Lung squamous cell carcinoma （LUSC） causes approximately 400 000 deaths each year worldwide. The occurrence of LUSC is attributed to exposure to cigarette smoke, which induces the development of numerous genomic abn...Lung squamous cell carcinoma （LUSC） causes approximately 400 000 deaths each year worldwide. The occurrence of LUSC is attributed to exposure to cigarette smoke, which induces the development of numerous genomic abnormalities. However, few studies have investigated the genomic variations that occur only in normal tissues that have been similarly exposed to tobacco smoke as tumor tissues. In this study, we sequenced the whole genomes of three normal lung tissue samples and their paired adjacent squamous cell carcinomas. We then called genomic variations specific to the normal lung tissues through filtering the genomic sequence of the normal lung tissues against that of the paired tumors, the reference human genome, the dbSNP138 common germline variants, and the variations derived from sequencing artifacts. To expand these observations, the whole exome sequences of 478 counterpart normal controls （CNCs） and paired LUSCs of The Cancer Genome Atlas （TCGA） dataset were analyzed. Sixteen genomic variations were called in the three normal lung tissues. These variations were confirmed by Sanger capillary sequencing. A mean of 0.5661 exonic variations/Mb and 7.7887 altered genes per sample were identified in the CNC genome sequences of TCGA. In these CNCs, C：G→T：A transitions, which are the genomic signatures of tobacco carcinogen N-methyl-N-nitro-N-nitrosoguanidine, were the predominant nucleotide changes. Twenty five genes in CNCs had a variation rate that exceeded 2%, including ARSD （18.62%）, MUC4 （8.79%）, and RBMX（7.11%）. CNC variations in CTAGE5 and USP17L7were associated with the poor prognosis of patients with LUSC. Our results uncovered previously unreported genomic variations in CNCs, rather than LUSCs, that may be involved in the develooment of LUSC.展开更多
Tea green leafhopper(TGL),Empoasca onukii,is of biological and economic interest.Despite numerous studies,the mechanisms underlying its adaptation and evolution remain enigmatic.Here,we use previously untapped genome ...Tea green leafhopper(TGL),Empoasca onukii,is of biological and economic interest.Despite numerous studies,the mechanisms underlying its adaptation and evolution remain enigmatic.Here,we use previously untapped genome and population genetics approaches to examine how the pest adapted to different environmental variables and thus has expanded geographically.We complete a chromosome-level assembly and annotation of the E.onukii genome,showing notable expansions of gene families associated with adaptation to chemoreception and detoxification.Genomic signals indicating balancing selection highlight metabolic pathways involved in adaptation to a wide range of tea varieties grown across ecologically diverse regions.Patterns of genetic variations among 54 E.onukii samples unveil the population structure and evolutionary history across different tea-growing regions in China.Our results demonstrate that the genomic changes in key pathways,including those linked to metabolism,circadian rhythms,and immune system functions,may underlie the successful spread and adaptation of E.onukii.This work highlights the genetic and molecular basis underlying the evolutionary success of a species with broad economic impacts,and provides insights into insect adaptation to host plants,which will ultimately facilitate more sustainable pest management.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
Objective:To investigate mutations in the Chikungunya(CHIKV)envelope genome region and evaluate their potential impact on B lymphocyte epitopes via in silico analysis.Methods:E1,E2 and 6K protein genes were sequenced ...Objective:To investigate mutations in the Chikungunya(CHIKV)envelope genome region and evaluate their potential impact on B lymphocyte epitopes via in silico analysis.Methods:E1,E2 and 6K protein genes were sequenced from viral RNA isolated from 13 CHIKV-positive serum samples from Alagoas State,Brazil,during the 2016 outbreak.Phylogenetic analysis,experimental epitope identification in the immune epitope database(IEDB)and in silico approaches were employed to predict the potential impact of the detected mutations.Results:The sequences were clustered via phylogenetic analysis.The CHIKV isolates belong to the ECSA genotype,with 13 detected amino acid mutations.Five mutations are located on the surface of the viral particle in regions critical for cellular receptor interaction.Nine mutations are known experimentally validated epitopes for B and T cells.In B-cell epitope predictions,mutations affect sequences within three conformational epitopes in E2 and one in E1,as well as linear epitopes.Notably,the E2-G60D mutation found in the Alagoas strain has been previously reported to influence the vector competence of Aedes aegypti,the primary vector in Brazil.Conclusions:Genomic surveillance and an in-depth understanding of viral mutations are crucial for adapting public health strategies and improving the outbreak response.These findings could have significant public health implications,such as the development of more effective vaccines,diagnostic tests,and antiviral therapies.展开更多
Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression...Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.展开更多
Objective:Histology grade,subtypes and TNM stage of lung adenocarcinomas are useful predictors of prognosis and survival.The aim of the study was to investigate the relationship between chromosomal instability,morphol...Objective:Histology grade,subtypes and TNM stage of lung adenocarcinomas are useful predictors of prognosis and survival.The aim of the study was to investigate the relationship between chromosomal instability,morphological subtypes and the grading system used in lung non-mucinous adenocarcinoma(LNMA).Methods:We developed a whole genome copy number variation(WGCNV)scoring system and applied next generation sequencing to evaluate CNVs present in 91 LNMA tumor samples.Results:Higher histological grades,aggressive subtypes and more advanced TNM staging were associated with an increased WGCNV score,particularly in CNV regions enriched for tumor suppressor genes and oncogenes.In addition,we demonstrate that 24-chromosome CNV profiling can be performed reliably from specific cell types(<100 cells)isolated by sample laser capture microdissection.Conclusions:Our findings suggest that the WGCNV scoring system we developed may have potential value as an adjunct test for predicting the prognosis of patients diagnosed with LNMA.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
Approximately 20%of colorectal cancer(CRC)patients present with metastasis at diagnosis.Among Stage I-III CRC patients who undergo surgical resection,18%typically suffer from distal metastasis within the first three y...Approximately 20%of colorectal cancer(CRC)patients present with metastasis at diagnosis.Among Stage I-III CRC patients who undergo surgical resection,18%typically suffer from distal metastasis within the first three years following initial treatment.The median survival duration after the diagnosis of metastatic CRC(mCRC)is only 9 mo.mCRC is traditionally considered to be an advanced stage malignancy or is thought to be caused by incomplete resection of tumor tissue,allowing cancer cells to spread from primary to distant organs;however,increa-sing evidence suggests that the mCRC process can begin early in tumor development.CRC patients present with high heterogeneity and diverse cancer phenotypes that are classified on the basis of molecular and morphological alterations.Different genomic and nongenomic events can induce subclone diversity,which leads to cancer and metastasis.Throughout the course of mCRC,metastatic cascades are associated with invasive cancer cell migration through the circulatory system,extravasation,distal seeding,dormancy,and reactivation,with each step requiring specific molecular functions.However,cancer cells presenting neoantigens can be recognized and eliminated by the immune system.In this review,we explain the biological factors that drive CRC metastasis,namely,genomic instability,epigenetic instability,the metastatic cascade,the cancer-immunity cycle,and external lifestyle factors.Despite remarkable progress in CRC research,the role of molecular classification in therapeutic intervention remains unclear.This review shows the driving factors of mCRC which may help in identifying potential candidate biomarkers that can improve the diagnosis and early detection of mCRC cases.展开更多
Mutation breeding is based on the induction of genetic variations; hence knowledge of the frequency and type of induced mutations is of paramount importance for the design and implementation of a mutation breeding pro...Mutation breeding is based on the induction of genetic variations; hence knowledge of the frequency and type of induced mutations is of paramount importance for the design and implementation of a mutation breeding program. Although γ ray irradiation has been widely used since the 1960 s in the breeding of about 200 economically important plant species, molecular elucidation of its genetic effects has so far been achieved largely by analysis of target genes or genomic regions. In the present study, the whole genomes of six γ-irradiated M2 rice plants were sequenced; a total of 144–188 million high-quality（Q〉20） reads were generated for each M2 plant, resulting in genome coverage of 45 times for each plant. Single base substitution（SBS） and short insertion/deletion（Indel） mutations were detected at the average frequency of 7.5×10^-6～9.8×10^-6 in the six M2 rice plants（SBS being about 4 times more frequent than Indels）. Structural and copy number variations, though less frequent than SBS and Indel, were also identified and validated. The mutations were scattered in all genomic regions across 12 rice chromosomes without apparent hotspots. The present study is the first genome-wide single-nucleotide resolution study on the feature and frequency of γ irradiation-induced mutations in a seed propagated crop; the findings are of practical importance for mutation breeding of rice and other crop species.展开更多
The cultivated soybean（Glycine max（L.） Merr.） was distinguished from its wild progenitor Glycine soja Sieb.＆ Zucc.in growth period structure,by a shorter vegetative phase（V）,a prolonged reproductive phase（R） ...The cultivated soybean（Glycine max（L.） Merr.） was distinguished from its wild progenitor Glycine soja Sieb.＆ Zucc.in growth period structure,by a shorter vegetative phase（V）,a prolonged reproductive phase（R） and hence a larger R/V ratio.However,the genetic basis of the domestication of soybean from wild materials is unclear.Here,a panel of 123 cultivated and 97 wild accessions were genotyped using a set of 24 presence/absence variants（PAVs） while at the same time the materials were phenotyped with respect to flowering and maturity times at two trial sites located at very different latitudes.The major result of this study showed that variation at PAVs is informative for assessing patterns of genetic diversity in Glycine spp.The genotyping was largely consistent with the taxonomic status,although a few accessions were intermediate between the two major clades identified.Allelic diversity was much higher in the wild germplasm than in the cultivated materials.A significant domestication signal was detected at 11 of the PAVs at 0.01 level.In particular,this study has provided information for revealing the genetic basis of photoperiodism which was a prominent feature for the domestication of soybean.A significant marker-trait association with R/V ratio was detected at 14 of the PAVs,but stripping out population structure reduced this to three.These results will provide markers information for further finding of R/V related genes that can help to understand the domestication process and introgress novel genes in wild soybean to broaden the genetic base of modern soybean cultivars.展开更多
Common wheat （Triticum aestivum L.） is one of the most important crops, and intra-specific wheat hybrids have obvious heterosis in yield and protein quality. Therefore, utilization of hybrid wheat varieties offers a...Common wheat （Triticum aestivum L.） is one of the most important crops, and intra-specific wheat hybrids have obvious heterosis in yield and protein quality. Therefore, utilization of hybrid wheat varieties offers an effective way to increase yield and nutrition. Cytoplasmic male sterility （CMS） systems are a useful genetic tool for hybrid crop breeding, and are ideal models for studying the genetic interaction and cooperative function of mitochondrial and nuclear genomes in plants （Schnable and Wise, 1998; Hanson and Bentolila, 2004）.展开更多
Global climate change is expected to accelerate biological invasions,necessitating accurate risk forecasting and management strategies.However,current invasion risk assessments often overlook adaptive genomic variatio...Global climate change is expected to accelerate biological invasions,necessitating accurate risk forecasting and management strategies.However,current invasion risk assessments often overlook adaptive genomic variation,which plays a significant role in the persistence and expansion of invasive populations.Here we used Molgula manhattensis,a highly invasive ascidian,as a model to assess its invasion risks along Chinese coasts under climate change.Through population genomics analyses,we identified two genetic clusters,the north and south clusters,based on geographic distributions.To predict invasion risks,we employed the gradient forest and species distribution models to calculate genomic offset and species habitat suitability,respectively.These approaches yielded distinct predictions:the gradient forest model suggested a greater genomic offset to future climatic conditions for the north cluster(i.e.,lower invasion risks),while the species distribution model indicated higher future habitat suitability for the same cluster(i.e,higher invasion risks).By integrating these models,we found that the south cluster exhibited minor genome-niche disruptions in the future,indicating higher invasion risks.Our study highlights the complementary roles of genomic offset and habitat suitability in assessing invasion risks under climate change.Moreover,incorporating adaptive genomic variation into predictive models can significantly enhance future invasion risk predictions and enable effective management strategies for biological invasions in the future.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
Objective:To summarize the application value of copy number variant sequencing(CNV-seq)in the detection of fetal chromosome and cytomegalovirus load.Methods:The study analyzed the clinical basic data,relevant laborato...Objective:To summarize the application value of copy number variant sequencing(CNV-seq)in the detection of fetal chromosome and cytomegalovirus load.Methods:The study analyzed the clinical basic data,relevant laboratory tests,treatment process,and outcomes of three patients with positive cytomegalovirus load detected by CNV-seq for fetal chromosomes and cytomegalovirus load,and literature review was done simutaneoubly.Results:In all three cases,the amniotic fluid cytomegalovirus load was less than 105 Copies/ml,and there were no significant neurological abnormalities observed during pregnancy or postpartum follow-up.There is no literature review on the application of CNV-seq technology in the detection of cytomegalovirus infection,only literature reports on genome analysis of CMV-DNA in confirmed patients were available.Conclusion:CNV-seq can be used to detect cytomegalovirus load,which may have a certain degree of predictive value for fetal outcome.CNV-seq can simultaneously detect fetal chromosomes and pathogenic microorganisms,which is of great significance for the prevention and control of birth defects.展开更多
In this study, we conducted a cross of white crucian carp （♀）xred crucian carp （♂） （WR）, and characterized the morphology, reproduction and genetics of the progeny. Different from parents, WR with the gray col...In this study, we conducted a cross of white crucian carp （♀）xred crucian carp （♂） （WR）, and characterized the morphology, reproduction and genetics of the progeny. Different from parents, WR with the gray color showed the hybrid morphological traits of both parents. WR possessed normal gonads producing mature eggs or sperm, and exhibited high fertilization rate （90.2%） and high hatchery rate （80.5%）, which contributed to produce and enlarge the population. WR with the same DNA content as parents was a diploid fish with 100 chromosomes （2n=100）. Amplified ITS of 45S rDNA, in WR the sequences consisting of 884 bp bases of the entire ITS-1 region, 5.8 S region, and entire ITS-2 region. The sequences showed high similarity between WR and its parents and leaned towards male inheritance. In WR, NTS of 5S rDNA consisted of three length types with total 654 bp bases. From sequence analysis of NTS, WR shared 94.2% and 95.1% similarities with their female and male parent, respectively. Sequence analysis of ITS and NTS revealed that there existed recombination and variation in the hybrid progeny, which was the genetic base for adaptation and speciation. In conclusion, we obtained WR from hybridization and it exhibited hybrid traits in morphology and variation in genetic composition showing essential difference with its parents. The obtainment of WR has important significance in fish genetic breeding.展开更多
Advances in DNA sequencing technology have sparked a genomics revolution,driving breakthroughs in plant genetics and crop breeding.Recently,the focus has shifted from cataloging genetic diversity in plants to explorin...Advances in DNA sequencing technology have sparked a genomics revolution,driving breakthroughs in plant genetics and crop breeding.Recently,the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement.This transformation has been facilitated by the increasing adoption of whole-genome resequencing.In this review,we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding.A total of 187 land plants from 163 countries have been resequenced,comprising 54413 accessions.As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted.Economically important crops,particularly cereals,vegetables,and legumes,have dominated the resequencing efforts,leaving a gap in 49 orders,including Lycopodiales,Liliales,Acorales,Austrobaileyales,and Commelinales.The resequenced germplasm is distributed across diverse geographic locations,providing a global perspective on plant genomics.We highlight genes that have been selected during domestication,or associated with agronomic traits,and form a repository of candidate genes for future research and application.Despite the opportunities for cross-species comparative genomics,many population genomic datasets are not accessible,impeding secondary analyses.We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy.The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs,coupled with advances in analysis and computational technologies.This expansion,in terms of both scale and quality,holds promise for deeper insights into plant trait genetics and breeding design.展开更多
Plants produce a remarkable diversity of structurally and functionally diverse natural chemicals that serve as adaptive compounds throughout their life cycles.However,unlocking this metabolic diversity is significantl...Plants produce a remarkable diversity of structurally and functionally diverse natural chemicals that serve as adaptive compounds throughout their life cycles.However,unlocking this metabolic diversity is significantly impeded by the size,complexity,and abundant repetitive elements of typical plant genomes.As genome sequencing becomes routine,we anticipate that links between metabolic diversity and genetic variation will be strengthened.In addition,an ever-increasing number of plant genomes have revealed that biosynthetic gene clusters are not only a hallmark of microbes and fungi;gene clusters for various classes of compounds have also been found in plants,and many are associated with important agronomic traits.We present recent examples of plant metabolic diversification that have been discovered through the exploration and exploitation of various genomic and pan-genomic data.We also draw attention to the fundamental genomic and pan-genomic basis of plant chemodiversity and discuss challenges and future perspectives for investigating metabolic diversity in the coming pan-genomics era.展开更多
As a typical representative of global complex diseases,psoriasis has attracted widespread attention because of its high heritability,heterogeneity,and incidence.Environmentally induced activation of the inflammatory-i...As a typical representative of global complex diseases,psoriasis has attracted widespread attention because of its high heritability,heterogeneity,and incidence.Environmentally induced activation of the inflammatory-immune axis in patients with psoriasis relies on genetic regulation of genomic variation.The heritability of psoriasis exceeds 80%,and research of genomic variation in psoriasis is of great significance to the interpretation of the biological pathogenesis of the disease.The development of genome-wide association studies(GWASs)has provided a powerful means for the capture of psoriasis susceptibility genes.More than 100 psoriasis susceptibility loci have been captured,enabling humans to gain a breakthrough understanding of the genetics and traits of psoriasis.With the advancement of research methods,increasingly more genetic methodologies are being used to capture the locations and types of variants outside the scope of GWAS scanning,making up for the inclinations and deficiencies of traditional GWAS capture of gene loci in a more detailed manner.This review covers several decades of research on genomic variation in psoriasis,including GWASs in psoriasis,the capture of functional gene variant types,and the translation of genomic variation into precision medicine;summarizes the research progress of genomic variation in psoriasis;and provides a theoretical reference for future genetic-based research of the mechanisms underlying psoriasis.展开更多
On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS...On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates,which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline.Of particular note,2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale.It provides all identified variants and their detailed statistics for each virus isolate,and congregates the quality score,functional annotation,and population frequency for each variant.Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available.Moreover,2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019(COVID-19),including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC.Furthermore,by linking with relevant databases in CNCB,2019nCoVR offers data submission services for raw sequence reads and assembled genomes,and data sharing with NCBI.Collectively,SARS-CoV-2 is updated daily to collect the latest information on genome sequences,variants,haplotypes,and literature for a timely reflection,making 2019nCoVR a valuable resource for the global research community.2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.展开更多
Polyploidization via whole-genome duplications （WGD） is a common phenomenon in organisms. However, investigations into this phenomenon differ greatly between plants and animals. Recent research on polyploid plants i...Polyploidization via whole-genome duplications （WGD） is a common phenomenon in organisms. However, investigations into this phenomenon differ greatly between plants and animals. Recent research on polyploid plants illustrates the immediate changes that follow WGDs and the mechanisms behind in both genetic and epigenetic consequences. Unfortunately, equivalent questions remain to be explored in animals. Enlightened by botanical research, the study of polyploidization in vertebrates involves the identification of model animals and the establishment of strategies. Here we review and compare the research on plants and vertebrates while considering intrageneric or intraspecific variation in genome size. Suitable research methods on recently established poly- ploidy systems could provide important clues for under- standing what happens after WGDs in vertebrates. The approach yields insights into survival and the rarity of polyploidization in vertebrates. The species of Carassius and the allopolyploid system of goldfish × common carp hybridization appear to be suitable models for unraveling the evolution and adaptation of polyploid vertebrates.展开更多
基金This work was supported by the National Natural Science Funds of China for Distinguished Young Scholar （No. 81425025）, the National Key Research and Development Program of China （No. 2016YFC0905500）, the National Natural Science Foundation of China （No. 81672765）, the Strategic Priority Research Program of the Chinese Academy of Sciences （No. XDA 12010307）, and grants from the State Key Laboratory of Membrane Biology. The funders had no role in the design, data collection, and analysis of the study or in the preparation of and the decision to publish the manuscript. The results shown here are partly based on the data generated by The Cancer Genome Atlas, which is managed by the NCI and NHGRI. Information about TCGA can be found at http：//cancergenome.nih. gov. The dbGaP accession number is phs000178.v9.p8.
文摘Lung squamous cell carcinoma （LUSC） causes approximately 400 000 deaths each year worldwide. The occurrence of LUSC is attributed to exposure to cigarette smoke, which induces the development of numerous genomic abnormalities. However, few studies have investigated the genomic variations that occur only in normal tissues that have been similarly exposed to tobacco smoke as tumor tissues. In this study, we sequenced the whole genomes of three normal lung tissue samples and their paired adjacent squamous cell carcinomas. We then called genomic variations specific to the normal lung tissues through filtering the genomic sequence of the normal lung tissues against that of the paired tumors, the reference human genome, the dbSNP138 common germline variants, and the variations derived from sequencing artifacts. To expand these observations, the whole exome sequences of 478 counterpart normal controls （CNCs） and paired LUSCs of The Cancer Genome Atlas （TCGA） dataset were analyzed. Sixteen genomic variations were called in the three normal lung tissues. These variations were confirmed by Sanger capillary sequencing. A mean of 0.5661 exonic variations/Mb and 7.7887 altered genes per sample were identified in the CNC genome sequences of TCGA. In these CNCs, C：G→T：A transitions, which are the genomic signatures of tobacco carcinogen N-methyl-N-nitro-N-nitrosoguanidine, were the predominant nucleotide changes. Twenty five genes in CNCs had a variation rate that exceeded 2%, including ARSD （18.62%）, MUC4 （8.79%）, and RBMX（7.11%）. CNC variations in CTAGE5 and USP17L7were associated with the poor prognosis of patients with LUSC. Our results uncovered previously unreported genomic variations in CNCs, rather than LUSCs, that may be involved in the develooment of LUSC.
基金supported by the National Key R&D Program of China(Grant No.2019YFD1002100)the Natural Science Foundation of Fujian Province,China(Grant No.2020J01525)+1 种基金the Fujian Agriculture and Forestry University Construction Project for Technological Innovation and Service System of Tea Industry,China(Grant No.K1520005A03)the Key International Science and Technology cooperation Project of China(Grant No.2016YFE0102100).
文摘Tea green leafhopper(TGL),Empoasca onukii,is of biological and economic interest.Despite numerous studies,the mechanisms underlying its adaptation and evolution remain enigmatic.Here,we use previously untapped genome and population genetics approaches to examine how the pest adapted to different environmental variables and thus has expanded geographically.We complete a chromosome-level assembly and annotation of the E.onukii genome,showing notable expansions of gene families associated with adaptation to chemoreception and detoxification.Genomic signals indicating balancing selection highlight metabolic pathways involved in adaptation to a wide range of tea varieties grown across ecologically diverse regions.Patterns of genetic variations among 54 E.onukii samples unveil the population structure and evolutionary history across different tea-growing regions in China.Our results demonstrate that the genomic changes in key pathways,including those linked to metabolism,circadian rhythms,and immune system functions,may underlie the successful spread and adaptation of E.onukii.This work highlights the genetic and molecular basis underlying the evolutionary success of a species with broad economic impacts,and provides insights into insect adaptation to host plants,which will ultimately facilitate more sustainable pest management.
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 Decit/SCTIE-Ministério da Saúde,Conselho Nacional de Desenvolvimento Científico e Tecnológico(CNPq),Fundação de AmparoàPesquisa do Estado de Alagoas(FAPEAL)and Secretaria de Estado da Saúde de Alagoas(SESAU-AL)[PPSUS 60030000841/2016].
文摘Objective:To investigate mutations in the Chikungunya(CHIKV)envelope genome region and evaluate their potential impact on B lymphocyte epitopes via in silico analysis.Methods:E1,E2 and 6K protein genes were sequenced from viral RNA isolated from 13 CHIKV-positive serum samples from Alagoas State,Brazil,during the 2016 outbreak.Phylogenetic analysis,experimental epitope identification in the immune epitope database(IEDB)and in silico approaches were employed to predict the potential impact of the detected mutations.Results:The sequences were clustered via phylogenetic analysis.The CHIKV isolates belong to the ECSA genotype,with 13 detected amino acid mutations.Five mutations are located on the surface of the viral particle in regions critical for cellular receptor interaction.Nine mutations are known experimentally validated epitopes for B and T cells.In B-cell epitope predictions,mutations affect sequences within three conformational epitopes in E2 and one in E1,as well as linear epitopes.Notably,the E2-G60D mutation found in the Alagoas strain has been previously reported to influence the vector competence of Aedes aegypti,the primary vector in Brazil.Conclusions:Genomic surveillance and an in-depth understanding of viral mutations are crucial for adapting public health strategies and improving the outbreak response.These findings could have significant public health implications,such as the development of more effective vaccines,diagnostic tests,and antiviral therapies.
基金supported by the National Natural Science Foundation of China(32172010)the Major Program of Guangdong Basic and Applied Basic Research(2019B030302006).
文摘Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.
基金grants from Beijing Hospital Key Research Program(121 Research Program,No.BJ2019-195)。
文摘Objective:Histology grade,subtypes and TNM stage of lung adenocarcinomas are useful predictors of prognosis and survival.The aim of the study was to investigate the relationship between chromosomal instability,morphological subtypes and the grading system used in lung non-mucinous adenocarcinoma(LNMA).Methods:We developed a whole genome copy number variation(WGCNV)scoring system and applied next generation sequencing to evaluate CNVs present in 91 LNMA tumor samples.Results:Higher histological grades,aggressive subtypes and more advanced TNM staging were associated with an increased WGCNV score,particularly in CNV regions enriched for tumor suppressor genes and oncogenes.In addition,we demonstrate that 24-chromosome CNV profiling can be performed reliably from specific cell types(<100 cells)isolated by sample laser capture microdissection.Conclusions:Our findings suggest that the WGCNV scoring system we developed may have potential value as an adjunct test for predicting the prognosis of patients diagnosed with LNMA.
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;
文摘Approximately 20%of colorectal cancer(CRC)patients present with metastasis at diagnosis.Among Stage I-III CRC patients who undergo surgical resection,18%typically suffer from distal metastasis within the first three years following initial treatment.The median survival duration after the diagnosis of metastatic CRC(mCRC)is only 9 mo.mCRC is traditionally considered to be an advanced stage malignancy or is thought to be caused by incomplete resection of tumor tissue,allowing cancer cells to spread from primary to distant organs;however,increa-sing evidence suggests that the mCRC process can begin early in tumor development.CRC patients present with high heterogeneity and diverse cancer phenotypes that are classified on the basis of molecular and morphological alterations.Different genomic and nongenomic events can induce subclone diversity,which leads to cancer and metastasis.Throughout the course of mCRC,metastatic cascades are associated with invasive cancer cell migration through the circulatory system,extravasation,distal seeding,dormancy,and reactivation,with each step requiring specific molecular functions.However,cancer cells presenting neoantigens can be recognized and eliminated by the immune system.In this review,we explain the biological factors that drive CRC metastasis,namely,genomic instability,epigenetic instability,the metastatic cascade,the cancer-immunity cycle,and external lifestyle factors.Despite remarkable progress in CRC research,the role of molecular classification in therapeutic intervention remains unclear.This review shows the driving factors of mCRC which may help in identifying potential candidate biomarkers that can improve the diagnosis and early detection of mCRC cases.
基金supported by the National Natural Science Foundation of China(No.11275171)the National Key Technology R&D Program of China(No.2014BAA03B04)the Mutation Breeding Project of the Forum for Nuclear Cooperation in Asia(FNCA)
文摘Mutation breeding is based on the induction of genetic variations; hence knowledge of the frequency and type of induced mutations is of paramount importance for the design and implementation of a mutation breeding program. Although γ ray irradiation has been widely used since the 1960 s in the breeding of about 200 economically important plant species, molecular elucidation of its genetic effects has so far been achieved largely by analysis of target genes or genomic regions. In the present study, the whole genomes of six γ-irradiated M2 rice plants were sequenced; a total of 144–188 million high-quality（Q〉20） reads were generated for each M2 plant, resulting in genome coverage of 45 times for each plant. Single base substitution（SBS） and short insertion/deletion（Indel） mutations were detected at the average frequency of 7.5×10^-6～9.8×10^-6 in the six M2 rice plants（SBS being about 4 times more frequent than Indels）. Structural and copy number variations, though less frequent than SBS and Indel, were also identified and validated. The mutations were scattered in all genomic regions across 12 rice chromosomes without apparent hotspots. The present study is the first genome-wide single-nucleotide resolution study on the feature and frequency of γ irradiation-induced mutations in a seed propagated crop; the findings are of practical importance for mutation breeding of rice and other crop species.
基金supported by the Agricultural Science and Technology Innovation Program(ASTIP) of Chinese Academy of Agricultural Sciences and the Platform of National Crop Germplasm Resources of China(nos.2012-004 and 2013-004)
文摘The cultivated soybean（Glycine max（L.） Merr.） was distinguished from its wild progenitor Glycine soja Sieb.＆ Zucc.in growth period structure,by a shorter vegetative phase（V）,a prolonged reproductive phase（R） and hence a larger R/V ratio.However,the genetic basis of the domestication of soybean from wild materials is unclear.Here,a panel of 123 cultivated and 97 wild accessions were genotyped using a set of 24 presence/absence variants（PAVs） while at the same time the materials were phenotyped with respect to flowering and maturity times at two trial sites located at very different latitudes.The major result of this study showed that variation at PAVs is informative for assessing patterns of genetic diversity in Glycine spp.The genotyping was largely consistent with the taxonomic status,although a few accessions were intermediate between the two major clades identified.Allelic diversity was much higher in the wild germplasm than in the cultivated materials.A significant domestication signal was detected at 11 of the PAVs at 0.01 level.In particular,this study has provided information for revealing the genetic basis of photoperiodism which was a prominent feature for the domestication of soybean.A significant marker-trait association with R/V ratio was detected at 14 of the PAVs,but stripping out population structure reduced this to three.These results will provide markers information for further finding of R/V related genes that can help to understand the domestication process and introgress novel genes in wild soybean to broaden the genetic base of modern soybean cultivars.
基金supported by the National Natural Science Foundation of China(No.30971844)the Fundamental Research Funds of Northwest A & F University(No. QN2011003)+1 种基金China Postdoctoral Science Foundation to Wang Junwei(No.20070410835)the Tang Zhong-Ying Breeding Funding Project of Northwest A & F University
文摘Common wheat （Triticum aestivum L.） is one of the most important crops, and intra-specific wheat hybrids have obvious heterosis in yield and protein quality. Therefore, utilization of hybrid wheat varieties offers an effective way to increase yield and nutrition. Cytoplasmic male sterility （CMS） systems are a useful genetic tool for hybrid crop breeding, and are ideal models for studying the genetic interaction and cooperative function of mitochondrial and nuclear genomes in plants （Schnable and Wise, 1998; Hanson and Bentolila, 2004）.
基金supported by the National Natural Science Foundation of China(grant numbers 32061143012,42106098,and 42276126).
文摘Global climate change is expected to accelerate biological invasions,necessitating accurate risk forecasting and management strategies.However,current invasion risk assessments often overlook adaptive genomic variation,which plays a significant role in the persistence and expansion of invasive populations.Here we used Molgula manhattensis,a highly invasive ascidian,as a model to assess its invasion risks along Chinese coasts under climate change.Through population genomics analyses,we identified two genetic clusters,the north and south clusters,based on geographic distributions.To predict invasion risks,we employed the gradient forest and species distribution models to calculate genomic offset and species habitat suitability,respectively.These approaches yielded distinct predictions:the gradient forest model suggested a greater genomic offset to future climatic conditions for the north cluster(i.e.,lower invasion risks),while the species distribution model indicated higher future habitat suitability for the same cluster(i.e,higher invasion risks).By integrating these models,we found that the south cluster exhibited minor genome-niche disruptions in the future,indicating higher invasion risks.Our study highlights the complementary roles of genomic offset and habitat suitability in assessing invasion risks under climate change.Moreover,incorporating adaptive genomic variation into predictive models can significantly enhance future invasion risk predictions and enable effective management strategies for biological invasions in the future.
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Hainan Natural Science Foundation(821RC699)Hainan Natural Science Foundation(822RC825)+1 种基金Hainan Provincial Health Industry Research Project(22A200242)Key R&D Plan of Hainan Province(ZDYF2020225)。
文摘Objective:To summarize the application value of copy number variant sequencing(CNV-seq)in the detection of fetal chromosome and cytomegalovirus load.Methods:The study analyzed the clinical basic data,relevant laboratory tests,treatment process,and outcomes of three patients with positive cytomegalovirus load detected by CNV-seq for fetal chromosomes and cytomegalovirus load,and literature review was done simutaneoubly.Results:In all three cases,the amniotic fluid cytomegalovirus load was less than 105 Copies/ml,and there were no significant neurological abnormalities observed during pregnancy or postpartum follow-up.There is no literature review on the application of CNV-seq technology in the detection of cytomegalovirus infection,only literature reports on genome analysis of CMV-DNA in confirmed patients were available.Conclusion:CNV-seq can be used to detect cytomegalovirus load,which may have a certain degree of predictive value for fetal outcome.CNV-seq can simultaneously detect fetal chromosomes and pathogenic microorganisms,which is of great significance for the prevention and control of birth defects.
基金supported by Major International Cooperation Projects of the National Natural Science Foundation of China(31210103918)the National Natural Science Foundation of China(31201980,31430088 and 31272651)+5 种基金the National High Technology Research and Development Program of China(2011AA100403)the Natural Science Foundation of Hunan Province,China(14JJ3072)Science-Technology Foundation of Hunan Province,China(2014FJ3084)Research Foundation of Education Bureau of Hunan Province,China(13C523)the Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province(20134486)the Construct Program of the Key Discipline in Hunan Province,and Construct Program of the National Key Discipline
文摘In this study, we conducted a cross of white crucian carp （♀）xred crucian carp （♂） （WR）, and characterized the morphology, reproduction and genetics of the progeny. Different from parents, WR with the gray color showed the hybrid morphological traits of both parents. WR possessed normal gonads producing mature eggs or sperm, and exhibited high fertilization rate （90.2%） and high hatchery rate （80.5%）, which contributed to produce and enlarge the population. WR with the same DNA content as parents was a diploid fish with 100 chromosomes （2n=100）. Amplified ITS of 45S rDNA, in WR the sequences consisting of 884 bp bases of the entire ITS-1 region, 5.8 S region, and entire ITS-2 region. The sequences showed high similarity between WR and its parents and leaned towards male inheritance. In WR, NTS of 5S rDNA consisted of three length types with total 654 bp bases. From sequence analysis of NTS, WR shared 94.2% and 95.1% similarities with their female and male parent, respectively. Sequence analysis of ITS and NTS revealed that there existed recombination and variation in the hybrid progeny, which was the genetic base for adaptation and speciation. In conclusion, we obtained WR from hybridization and it exhibited hybrid traits in morphology and variation in genetic composition showing essential difference with its parents. The obtainment of WR has important significance in fish genetic breeding.
基金supported by the National Key Research and Development Program of China(2020YFE0202300)Science and Technology Major Project of Guangxi(GuiKeAA20108005-2)+1 种基金Guangdong Innovation Research Team Fund(grant number:2014ZT05S078)National Key Research and Development Program of China(2019YFA0707000).No conflict of interest declared.
文摘Advances in DNA sequencing technology have sparked a genomics revolution,driving breakthroughs in plant genetics and crop breeding.Recently,the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement.This transformation has been facilitated by the increasing adoption of whole-genome resequencing.In this review,we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding.A total of 187 land plants from 163 countries have been resequenced,comprising 54413 accessions.As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted.Economically important crops,particularly cereals,vegetables,and legumes,have dominated the resequencing efforts,leaving a gap in 49 orders,including Lycopodiales,Liliales,Acorales,Austrobaileyales,and Commelinales.The resequenced germplasm is distributed across diverse geographic locations,providing a global perspective on plant genomics.We highlight genes that have been selected during domestication,or associated with agronomic traits,and form a repository of candidate genes for future research and application.Despite the opportunities for cross-species comparative genomics,many population genomic datasets are not accessible,impeding secondary analyses.We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy.The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs,coupled with advances in analysis and computational technologies.This expansion,in terms of both scale and quality,holds promise for deeper insights into plant trait genetics and breeding design.
基金The Z.L.laboratory is supported by a startup grant provided by Shanghai Jiao Tong University,School of Agriculture and Biology and the Shanghai Pujiang Program(20PJ1405900).
文摘Plants produce a remarkable diversity of structurally and functionally diverse natural chemicals that serve as adaptive compounds throughout their life cycles.However,unlocking this metabolic diversity is significantly impeded by the size,complexity,and abundant repetitive elements of typical plant genomes.As genome sequencing becomes routine,we anticipate that links between metabolic diversity and genetic variation will be strengthened.In addition,an ever-increasing number of plant genomes have revealed that biosynthetic gene clusters are not only a hallmark of microbes and fungi;gene clusters for various classes of compounds have also been found in plants,and many are associated with important agronomic traits.We present recent examples of plant metabolic diversification that have been discovered through the exploration and exploitation of various genomic and pan-genomic data.We also draw attention to the fundamental genomic and pan-genomic basis of plant chemodiversity and discuss challenges and future perspectives for investigating metabolic diversity in the coming pan-genomics era.
文摘As a typical representative of global complex diseases,psoriasis has attracted widespread attention because of its high heritability,heterogeneity,and incidence.Environmentally induced activation of the inflammatory-immune axis in patients with psoriasis relies on genetic regulation of genomic variation.The heritability of psoriasis exceeds 80%,and research of genomic variation in psoriasis is of great significance to the interpretation of the biological pathogenesis of the disease.The development of genome-wide association studies(GWASs)has provided a powerful means for the capture of psoriasis susceptibility genes.More than 100 psoriasis susceptibility loci have been captured,enabling humans to gain a breakthrough understanding of the genetics and traits of psoriasis.With the advancement of research methods,increasingly more genetic methodologies are being used to capture the locations and types of variants outside the scope of GWAS scanning,making up for the inclinations and deficiencies of traditional GWAS capture of gene loci in a more detailed manner.This review covers several decades of research on genomic variation in psoriasis,including GWASs in psoriasis,the capture of functional gene variant types,and the translation of genomic variation into precision medicine;summarizes the research progress of genomic variation in psoriasis;and provides a theoretical reference for future genetic-based research of the mechanisms underlying psoriasis.
基金This work was supported by grants from the Strategic PriorityResearch Program of Chinese Academy of Sciences(GrantNos.XDA19090116,XDA19050302,and XDB38030400)awarded to SS,ZZ,and MLthe National Key R&D Programof China(Grant Nos.2020YFC0848900,2020YFC0847000,2016YFE0206600,and 2017YFC0907502)+5 种基金the 13th Five-yearInformatization Plan of Chinese Academy of Sciences(GrantNo.XXH13505-05)Genomics Data Center Construction ofChinese Academy of Sciences(Grant No.XXH-13514-0202)the Open Biodiversity and Health Big Data Programme ofInternational Union of Biological Sciences,International Part-nership Program of Chinese Academy of Sciences(Grant No.153F11KYSB20160008)the Professional Association of theAlliance of International Science Organizations(Grant No.ANSO-PA-2020-07)This work was also supported by KCWong Education Foundation to ZZthe YouthInnovation Promotion Association of Chinese Academy ofSciences(Grant Nos.2017141 and 2019104)awarded to SSand ML.
文摘On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates,which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline.Of particular note,2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale.It provides all identified variants and their detailed statistics for each virus isolate,and congregates the quality score,functional annotation,and population frequency for each variant.Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available.Moreover,2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019(COVID-19),including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC.Furthermore,by linking with relevant databases in CNCB,2019nCoVR offers data submission services for raw sequence reads and assembled genomes,and data sharing with NCBI.Collectively,SARS-CoV-2 is updated daily to collect the latest information on genome sequences,variants,haplotypes,and literature for a timely reflection,making 2019nCoVR a valuable resource for the global research community.2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.
基金supported by the National Natural Science Foundation of China(91331105,31360514)
文摘Polyploidization via whole-genome duplications （WGD） is a common phenomenon in organisms. However, investigations into this phenomenon differ greatly between plants and animals. Recent research on polyploid plants illustrates the immediate changes that follow WGDs and the mechanisms behind in both genetic and epigenetic consequences. Unfortunately, equivalent questions remain to be explored in animals. Enlightened by botanical research, the study of polyploidization in vertebrates involves the identification of model animals and the establishment of strategies. Here we review and compare the research on plants and vertebrates while considering intrageneric or intraspecific variation in genome size. Suitable research methods on recently established poly- ploidy systems could provide important clues for under- standing what happens after WGDs in vertebrates. The approach yields insights into survival and the rarity of polyploidization in vertebrates. The species of Carassius and the allopolyploid system of goldfish × common carp hybridization appear to be suitable models for unraveling the evolution and adaptation of polyploid vertebrates.
