions.However,the effect of genome architecture on SOC regulation remains unclear.Here,we used high-throughput chromatin conformation capture to characterize differences in the three-dimen-sional(3D)landscape of genome architecture of seeds from two B.napus lines,N53-2(with high SOC)and Ken-C8(with low SOC).Bioinformatics analysis demonstrated that differentially accessible regions and differentially expressed genes between N53-2 and Ken-C8 were preferentially enriched in regions with quantitative trait loci(QTLs)/associated genomic regions(AGRs)for SOC.A multi-omics analysis demonstrated that expression of SOC-related genes was tightly correlated with genome structural varia-tions in QTLs/AGRs of B.napus.The candidate gene BnaA09g48250D,which showed structural variation in a QTL/AGR on chrA09,was identified byfine-mapping of a KN double-haploid population derived from hybridization of N53-2 and Ken-C8.Overexpression and knockout of BnaA09g48250D led to significant in-creases and decreases in SOC,respectively,in the transgenic lines.Taken together,our results reveal the 3D genome architecture of B.napus seeds and the roles of genome structural variations in SOC regulation,enriching our understanding of the molecular mechanisms of SOC regulation from the perspective of spatial chromatin structure.展开更多
A genome-wide association study(GWAS)identifies trait-associated loci,but identifying the causal genes can be a bottleneck,due in part to slow decay of linkage disequilibrium(LD).A transcriptome-wide association study...A genome-wide association study(GWAS)identifies trait-associated loci,but identifying the causal genes can be a bottleneck,due in part to slow decay of linkage disequilibrium(LD).A transcriptome-wide association study(TWAS)addresses this issue by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci with GWAS results.Here,we used self-pollinated soybean(Glycine max[L.]Merr.)as a model to evaluate the application of TWAS to the genetic dissection of traits in plant species with slow LD decay.We generated RNA sequencing data for a soybean diversity panel and identified the genetic expression regulation of 29286 soybean genes.Different TWAS solutions were less affected by LD and were robust to the source of expression,identifing known genes related to traits from different tissues and developmental stages.The novel pod-color gene L2 was identified via TWAS and functionally validated by genome editing.By introducing a new exon proportion feature,we significantly improved the detection of expression variations that resulted from structural variations and alternative splicing.As a result,the genes identified through our TWAS approach exhibited a diverse range of causal variations,including SNPs,insertions or deletions,gene fusion,copy number variations,and alternative splicing.Using this approach,we identified genes associated with flowering time,including both previously known genes and novel genes that had not previously been linked to this trait,providing insights complementary to those from GWAS.In summary,this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.展开更多
Structural variations(SVs)have long been described as being involved in the origin,adaption,and domes-tication of species.However,the underlying genetic and genomic mechanisms are poorly understood.Here,we report a hi...Structural variations(SVs)have long been described as being involved in the origin,adaption,and domes-tication of species.However,the underlying genetic and genomic mechanisms are poorly understood.Here,we report a high-quality genome assembly of Gossypium barbadense acc.Tanguis,a landrace that is closely related to formation of extra-long-staple(ELS)cultivated cotton.An SV-based pan-genome(Pan-SV)was then constructed using a total of 182593 non-redundant SVs,including 2236 inversions,97398 insertions,and 82959 deletions from 11 assembled genomes of allopolyploid cotton.The utility of this Pan-sV was then demonstrated through population structure analysis and genome-wide association studies(GWASs).Using segregation mapping populations produced through crossing ELS cotton and the landrace along with an Sv-based GWAs,certain SVs responsible for speciation,domestication,and improvement in tetraploid cottons were identified.Importantly,some of the SVs presently identified as associated with the yield and fiber quality improvement had not been identified in previous SNP-based GWAS.In particular,a 9-bp insertion or deletion was found to associate with elimination of the interspecific reproductive isolation between Gossypium hirsutum and G.barbadense.Collectively,this study provides new insights into genome-wide,gene-scale SVs linked to important agronomic traits in a major crop spe-cies and highlights the importance of sVs during the speciation,domestication,and improvement of culti-vated crop species.展开更多
Naturally occurring structural variations(SVs)are a considerable source of genomic variation that can reshape the 3D architecture of chromosomes.Controllable methods aimed at introducing the complex SVs and their rela...Naturally occurring structural variations(SVs)are a considerable source of genomic variation that can reshape the 3D architecture of chromosomes.Controllable methods aimed at introducing the complex SVs and their related molecular mechanisms have remained farfetched.In this study,an SV-prone yeast strain was developed using Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE)technology with two synthetic chromosomes,namely synV and synX.The biosynthesis of astaxanthin is used as a readout and a proof of concept for the application of SVs in industries.Our findings showed that complex SVs,including a pericentric inversion and a trans-chromosome translocation between synV and synX,resulted in two neo-chromosomes and a 2.7-fold yield of astaxanthin.Also,genetic targets were mapped,which resulted in a higher astaxanthin yield,thus demonstrating the SVs’ability to reorganize genetic information along the chromosomes.The rational design of trans-chromosome translocation and pericentric inversion enabled precise induction of these phenomena.Collectively,this study provides an effective tool to not only accelerate the directed genome evolution but also to reveal the mechanistic insight of complex SVs for altering phenotypes.展开更多
Advanced three-dimensional structure variations of chromatin in large genome fragments,such as conversion of A/B compartment,topologically associated domains(TADs)and chromatin loops are related closely to occurrence ...Advanced three-dimensional structure variations of chromatin in large genome fragments,such as conversion of A/B compartment,topologically associated domains(TADs)and chromatin loops are related closely to occurrence of malignant tumors.However,the structural characteristics of lung cancer still remain uncovered.In this study,we used high-throughput chromosome(Hi-C)conformation capture technology to detect the advanced structural variations in chromatin of two nonsmoking lung adenocarcinoma(LUAD)tumor and paired normal tissues.The results indicate that significant chromatin variations are detected in tumor tissues compared with normal tissues.At compartment scale,the main conversion type of compartment is A→B in tumor tissues,which are concentrated mainly on chromosome 3(Chr3)(33.6%).A total of 216 tumor-specific TADs are identified in tumor tissues,which are distributed mainly in Chr1(19),Chr2(15)and Chr3(17).Forty-one distinct enhancer-promoter loops are observed in tumor tissue,which are associated closely to tumor-related pathways including mitogen-activated protein kinase(MAPK),Phosphatidylinositol-3-kinase-Protein kinase B(PI3K-AKT),Ras,Wnt and Ras1.The most important observation in this study is that we identify five important genes(SYT16,NCEH1,NXPE3,MB21D2,and DZIP1L),which are detected in both A→B compartment,TADs and chromatin loops in tumor samples,and four of these genes(NCEH1,NXPE3,MB21D2,and DZIP1L)locate on q arm of Chr3.Further gene expression and invasion experiment analysis show that NCEH1,MB21D2 and SYT16 are involved in the tumor development.Thus,we provide a comprehensive overview of advanced structures in LUAD for the first time and provide a basis for further research on the genetic variation of this tumor.展开更多
Structural variants(SVs),such as deletions(DELs)and insertions(INSs),contribute substantially to pig genetic diversity and phenotypic variation.Using a library of SVs discovered from long-read primary assemblies and s...Structural variants(SVs),such as deletions(DELs)and insertions(INSs),contribute substantially to pig genetic diversity and phenotypic variation.Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes,we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes.Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation.Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements.We identify that the genotypes of two DELs(296-bp DEL,chr7:52,172,101e52,172,397;278-bp DEL,chr18:23,840,143 e23,840,421)located in muscle-specific enhancers are associated with the expression of target genes related to meat quality(FSD2)and muscle fiber hypertrophy(LMOD2 and WASL)in pigs.Our results highlight the role of SVs in domestic porcine evolution,and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.展开更多
Global warming adversely affects crop production worldwide.Massive efforts have been undertaken to study mechanisms regulating heat tolerance in plants.However,the roles of structural variations(SVs)in heat stress tol...Global warming adversely affects crop production worldwide.Massive efforts have been undertaken to study mechanisms regulating heat tolerance in plants.However,the roles of structural variations(SVs)in heat stress tolerance remain unclear.In a recent article,Yan et al.(Nat Genet 1-12,2023)constructed the first pan-genome of pearl millet(Pennisetum glaucum)and identified key SVs linked to genes involved in regulating plant tolerance to heat stress for an important crop with a superior ability to thrive in extremely hot and arid climates.Through multi-omics analyses integrating by pan-genomics,comparative genomics,transcriptomics,population genetics and and molecular biological technologies,they found RWP-RK transcription factors cooperating with endoplasmic reticulum-related genes play key roles in heat tolerance in pearl millet.The results in this paper provided novel insights to advance the understanding of the genetic and genomic basis of heat tolerance and an exceptional resource for molecular breeding to improve heat tolerance in pearl millet and other crops.展开更多
文摘Fig.1.The GenomeSyn tool for visualizing genome synteny and characterizing structural variations.A:The first synteny visualization map showed the detailed information of two or three genomes and can display structural variations and other annotation information.B:The second type of visualization map was simple and only showed the synteny relationship between the chromosomes of two or three genomes.C:Multiplatform general GenomeSyn submission page,applicable to Windows,MAC and web platforms;other analysis files can be entered in the"other"option.The publisher would like to apologise for any inconvenience caused.
基金supported by National Natural Science Foundation of China(32201759,32172002)Inner Mongolia Innovation Center of Biological Breeding Technology,National Key Research and Development Program of China(2021YFD1201600)+1 种基金Earmarked Fund for CARS(CARS-04-PS01)Agricultural Science and Technology Innovation Program(ASTIP).
文摘Soybean(Glycine max)is a globally important crop that serves as a primary source of edible oil and protein for both humans and animals.Cultivated soybean varieties exhibit considerable genetic diversity depending on their geographical origin.Heinong 531(HN531)is an elite cultivar that was released in China in June 2021 with 22.34%seed oil,high resistance to soybean cyst nematode(SCN)race 3,and enhanced yield.However,the genetic basis for these desirable agronomic traits is unclear.In this study,we generated a high-quality genome assembly for HN531 and used it to systematically analyze genes related to agronomic traits such as resistance to SCN.The assembled genome spans 981.20 Mb,featuring a contig N50 of 19.47 Mb,and contains 58,151 predicted gene models.Pan-genomic comparison with 27 previously reported soybean genomes revealed 95,071 structural variants(SVs)of>50 bp,of which 602 were HN531-specific.Furthermore,we identified a copy number variation at rhg1 that underlies resistance to SCN,and we found elite alleles of functional genes underlying important agronomic traits such as seed oil content,adaptability,and yield.This high-quality HN531 genome can be used to explore the genetic basis for the excellent agronomic traits of this cultivar,and is a valuable resource for breeders aiming to improve HN531 and related cultivars.
基金supported by the National Key Research and Development Program of China(2023YFF1000100 and 2023YFA0914601)the Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District(PT202101-01).
文摘Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lacking.Here,we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size,gene number,and TE component,which indicates their representativeness of wheat genetic diversity.Pan-gene analyses uncover 140,261 distinct gene families,of which only 23.2%are shared in all accessions.Moreover,we build a∼16.15 Gb graph pangenome containing 695,897 bubbles,intersecting 5132 genes and 230,307 cis-regulatory regions.Pairwise genome comparisons identify∼1,978,221 non-redundant SVs and 497 SV hotspots.Notably,the density of bubbles as well as SVs show remarkable aggregation in centromeres,which probably play an important role in chromosome plasticity and stability.As for functional SVs exploration,we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups.Additionally,several reported functional genes in wheat display complex structural graphs,for example,PPD-A1,VRT-A2,and TaNAAT2-A.These findings deepen our understanding of wheat genetic diversity,providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.
基金supported by grants from the Zhejiang Science and Technology Department Project(2023C04004)Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding(2021C02068-6)+2 种基金Department of Science Technology of Huzhou City(2023GZ33)Zhejiang Team Technology Ambassador Project(Tongxiang)the National Natural Science Foundation of China(32172724).
文摘Hu sheep is an indigenous breed from the Taihu Lake Plain in China,known for its high fertility.Although Hu sheep belong to the Mongolian group,their demographic history and genetic architecture remain inconclusive.Here,we analyze 697 sheep genomes from representatives of Mongolian sheep breeds.Our study suggests that the ancestral Hu sheep first separated from the Mongolian group approximately 3000 years ago.As Hu sheep migrated from the north and flourished in the Taihu Lake Plain around 1000 years ago,they developed a unique genetic foundation and phenotypic characteristics,which are evident in the genomic footprints of selective sweeps and structural variation landscape.Genes associated with reproductive traits(BMPR1B and TDRD10)and horn phenotype(RXFP2)exhibit notable selective sweeps in the genome of Hu sheep.A genome-wide association analysis reveals that structural variations at LOC101110773,MAST2,and ZNF385B may significantly impact polledness,teat number,and early growth in Hu sheep,respectively.Our study offers insights into the evolutionary history of Hu sheep and may serve as a valuable genetic resource to enhance the understanding of complex traits in Hu sheep.
基金supported by the Foundation of Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration in Longdong (LDSWZY202103)Natural Science Foundation of Gansu Province (22JR5RM210)to B.P.L.Gansu Ziwuling Ecosystem Observation and Research Station (20JR10RA658)。
文摘Avian genomes exhibit compact organization and remarkable chromosomal stability.However,the extent and mechanisms by which structural variation in avian genomes differ from those in other vertebrate lineages are poorly explored.This study generated a diploid genome assembly for the golden pheasant(Chrysolophus pictus),a species distinguished by the vibrant plumage of males.Each haploid genome assembly included complete chromosomalmodels,incorporatingall microchromosomes.Analysis revealed extensive tandem amplification of immune-related genes across the smallest microchromosomes(dot chromosomes),with an average copy number of 54.Structural variation between the haploid genomes was primarily shaped by large insertions and deletions(indels),with minimal contributions from inversions or duplications.Approximately 28%of these large indels were associated with recent insertions of transposable elements,despite their typically low activity in bird genomes.Evidence for significant effects of transposable elements on gene expression was minimal.Evolutionary strata on the sex chromosomes were identified,along with a drastic rearrangement of the W chromosome.These analyses of the high-quality diploid genome of the golden pheasant provide valuable insights into the evolutionary patterns of structural variation in avian genomes.
基金supported by the National Natural Science Foundation of China(NSFC,31970564,32000397,32171982)the Fundamental Research Funds for the Central Universities(2662023PY004)。
文摘"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.
基金supported by the National Key R&D Program of China(2021YFD1301101)National Swine Industry Technology System(CARS-35)Agricultural Science and Technology Innovation Program(ASTIP-IAS02)。
文摘Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.
基金funded by the National Natural Science Foundation of China(32370693 and U20A2034)Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-CSIAF-202402)+1 种基金the Young Top-notch Talent Cultivation Program of Hubei Province for Dr.Chaobo Tong,the National Key Research and Development Program of China(2021YFD1600500)Central Public-interest Scientific Institution Basal Research Fund(2021-2060302-061-027,2021-2060302-061-029).
文摘Structural variations(SVs),a newly discovered genetic variation,have gained increasing recognition for their importance,yet much about them remains unknown.With the completion of whole-genome sequencing projects in oil crops,more SVs have been identified,revealing their types,genomic distribution,and characteristics.These findings have demonstrated the crucial roles of SVs in regulating gene expression,driving trait innovation,facilitating domestication,making this an opportune time for a systematic review.We summarized the progress of SV-related studies in oil crops,focusing on the types of SVs and their mechanisms of occurrence,the strategies and methods for SV detection,and the SVs identified in oil crops such as rapeseed,soybean,peanut,and sesame.The various types of SVs,such as presence-absence variations(PAVs),copy number variations(CNVs),and homeologous exchanges(HEs),have been shown.Along with their genomic characterization,their roles in crop domestication and breeding,and regulatory impact on gene expression and agronomic traits have also been demonstrated.This review will provide an overview of the SV research process in oil crops,enabling researchers to quickly understand key information and apply this knowledge in future studies and crop breeding.
基金funded by the National Natural Science Foundation of China(No.31270408)the National High Technology Research and Development Program(863 Program) of China(No.2014AA022001)
文摘Zeocin can cause double strand breaks of DNA and thus may be employed as a mutagen. In this study, two strains of Nannochloropsis oceanica, the wild and the Zeocin-tolerant strains, were re-sequenced to verify such function of Zeocin, The results showed that Zeocin can mutate the N. oceanica genome and cause the structural variation. Zeocin either swept away or selected the alleles of genes functioning in ubiquitin-mediated proteolysis, alpha-linolenic acid metabolism, ascorbate and aldarate metabolism, ribosome biogenesis, and circadian rhythm, indicating that N. oceanica may have adjusted its metabolic performances for protein, carbohydrate, and lipid, and changed its ribosome biosynthesis and living rhythm to survive in Zeocin containing medium. In addition, Zeocin caused mutation may have influenced the expression of a set of tanscription factors. It was concluded that Zeocin effectively caused the structural variation of the genome of N. oceanica, and forced the microalgae to select out the alleles of a set of genes around these variations in order to adapt to Zeocin containing medium. Further studies on the genetic basis of the phenotypic adaptation of this haploid and asexual microalga and the application of Zeocin to its genetic improvement are very important.
基金support from the Ministry of Science and Technology (Nos.2012BAC20B10)the National Natural Science Foundation of China (Nos. 21321061 and 20976109)
文摘In this work,the influence of CO2 on the structural variation and catalytic performance of Na2WO4/Mn/Si O2 for oxidative coupling of methane to ethylene was investigated. The catalyst was prepared by impregnation method and characterized by XRD,Raman and XPS techniques. Appropriate amount of CO2 in the reactant gases enhanced the formation of surface tetrahedral Na2WO4 species and promoted the migration of O in MOx,Na,W from the catalyst bulk to surface,which were favorable for oxidative coupling of methane. When the molar ratio of CH4/O2/CO2 was 3/1/2,enriched surface tetrahedral Na2WO4 species and high surface concentration of O in MOx,Na,W were detected,and then high CH4 conversion of 33.1% and high C2H4 selectivity of 56.2% were obtained. With further increase of CO2 in the reagent gases,the content of active surface tetrahedral Na2WO4 species and surface concentration of O in MOx,Na,W decreased,while that of inactive species（Mn WO4 and Mn2O3） increased dramatically,leading to low CH4 conversion and low C2H4 selectivity. It could be speculated that Na2WO4 crystal was transformed into Mn WO4 crystal with excessive CO2 added under the reaction conditions. Pretreatment of Na2WO4/Mn/Si O2 catalyst by moderate amount of CO2 before OCM also promoted the formation of Na2WO4 species.
基金supported by the National High Technology Research and Development Program of China(863 Program)(No.2013AA102502)the National Natural Science Foundation of China(Nos.31372284 and 31402046)+1 种基金the Fund of Fok Ying-Tung Education Foundation(No.141117)the Fund for Distinguished Young Scientists of Sichuan Province(No. 2013JQ0013)
文摘Genomic structural variations （SVs）, particularly insertions, deletions and inversions, can contribute to the heterogeneity of millions of nucleotides within a genome, and are likely to make an important contribution to biological diversity and phenotypic variation （Alkan et al., 2011; Bickhart and Liu, 2014）. With the rapid development of the next-generation sequencing technologies and the new assembly methodolo- gies, the multiple de novo assemblies of genomes within a species allow researchers to explore more detailed SV maps （Li et al., 2011）. Compared with the traditional read depth algorithm using the whole-genome resequencing approach and array-based technologies （Baker, 2012; Wang et al., 2012;
基金supported by the National Key Research and Development Program of China(2023YFF1001000)。
文摘Chickens are one of the most important domesticated animals,serving as an important protein source.Studying genetic variations in chickens to enhance their production performance is of great potential value.The emergence of next-generation sequencing has enabled precise analysis of single nucleotide polymorphisms and insertions/deletions in chicken,while third-generation sequencing achieves the accurate structural variant identification.However,the high cost of third-generation sequencing technology limits its application in population studies.The graph-based pan-genome strategy can overcome this challenge by enabling the detection of structural variations using cost-effective next-generation sequencing data.This study constructed a graph-based pangenome for chickens using 12 high-quality genomes.This pan-genome used linear genome GRCg6a as the reference genome,containing variant information from two commercial and nine native chicken breeds.Compared to the linear genome,the pan-genome provided significant improvements in the efficiency of structural variation identification.On the basis of the graph-based pan-genome,high-frequency structural variations related to high egg production in Leghorn chicken were predicted.Additionally,it was discovered that potential structural variations was associated with highland adaptation in Tibetan chickens according to next-generation sequencing and transcriptomics data.Using the pan-genome graph,a new strategy to identify structural variations related to traits of interest in chickens is presented.
基金supported by the National Natural Science Foundation of China (32172626, 32261133519, 32002086, U20A2045)the National Key Research and Development Program of China (2022YFF1003103)+3 种基金the Natural Science Foundation of Anhui Province, Outstanding Youth Project (2308085J17)the Outstanding Youth Project of Anhui Provincial University (2022AH020060)the Natural Science Research Project of Anhui Provincial University (2022AH050867, 2022AH050893, 2023AH051303)the Open Fund of State Key Laboratory of Tea Plant Biology and Utilization (SKLTOF20220120, SKLTOF20230127)。
文摘Domestication has shaped the population structure and agronomic traits of tea plants, yet the complexity of tea population structure and genetic variation that determines these traits remains unclear.We here investigated the resequencing data of 363 diverse tea accessions collected extensively from almost all tea distributions and found that the population structure of tea plants was divided into eight subgroups, which were basically consistent with their geographical distributions. The genetic diversity of tea plants in China decreased from southwest to east as latitude increased. Results also indicated that Camellia sinensis var. assamica(CSA) illustrated divergent selection signatures with Camellia sinensis var. sinensis(CSS). The domesticated genes of CSA were mainly involved in leaf development, flavonoid and alkaloid biosynthesis, while the domesticated genes in CSS mainly participated in amino acid metabolism, aroma compounds biosynthesis,and cold stress. Comparative population genomics further identified ~730 Mb novel sequences, generating 6,058 full-length protein-encoding genes,significantly expanding the gene pool of tea plants.We also discovered 217,376 large-scale structural variations and 56,583 presence and absence variations(PAVs) across diverse tea accessions, some of which were associated with tea quality and stress resistance. Functional experiments demonstrated that two PAV genes(CSS0049975 and CSS0006599)were likely to drive trait diversification in cold tolerance between CSA and CSS tea plants. The overall findings not only revealed the genetic diversity and domestication of tea plants, but also underscored the vital role of structural variations in the diversification of tea plant traits.
基金supported by the National Key Research and Development Program of China (2022YFD1200402)the National Natural Science Foundation of China (32272067 and 32072098).
文摘Dissecting the complex regulatory mechanism of seed oil content(SOC)is one of the main research goals in Brassica napus.Increasing evidence suggests that genome architecture is linked to multiple biological functions.However,the effect of genome architecture on SOC regulation remains unclear.Here,we used high-throughput chromatin conformation capture to characterize differences in the three-dimen-sional(3D)landscape of genome architecture of seeds from two B.napus lines,N53-2(with high SOC)and Ken-C8(with low SOC).Bioinformatics analysis demonstrated that differentially accessible regions and differentially expressed genes between N53-2 and Ken-C8 were preferentially enriched in regions with quantitative trait loci(QTLs)/associated genomic regions(AGRs)for SOC.A multi-omics analysis demonstrated that expression of SOC-related genes was tightly correlated with genome structural varia-tions in QTLs/AGRs of B.napus.The candidate gene BnaA09g48250D,which showed structural variation in a QTL/AGR on chrA09,was identified byfine-mapping of a KN double-haploid population derived from hybridization of N53-2 and Ken-C8.Overexpression and knockout of BnaA09g48250D led to significant in-creases and decreases in SOC,respectively,in the transgenic lines.Taken together,our results reveal the 3D genome architecture of B.napus seeds and the roles of genome structural variations in SOC regulation,enriching our understanding of the molecular mechanisms of SOC regulation from the perspective of spatial chromatin structure.
基金supported by the National Key Research and Development Program of China(2021YFD1201600)the National Natural Science Foundation of China(32201759 and U22A20473)+3 种基金the China Scientific Innovation 2030 Project(2022ZD0401703)the Earmarked Fund for CARS(CARS-04-PS01)the Agricultural Science and Technology Innovation Program(ASTIPCAAS-ZDRW202109).
文摘A genome-wide association study(GWAS)identifies trait-associated loci,but identifying the causal genes can be a bottleneck,due in part to slow decay of linkage disequilibrium(LD).A transcriptome-wide association study(TWAS)addresses this issue by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci with GWAS results.Here,we used self-pollinated soybean(Glycine max[L.]Merr.)as a model to evaluate the application of TWAS to the genetic dissection of traits in plant species with slow LD decay.We generated RNA sequencing data for a soybean diversity panel and identified the genetic expression regulation of 29286 soybean genes.Different TWAS solutions were less affected by LD and were robust to the source of expression,identifing known genes related to traits from different tissues and developmental stages.The novel pod-color gene L2 was identified via TWAS and functionally validated by genome editing.By introducing a new exon proportion feature,we significantly improved the detection of expression variations that resulted from structural variations and alternative splicing.As a result,the genes identified through our TWAS approach exhibited a diverse range of causal variations,including SNPs,insertions or deletions,gene fusion,copy number variations,and alternative splicing.Using this approach,we identified genes associated with flowering time,including both previously known genes and novel genes that had not previously been linked to this trait,providing insights complementary to those from GWAS.In summary,this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.
基金supported in part by the 2021 Research Program of Sanya Yazhou Bay Science and Technology City(SKJC-2021-02-001)the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang(2019R01002)the Fundamental Research Funds for the Central Universities(226-2022-00100 and 2022QZJH43).
文摘Structural variations(SVs)have long been described as being involved in the origin,adaption,and domes-tication of species.However,the underlying genetic and genomic mechanisms are poorly understood.Here,we report a high-quality genome assembly of Gossypium barbadense acc.Tanguis,a landrace that is closely related to formation of extra-long-staple(ELS)cultivated cotton.An SV-based pan-genome(Pan-SV)was then constructed using a total of 182593 non-redundant SVs,including 2236 inversions,97398 insertions,and 82959 deletions from 11 assembled genomes of allopolyploid cotton.The utility of this Pan-sV was then demonstrated through population structure analysis and genome-wide association studies(GWASs).Using segregation mapping populations produced through crossing ELS cotton and the landrace along with an Sv-based GWAs,certain SVs responsible for speciation,domestication,and improvement in tetraploid cottons were identified.Importantly,some of the SVs presently identified as associated with the yield and fiber quality improvement had not been identified in previous SNP-based GWAS.In particular,a 9-bp insertion or deletion was found to associate with elimination of the interspecific reproductive isolation between Gossypium hirsutum and G.barbadense.Collectively,this study provides new insights into genome-wide,gene-scale SVs linked to important agronomic traits in a major crop spe-cies and highlights the importance of sVs during the speciation,domestication,and improvement of culti-vated crop species.
基金This work was supported by the Ministry of Science and Technology,the National Key Research and Development Program of China(2021YFC2100800)the National Natural Science Foundation of China(31800719,31861143017,21621004).
文摘Naturally occurring structural variations(SVs)are a considerable source of genomic variation that can reshape the 3D architecture of chromosomes.Controllable methods aimed at introducing the complex SVs and their related molecular mechanisms have remained farfetched.In this study,an SV-prone yeast strain was developed using Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE)technology with two synthetic chromosomes,namely synV and synX.The biosynthesis of astaxanthin is used as a readout and a proof of concept for the application of SVs in industries.Our findings showed that complex SVs,including a pericentric inversion and a trans-chromosome translocation between synV and synX,resulted in two neo-chromosomes and a 2.7-fold yield of astaxanthin.Also,genetic targets were mapped,which resulted in a higher astaxanthin yield,thus demonstrating the SVs’ability to reorganize genetic information along the chromosomes.The rational design of trans-chromosome translocation and pericentric inversion enabled precise induction of these phenomena.Collectively,this study provides an effective tool to not only accelerate the directed genome evolution but also to reveal the mechanistic insight of complex SVs for altering phenotypes.
基金supported by National Guided Science and Technology Development Project of Sichuan Province(No:2020ZYD009)Clinical Research Incubation Project of West China Hospital of Sichuan University(No:2018HXFH012)+3 种基金Hospital-enterprise cooperation clinical research innovation project(Sichuan University West China Hospital-Shanghai Pharmaceutical)(No:2019HXCX04)Sichuan Science and Technology Program(No:2020ZYD007)Science and Technology Achievement Transformation Fund of Sichuan University West China Hospital(No:CGZH19013)we sincerely thanks to Biomarker Technologies Corporation(Beijing,China)for the analyses of bioinformation in this study.
文摘Advanced three-dimensional structure variations of chromatin in large genome fragments,such as conversion of A/B compartment,topologically associated domains(TADs)and chromatin loops are related closely to occurrence of malignant tumors.However,the structural characteristics of lung cancer still remain uncovered.In this study,we used high-throughput chromosome(Hi-C)conformation capture technology to detect the advanced structural variations in chromatin of two nonsmoking lung adenocarcinoma(LUAD)tumor and paired normal tissues.The results indicate that significant chromatin variations are detected in tumor tissues compared with normal tissues.At compartment scale,the main conversion type of compartment is A→B in tumor tissues,which are concentrated mainly on chromosome 3(Chr3)(33.6%).A total of 216 tumor-specific TADs are identified in tumor tissues,which are distributed mainly in Chr1(19),Chr2(15)and Chr3(17).Forty-one distinct enhancer-promoter loops are observed in tumor tissue,which are associated closely to tumor-related pathways including mitogen-activated protein kinase(MAPK),Phosphatidylinositol-3-kinase-Protein kinase B(PI3K-AKT),Ras,Wnt and Ras1.The most important observation in this study is that we identify five important genes(SYT16,NCEH1,NXPE3,MB21D2,and DZIP1L),which are detected in both A→B compartment,TADs and chromatin loops in tumor samples,and four of these genes(NCEH1,NXPE3,MB21D2,and DZIP1L)locate on q arm of Chr3.Further gene expression and invasion experiment analysis show that NCEH1,MB21D2 and SYT16 are involved in the tumor development.Thus,we provide a comprehensive overview of advanced structures in LUAD for the first time and provide a basis for further research on the genetic variation of this tumor.
基金supported by Creative Research Team Project of the National Natural Science Foundation of China(32221005 to S.Zhao)grants from the National Natural Science Foundation of China(32202637 to Z.Zheng and 31972536 to X.Li)the earmarked fund for CARS-35,and China Postdoctoral Science Foundation(2020M682446 to Z.Zheng).
文摘Structural variants(SVs),such as deletions(DELs)and insertions(INSs),contribute substantially to pig genetic diversity and phenotypic variation.Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes,we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes.Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation.Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements.We identify that the genotypes of two DELs(296-bp DEL,chr7:52,172,101e52,172,397;278-bp DEL,chr18:23,840,143 e23,840,421)located in muscle-specific enhancers are associated with the expression of target genes related to meat quality(FSD2)and muscle fiber hypertrophy(LMOD2 and WASL)in pigs.Our results highlight the role of SVs in domestic porcine evolution,and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.
文摘Global warming adversely affects crop production worldwide.Massive efforts have been undertaken to study mechanisms regulating heat tolerance in plants.However,the roles of structural variations(SVs)in heat stress tolerance remain unclear.In a recent article,Yan et al.(Nat Genet 1-12,2023)constructed the first pan-genome of pearl millet(Pennisetum glaucum)and identified key SVs linked to genes involved in regulating plant tolerance to heat stress for an important crop with a superior ability to thrive in extremely hot and arid climates.Through multi-omics analyses integrating by pan-genomics,comparative genomics,transcriptomics,population genetics and and molecular biological technologies,they found RWP-RK transcription factors cooperating with endoplasmic reticulum-related genes play key roles in heat tolerance in pearl millet.The results in this paper provided novel insights to advance the understanding of the genetic and genomic basis of heat tolerance and an exceptional resource for molecular breeding to improve heat tolerance in pearl millet and other crops.
