Emerging and powerful genome editing tools,particularly CRISPR/Cas9,are facilitating functional genomics research and accelerating crop improvement(Jiang et al.2021;Cao et al.2023;Chen C et al.2023;Liu et al.2023a).Ho...Emerging and powerful genome editing tools,particularly CRISPR/Cas9,are facilitating functional genomics research and accelerating crop improvement(Jiang et al.2021;Cao et al.2023;Chen C et al.2023;Liu et al.2023a).However,the detection and screening of transgenic lines remain major bottlenecks,being time-consuming,labor-intensive,and inefficient during transformation and subsequent mutation identification.A simple and efficient visual marker system plays a critical role in addressing these challenges.Recent studies demonstrated that the GmW1 and RUBY reporter systems were used to obtain visual transgenic soybean(Glycine max) plants(Chen L et al.2023;Chen et al.2024).展开更多
Due to the economic value of natural textile fiber, cotton has attracted much research attention, which has led to the publication of two diploid genomes and two tetraploid genomes. These big data facilitate functiona...Due to the economic value of natural textile fiber, cotton has attracted much research attention, which has led to the publication of two diploid genomes and two tetraploid genomes. These big data facilitate functional genomic study in cotton, and allow researchers to investigate cotton genome structure, gene expression, and protein function on the global scale using high-throughput methods. In this review, we summarized recent studies of cotton genomes. Population genomic analyses revealed the domestication history of cultivated upland cotton and the roles of transposable elements in cotton genome evolution.Alternative splicing of cotton transcriptomes was evaluated genome-widely. Several important gene families like MYC, NAC, Sus and GhPLDal were systematically identified and classified based on genetic structure and biological function. High-throughput proteomics also unraveled the key functional proteins correlated with fiber development. Functional genomic studies have provided unprecedented insights into global-scale methods for cotton research.展开更多
The translatome,a profile of the translational status of genetic information within cells,provides a new perspective on gene expression.Although many plant genomes have been sequenced,comprehensive translatomic annota...The translatome,a profile of the translational status of genetic information within cells,provides a new perspective on gene expression.Although many plant genomes have been sequenced,comprehensive translatomic annotations are not available for plants due to a lack of efficient translatome profiling techniques.Here,we developed a new technique termed 30 ribosome-profiling sequencing(30Ribo-seq)for reliable,robust translatomic profiling.30Ribo-seq combines polysome profiling and 30 selection with a barcoding and pooling strategy.Systematic translatome profiling of different tissues of Arabidopsis,rice,and maize using conventional ribosome profiling(Ribo-seq)and 30Ribo-seq revealed many novel translational genomic loci,thereby complementing functional genome annotation in plants.Using the low-cost,efficient 30Ribo-seq technique and genome-wide association mapping of translatome expression(eGWAS),we performed a population-level dissection of the translatomes of 159 diverse maize inbred lines and identified 1,777 translational expression quantitative trait loci(eQTLs).Notably,local eQTLs are significantly enriched in the 30 untranslated regions of genes.Detailed eQTL analysis suggested that sequence variation around the polyadenylation(polyA)signal motif plays a key role in translatomic variation.Our study provides a comprehensive translatome annotation of plant functional genomes and introduces 30Ribo-seq,which paves the way for deep translatomic analysis at the population level.展开更多
The study of gene function in filamentous fungi is a field of research that has made great advances in very recent years. A number of transformation and gene manipulation strategies have been developed and applied to ...The study of gene function in filamentous fungi is a field of research that has made great advances in very recent years. A number of transformation and gene manipulation strategies have been developed and applied to a diverse and rapidly expanding list of economically important filamentous fungi and oomycetes. With the significant number of fungal genomes now sequenced or being sequenced, functional genomics promises to uncover a great deal of new information in coming years. This review discusses recent advances that have been made in examining gene function in filamentous fungi and describes the advantages and limitations of the different approaches.展开更多
In plants,transposable element(TE)-triggered mutants are important resources for functional genomic studies.However,conventional approaches for genome-wide identification of TE insertion sites are costly and laborious...In plants,transposable element(TE)-triggered mutants are important resources for functional genomic studies.However,conventional approaches for genome-wide identification of TE insertion sites are costly and laborious.This study developed a novel,rapid,and high-throughput TE insertion site identification workflow based on next-generation sequencing and named it Transposable Element Amplicon Sequencing(TEAseq).Using TEAseq,we systemically profiled the Dissociation(Ds)insertion sites in 1606 independent Ds insertional mutants in advanced backcross generation using K17 as background.The Ac-containing individuals were excluded for getting rid of the potential somatic insertions.We characterized 35,696 germinal Ds insertions tagging 10,323 genes,representing approximately 23.3%of the total genes in the maize genome.The insertion sites were presented in chromosomal hotspots around the ancestral Ds loci,and insertions occurred preferentially in gene body regions.Furthermore,we mapped a loss-of-function AGL2 gene using bulked segregant RNA-sequencing assay and proved that AGL2 is essential for seed development.We additionally established an open-access database named MEILAM for easy access to Ds insertional mutations.Overall,our results have provided an efficient workflow for TE insertion identification and rich sequence-indexed mutant resources for maize functional genomic studies.展开更多
A rapidly growing number of successful genome sequencing projects in plant pathogenic fungi greatly increase the demands for tools and methodologies to study fungal pathogenicity at genomic scale. Magnaporthe oryzae i...A rapidly growing number of successful genome sequencing projects in plant pathogenic fungi greatly increase the demands for tools and methodologies to study fungal pathogenicity at genomic scale. Magnaporthe oryzae is an economically important plant pathogenic fungus whose genome is fully sequenced. Recently we have reported the development and application of functional genomics platform technologies in M. oryzae. This model approach would have many practical ramifications in design and implementation of upcoming functional genomics studies of filamentous fungi aimed at understanding fungal pathogenicity.展开更多
Trichoderma is a fungal genus of great and demonstrable biotechnological value, but its genome is poorly surveyed compared with other model microorganisms. Due to their ubiquity and rapid substrate colonization, Trich...Trichoderma is a fungal genus of great and demonstrable biotechnological value, but its genome is poorly surveyed compared with other model microorganisms. Due to their ubiquity and rapid substrate colonization, Trichoderma species have been widely used as biocontrol organisms for agriculture, and their enzyme systems are widely used in industry. Therefore, there is a clear interest to explore beyond the phenotype to exploit the underlying genetic systems using functional genomics tools. The great diversity of species within the Trichoderma genus, the absence of optimized systems for its exploration, and the great variety of genes expressed under a wide range of ambient conditions are the main challenges to consider when starting a comprehensive functional genomics study. An initial project started by three Spanish groups has been extended into the project TRICHOEST, funded by the EU (FP5, QLRT-2001-02032) to target the transcriptome analysis of selected Trichoderma strains with biocontrol potential, in conditions related to antagonism, nutrient stress and plant interactions. Once specific conditions were defined, cDNA libraries were produced and used for EST sequencing. Nine strains from seven Trichoderma species have been considered in this study and an important amount of gene sequence data has been generated, analyzed and used to compare the gene expression in different strains. In parallel to sequencing, genomic expression studies were carried out by means of macro-arrays to identify genes expressed in specific conditions. In silico analysis of DNA sequencing data together with macro-array expression results have lead to a selection based on the potential use of the gene sequences. The selected clone sequences were completed and cloned in appropriate vectors to initiate functional analysis by means of expression studies in homologous and heterologous systems.展开更多
The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization...The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats(SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identified, among which dinucleotide repeats were the most frequent class(44.08%), followed by mononucleotides(29.67%), trinucleotides(18.96%), tetranucleotides(5.66%), hexanucleotides(1.07%), and pentanucleotides(0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci(90.0%) were successfully amplified with specific products and 24(80.0%) were polymorphic. For the amplified polymorphic loci, the alleles ranged from 5 to 17(with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had significant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identified SSRs significantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution.展开更多
Genome editing is a valuable tool to target specific DNA sequences for mutagenesis in the genomes of microbes, plants, and animals. Although different genome editing technologies are available, the clustered regularly...Genome editing is a valuable tool to target specific DNA sequences for mutagenesis in the genomes of microbes, plants, and animals. Although different genome editing technologies are available, the clustered regularly interspaced short palindromic repeats/Cas9 （CRISPR/ Cas9） system, which utilizes engineered endonucleases to generate a double-stranded DNA break （DSB） in the target DNA region and subsequently stimulates site-specific mutagenesis through DNA repair machineries, is emerging as a powerful genome editing tool for elucidating mecha- nisms of protection from plant viruses, plant disease resistance, and gene functions in basic and applied research. In this review, we provide an overview of recent advances in the CRISPR system associated genome editing in plants by focusing on application of this technology in model plants, crop plants, fruit plants, woody plants and grasses and discuss how genome editing associated with the CRISPR system can provide insights into genome modifications and functional genomics in plants.展开更多
CRISPR-Cas9 has emerged as a powerful tool for gene editing,and it has been widely used in plant functional genomics research and crop genetic breeding(Chen et al.2019).The target specificity of CRISPR-Cas9 relies on ...CRISPR-Cas9 has emerged as a powerful tool for gene editing,and it has been widely used in plant functional genomics research and crop genetic breeding(Chen et al.2019).The target specificity of CRISPR-Cas9 relies on the 20-base-pair single guide RNA(sgRNA),which makes creating plant-specific mutant libraries through large-scale synthesis of sgRNAs targeting multiple genes or even the whole genome relatively quick and straightforward.展开更多
Dear Editor,Cucumber,Cucumis sativus,is a major vegetable crop globally.In addition to being consumed fresh or sliced,pickling cucumber represents a key cultivated type,widely grown in open fields across regions inclu...Dear Editor,Cucumber,Cucumis sativus,is a major vegetable crop globally.In addition to being consumed fresh or sliced,pickling cucumber represents a key cultivated type,widely grown in open fields across regions including the Americas,Europe,and Asia(Shetty and Wehner,2002).展开更多
Genome editing in plants is a powerful strategy that can substantially advance functional genomics research,facilitating the discovery,enhancement,and development of novel traits with significant agricultural implicat...Genome editing in plants is a powerful strategy that can substantially advance functional genomics research,facilitating the discovery,enhancement,and development of novel traits with significant agricultural implications.Various methodologies,such as zinc finger nucleases(ZFNs),transcription activator-like effector nucleases(TALENs),and CRISPR/Cas systems,have been developed for this purpose.展开更多
Medicago,a genus in the Leguminosae or Fabaceae family,includes the most globally significant forage crops,notably alfalfa(Medicago sativa).Its close diploid relative Medicago truncatula serves as an exemplary model p...Medicago,a genus in the Leguminosae or Fabaceae family,includes the most globally significant forage crops,notably alfalfa(Medicago sativa).Its close diploid relative Medicago truncatula serves as an exemplary model plant for investigating legume growth and development,as well as symbiosis with rhizobia.Over the past decade,advances in Medicago genomics have significantly deepened our understanding of the molecular regulatory mechanisms that underlie various traits.In this review,we comprehensively summarize research progress on Medicago genomics,growth and development(including compound leaf development,shoot branching,flowering time regulation,inflorescence development,floral organ development,and seed dormancy),resistance to abiotic and biotic stresses,and symbiotic nitrogen fixation with rhizobia,as well as molecular breeding.We propose avenues for molecular biology research on Medicago in the coming decade,highlighting those areas that have yet to be investigated or that remain ambiguous.展开更多
As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,w...As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,we developed the first comprehensive Oleaceae Genome Research Platform(OGRP,https://oleaceae.cgrpoee.top/).In OGRP,70 genomes of 10 Oleaceae species and 46 eudicots and 366 transcriptomes involving 18 Oleaceae plant tissues can be obtained.We built 34 window-operated bioinformatics tools,collected 38 professional practical software programs,and proposed 3 new pipelines,namely ancient polyploidization identification,ancestral karyotype reconstruction,and gene family evolution.Employing these pipelines to reanalyze the Oleaceae genomes,we clarified the polyploidization,reconstructed the ancestral karyotypes,and explored the effects of paleogenome evolution on genes with specific biological regulatory roles.Significantly,we generated a series of comparative genomic resources focusing on the Oleaceae,comprising 108 genomic synteny dot plots,1952225 collinear gene pairs,multiple genome alignments,and imprints of paleochromosome rearrangements.Moreover,in Oleaceae genomes,researchers can efficiently search for 1785987 functional annotations,22584 orthogroups,29582 important trait genes from 74 gene families,12664 transcription factor-related genes,9178872 transposable elements,and all involved regulatory pathways.In addition,we provided downloads and usage instructions for the tools,a species encyclopedia,ecological resources,relevant literatures,and external database links.In short,ORGP integrates rich data resources and powerful analytical tools with the characteristic of continuous updating,which can efficiently empower genome research and agricultural breeding in Oleaceae and other plants.展开更多
In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects....In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects.Since the initial implementation of HTS in citrus virology,a substantial number of citrus viruses have been identified,with a notable increase in the last 7 years.The acquisition of viral genomes and various HTS-based omics analyses serve as crucial pillars for advancing research in the etiology,epidemiology,pathology,evolution,ecology,and biotechnology of citrus viruses.HTS has notably contributed to disease diagnosis,such as the diagnoses of concave gum and impietratura,as well as to the surveillance of new virus risks and the preparation of virus-free materials.However,certain inherent defects in HTS and coupled bioinformatics analysis,such as challenges with sequence assembly and the detection of viral dark matter,require improvement to enhance practical efficiency.In addition,the utilization of HTS for the systematic management of citrus viral diseases remains limited,and drawing insights from other virus-plant pathosystems while integrating emerging compatible techniques and ideas may broaden its specific applications.展开更多
RNA interference （RNAi）, caused by endogenous or exogenous double- stranded RNA （dsRNA） homologous with target genes, refers to gene silencing widely existing in animals and plants. It was first found in plants, a...RNA interference （RNAi）, caused by endogenous or exogenous double- stranded RNA （dsRNA） homologous with target genes, refers to gene silencing widely existing in animals and plants. It was first found in plants, and now it has developed into a kind of biotechnology as well as an important approach in post- genome era. This paper is to summarize the achievements of studies on RNAi tech- nology in basic biology, medicine, pharmacy, botany and other fields.展开更多
Gliomas are the most common and malignant intracranial tumors in adults.Recent studies have revealed the significance of functional genomics for glioma pathophysiological studies and treatments.However,access to compr...Gliomas are the most common and malignant intracranial tumors in adults.Recent studies have revealed the significance of functional genomics for glioma pathophysiological studies and treatments.However,access to comprehensive genomic data and analytical platforms is often limited.Here,we developed the Chinese Glioma Genome Atlas(CGGA),a user-friendly data portal for the storage and interactive exploration of cross-omics data,including nearly 2000 primary and recurrent glioma samples from Chinese cohort.Currently,open access is provided to whole-exome sequencing data(286 samples),mRNA sequencing(1018 samples)and microarray data(301 samples),DNA methylation microarray data(159 samples),and microRNA microarray data(198 samples),and to detailed clinical information(age,gender,chemoradiotherapy status,WHO grade,histological type,critical molecular pathological information,and survival data).In addition,we have developed several tools for users to analyze the mutation profiles,mRNA/microRNA expression,and DNA methylation profiles,and to perform survival and gene correlation analyses of specific glioma subtypes.This database removes the barriers for researchers,providing rapid and convenient access to high-quality functional genomic data resources for biological studies and clinical applications.CGGA is available at http://www.cgga.org.cn.展开更多
Rice is one of the most important crops worldwide, both as a staple food and as a model system for genomic research. In order to systematically assign functions to all predicted genes in the rice genome, a large numbe...Rice is one of the most important crops worldwide, both as a staple food and as a model system for genomic research. In order to systematically assign functions to all predicted genes in the rice genome, a large number of rice mutant lines, including those created by T-DNA insertion, Ds/dSpm tagging, Tos17 tagging, and chemical/irradiation mutagenesis, have been generated by groups around the world. In this study, we have reviewed the current status of mutant resources for functional analysis of the rice genome. A total of 246 566 flanking sequence tags from rice mutant libraries with T-DNA, Ds/dSpm, or Tos17 insertion have been collected and analyzed. The results show that, among 211 470 unique hits, inserts located in the genic region account for 68.16%, and 60.49% of nuclear genes contain at least one insertion. Currently, 57% of non-transposable-element-related genes in rice have insertional tags. In addition, chemical/irradiation-induced rice mutant libraries have contributed a lot to both gene identification and new technology for the identification of mutant sites. In this review, we summarize how these tools have been used to generate a large collection of mutants. In addition, we discuss the merits of classic mutation strategies. In order to achieve saturation of mutagenesis in rice, DNA targeting, and new resources like RiceFox for gene functional identification are reviewed from a perspective of the future generation of rice mutant resources.展开更多
The characterization of agronomically important genes has great potential for the improvement of wheat.However,progress in wheat genetics and functional genomics has been impeded by the high complexity and enormous si...The characterization of agronomically important genes has great potential for the improvement of wheat.However,progress in wheat genetics and functional genomics has been impeded by the high complexity and enormous size of the wheat genome.Recent advances in genome sequencing and sequence assembly have produced a high-quality genome sequence for wheat.Here,we suggest that the strategies used to characterize biological mechanisms in model species,including mutant preparation and characterization,gene cloning methods,and improved transgenic technology,can be applied to wheat biology.These strategies will accelerate progress in wheat biology and promote wheat breeding program development.We also outline recent advances in wheat functional genomics.Finally,we discuss the future of wheat functional genomics and the rational design-based molecular breeding of new wheat varieties to contribute to world food security.展开更多
RNA interference （RNAi）, a process that inhibits gene expression by the double-stranded RNA （dsRNA）, causes the degradation of target messenger RNA molecules. RNAi exists in almost all organisms. We review the rec...RNA interference （RNAi）, a process that inhibits gene expression by the double-stranded RNA （dsRNA）, causes the degradation of target messenger RNA molecules. RNAi exists in almost all organisms. We review the recent history of RNAi studies, RNAi molecular mechanisms, characteristics and RNAi applications in higher plants. At the same time, the prospect of RNAi applications in functional genomics and genetic improvement of higher plants and possible future problems and possibilities are also discussed.展开更多
基金supported by the Jilin Science and Technology Development Program,China (20240602032RC)the Jilin Agricultural Science and Technology Innovation Project,China (CXGC2024ZD001)+1 种基金the Jilin Agricultural Science and Technology Innovation Project,China (CXGC2024ZY012)the Jilin Province Development and Reform Commission-Project for Improving the Independent Innovation Capacity of Major Grain Crops,China (2024C002)。
文摘Emerging and powerful genome editing tools,particularly CRISPR/Cas9,are facilitating functional genomics research and accelerating crop improvement(Jiang et al.2021;Cao et al.2023;Chen C et al.2023;Liu et al.2023a).However,the detection and screening of transgenic lines remain major bottlenecks,being time-consuming,labor-intensive,and inefficient during transformation and subsequent mutation identification.A simple and efficient visual marker system plays a critical role in addressing these challenges.Recent studies demonstrated that the GmW1 and RUBY reporter systems were used to obtain visual transgenic soybean(Glycine max) plants(Chen L et al.2023;Chen et al.2024).
基金supported by the Natural Science Foundation of China(Nos.21602162 and 31690090)the National Science and Technology Major Project(No.2016ZX08005003-001)the Fundamental Research Funds for the Central Universities(No.104862016)
文摘Due to the economic value of natural textile fiber, cotton has attracted much research attention, which has led to the publication of two diploid genomes and two tetraploid genomes. These big data facilitate functional genomic study in cotton, and allow researchers to investigate cotton genome structure, gene expression, and protein function on the global scale using high-throughput methods. In this review, we summarized recent studies of cotton genomes. Population genomic analyses revealed the domestication history of cultivated upland cotton and the roles of transposable elements in cotton genome evolution.Alternative splicing of cotton transcriptomes was evaluated genome-widely. Several important gene families like MYC, NAC, Sus and GhPLDal were systematically identified and classified based on genetic structure and biological function. High-throughput proteomics also unraveled the key functional proteins correlated with fiber development. Functional genomic studies have provided unprecedented insights into global-scale methods for cotton research.
基金supported by the National Natural Science Foundation of China(31771798,92035302,31922068)the National Key Research and Development Program of China(2016YFD0100800)+1 种基金the Hubei Provincial Natural Science Foundation of China(2019CFA014)the Competition Fund of the National Key Laboratory of Crop Genetic Improvement,and Huazhong Agricultural University Scientific&Technological Selfinnovation Foundation(2015RC016).
文摘The translatome,a profile of the translational status of genetic information within cells,provides a new perspective on gene expression.Although many plant genomes have been sequenced,comprehensive translatomic annotations are not available for plants due to a lack of efficient translatome profiling techniques.Here,we developed a new technique termed 30 ribosome-profiling sequencing(30Ribo-seq)for reliable,robust translatomic profiling.30Ribo-seq combines polysome profiling and 30 selection with a barcoding and pooling strategy.Systematic translatome profiling of different tissues of Arabidopsis,rice,and maize using conventional ribosome profiling(Ribo-seq)and 30Ribo-seq revealed many novel translational genomic loci,thereby complementing functional genome annotation in plants.Using the low-cost,efficient 30Ribo-seq technique and genome-wide association mapping of translatome expression(eGWAS),we performed a population-level dissection of the translatomes of 159 diverse maize inbred lines and identified 1,777 translational expression quantitative trait loci(eQTLs).Notably,local eQTLs are significantly enriched in the 30 untranslated regions of genes.Detailed eQTL analysis suggested that sequence variation around the polyadenylation(polyA)signal motif plays a key role in translatomic variation.Our study provides a comprehensive translatome annotation of plant functional genomes and introduces 30Ribo-seq,which paves the way for deep translatomic analysis at the population level.
文摘The study of gene function in filamentous fungi is a field of research that has made great advances in very recent years. A number of transformation and gene manipulation strategies have been developed and applied to a diverse and rapidly expanding list of economically important filamentous fungi and oomycetes. With the significant number of fungal genomes now sequenced or being sequenced, functional genomics promises to uncover a great deal of new information in coming years. This review discusses recent advances that have been made in examining gene function in filamentous fungi and describes the advantages and limitations of the different approaches.
基金the Ministry of Science and Technology of China(2016YFD0101000 and 2016YFD0101001)the Natural Science Foundation of China(31901595).
文摘In plants,transposable element(TE)-triggered mutants are important resources for functional genomic studies.However,conventional approaches for genome-wide identification of TE insertion sites are costly and laborious.This study developed a novel,rapid,and high-throughput TE insertion site identification workflow based on next-generation sequencing and named it Transposable Element Amplicon Sequencing(TEAseq).Using TEAseq,we systemically profiled the Dissociation(Ds)insertion sites in 1606 independent Ds insertional mutants in advanced backcross generation using K17 as background.The Ac-containing individuals were excluded for getting rid of the potential somatic insertions.We characterized 35,696 germinal Ds insertions tagging 10,323 genes,representing approximately 23.3%of the total genes in the maize genome.The insertion sites were presented in chromosomal hotspots around the ancestral Ds loci,and insertions occurred preferentially in gene body regions.Furthermore,we mapped a loss-of-function AGL2 gene using bulked segregant RNA-sequencing assay and proved that AGL2 is essential for seed development.We additionally established an open-access database named MEILAM for easy access to Ds insertional mutations.Overall,our results have provided an efficient workflow for TE insertion identification and rich sequence-indexed mutant resources for maize functional genomic studies.
基金a grant from Biogreen 21 Project (No. 20080401034044)the Rural Development Administration of Korea, the Crop Functional Genomics Center (No. CG1141) of the 21st Century Frontier Research Program funded by the Ministry of Science and Technology of Koreathe Korean Research Foundation Grant (No. KRF-2006-005-J04701)
文摘A rapidly growing number of successful genome sequencing projects in plant pathogenic fungi greatly increase the demands for tools and methodologies to study fungal pathogenicity at genomic scale. Magnaporthe oryzae is an economically important plant pathogenic fungus whose genome is fully sequenced. Recently we have reported the development and application of functional genomics platform technologies in M. oryzae. This model approach would have many practical ramifications in design and implementation of upcoming functional genomics studies of filamentous fungi aimed at understanding fungal pathogenicity.
文摘Trichoderma is a fungal genus of great and demonstrable biotechnological value, but its genome is poorly surveyed compared with other model microorganisms. Due to their ubiquity and rapid substrate colonization, Trichoderma species have been widely used as biocontrol organisms for agriculture, and their enzyme systems are widely used in industry. Therefore, there is a clear interest to explore beyond the phenotype to exploit the underlying genetic systems using functional genomics tools. The great diversity of species within the Trichoderma genus, the absence of optimized systems for its exploration, and the great variety of genes expressed under a wide range of ambient conditions are the main challenges to consider when starting a comprehensive functional genomics study. An initial project started by three Spanish groups has been extended into the project TRICHOEST, funded by the EU (FP5, QLRT-2001-02032) to target the transcriptome analysis of selected Trichoderma strains with biocontrol potential, in conditions related to antagonism, nutrient stress and plant interactions. Once specific conditions were defined, cDNA libraries were produced and used for EST sequencing. Nine strains from seven Trichoderma species have been considered in this study and an important amount of gene sequence data has been generated, analyzed and used to compare the gene expression in different strains. In parallel to sequencing, genomic expression studies were carried out by means of macro-arrays to identify genes expressed in specific conditions. In silico analysis of DNA sequencing data together with macro-array expression results have lead to a selection based on the potential use of the gene sequences. The selected clone sequences were completed and cloned in appropriate vectors to initiate functional analysis by means of expression studies in homologous and heterologous systems.
基金Supported by the National High Technology Research and Development Program of China(863 Program)(No.2012AA10A409)
文摘The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats(SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identified, among which dinucleotide repeats were the most frequent class(44.08%), followed by mononucleotides(29.67%), trinucleotides(18.96%), tetranucleotides(5.66%), hexanucleotides(1.07%), and pentanucleotides(0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci(90.0%) were successfully amplified with specific products and 24(80.0%) were polymorphic. For the amplified polymorphic loci, the alleles ranged from 5 to 17(with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had significant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identified SSRs significantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution.
文摘Genome editing is a valuable tool to target specific DNA sequences for mutagenesis in the genomes of microbes, plants, and animals. Although different genome editing technologies are available, the clustered regularly interspaced short palindromic repeats/Cas9 （CRISPR/ Cas9） system, which utilizes engineered endonucleases to generate a double-stranded DNA break （DSB） in the target DNA region and subsequently stimulates site-specific mutagenesis through DNA repair machineries, is emerging as a powerful genome editing tool for elucidating mecha- nisms of protection from plant viruses, plant disease resistance, and gene functions in basic and applied research. In this review, we provide an overview of recent advances in the CRISPR system associated genome editing in plants by focusing on application of this technology in model plants, crop plants, fruit plants, woody plants and grasses and discuss how genome editing associated with the CRISPR system can provide insights into genome modifications and functional genomics in plants.
基金supported by the National Natural Science Foundation of China(32272670 and 31972986)the Key Research and Development Program of Shaanxi Province,China(2023-YBNY-059)。
文摘CRISPR-Cas9 has emerged as a powerful tool for gene editing,and it has been widely used in plant functional genomics research and crop genetic breeding(Chen et al.2019).The target specificity of CRISPR-Cas9 relies on the 20-base-pair single guide RNA(sgRNA),which makes creating plant-specific mutant libraries through large-scale synthesis of sgRNAs targeting multiple genes or even the whole genome relatively quick and straightforward.
基金supported by the Provincial Technology Innovation Program of Shandong,Ningbo Science and Technology Innovation Project 2021Z132Weifang Seed Innovation Group.
文摘Dear Editor,Cucumber,Cucumis sativus,is a major vegetable crop globally.In addition to being consumed fresh or sliced,pickling cucumber represents a key cultivated type,widely grown in open fields across regions including the Americas,Europe,and Asia(Shetty and Wehner,2002).
基金supported by the Agricultural Gongguan Project of Xinjiang Production and Construction Corps,China(NYHXGG,2023AA102)the Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-CSIAF-202402)+1 种基金the Outstanding Youth Foundation of Henan Scientific Committee,China(222300420097)the China Agriculture Research System of MOF and MARA(CARS-15-02).
文摘Genome editing in plants is a powerful strategy that can substantially advance functional genomics research,facilitating the discovery,enhancement,and development of novel traits with significant agricultural implications.Various methodologies,such as zinc finger nucleases(ZFNs),transcription activator-like effector nucleases(TALENs),and CRISPR/Cas systems,have been developed for this purpose.
基金supported by the National Key Research and Development Program of China(2023YFF1001400 to T.W.)the Young Elite Scientists Sponsorship Program by CAST(2023QNRC001 to Q.Y.)+1 种基金the National Natural Science Foundation of China(32370253 to J.D.,32325035 to H.L.)the US Department of Agriculture(USDA)US National Institute of Food and Agriculture(NIFA)grant(2022-38821-37353 to S.R.),and a US National Science Foundation Award(2217830 to S.R.).
文摘Medicago,a genus in the Leguminosae or Fabaceae family,includes the most globally significant forage crops,notably alfalfa(Medicago sativa).Its close diploid relative Medicago truncatula serves as an exemplary model plant for investigating legume growth and development,as well as symbiosis with rhizobia.Over the past decade,advances in Medicago genomics have significantly deepened our understanding of the molecular regulatory mechanisms that underlie various traits.In this review,we comprehensively summarize research progress on Medicago genomics,growth and development(including compound leaf development,shoot branching,flowering time regulation,inflorescence development,floral organ development,and seed dormancy),resistance to abiotic and biotic stresses,and symbiotic nitrogen fixation with rhizobia,as well as molecular breeding.We propose avenues for molecular biology research on Medicago in the coming decade,highlighting those areas that have yet to be investigated or that remain ambiguous.
基金supported by the National Natural Science Foundation of China(32470676 and 32170236)Central Guidance on Local Science and Technology Development Fund of Hebei Province(246Z2508G)+2 种基金Hebei Natural Science Foundation(C2020209064)Tangshan Science and Technology Program Project(21130217C)Key research project of North China University of Science and Technology(ZD-YG-202313-23).
文摘As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,we developed the first comprehensive Oleaceae Genome Research Platform(OGRP,https://oleaceae.cgrpoee.top/).In OGRP,70 genomes of 10 Oleaceae species and 46 eudicots and 366 transcriptomes involving 18 Oleaceae plant tissues can be obtained.We built 34 window-operated bioinformatics tools,collected 38 professional practical software programs,and proposed 3 new pipelines,namely ancient polyploidization identification,ancestral karyotype reconstruction,and gene family evolution.Employing these pipelines to reanalyze the Oleaceae genomes,we clarified the polyploidization,reconstructed the ancestral karyotypes,and explored the effects of paleogenome evolution on genes with specific biological regulatory roles.Significantly,we generated a series of comparative genomic resources focusing on the Oleaceae,comprising 108 genomic synteny dot plots,1952225 collinear gene pairs,multiple genome alignments,and imprints of paleochromosome rearrangements.Moreover,in Oleaceae genomes,researchers can efficiently search for 1785987 functional annotations,22584 orthogroups,29582 important trait genes from 74 gene families,12664 transcription factor-related genes,9178872 transposable elements,and all involved regulatory pathways.In addition,we provided downloads and usage instructions for the tools,a species encyclopedia,ecological resources,relevant literatures,and external database links.In short,ORGP integrates rich data resources and powerful analytical tools with the characteristic of continuous updating,which can efficiently empower genome research and agricultural breeding in Oleaceae and other plants.
基金supported by National Natural Science Foundation of China(Grant Nos.32370005,32072389)Chongqing Science Funds for Distinguished Young Scientists(Grant No.CSTB2022NSCQ-JQX0027)+3 种基金Innovation Research 2035 Pilot Plan of Southwest University(Grant Nos.SWU-XDPY22002,SWUXDZD22002)Special Fund for Youth Team of Southwest University(Grant No.SWU-XJLJ202310)Chongqing Talents of Exceptional Young Talents Project(Grant No.cstc2022ycjh-bgzxm0143)Chongqing Municipal Training Program of Innovation and Entrepreneurship for Undergraduates(Grant No.S202310635160)。
文摘In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects.Since the initial implementation of HTS in citrus virology,a substantial number of citrus viruses have been identified,with a notable increase in the last 7 years.The acquisition of viral genomes and various HTS-based omics analyses serve as crucial pillars for advancing research in the etiology,epidemiology,pathology,evolution,ecology,and biotechnology of citrus viruses.HTS has notably contributed to disease diagnosis,such as the diagnoses of concave gum and impietratura,as well as to the surveillance of new virus risks and the preparation of virus-free materials.However,certain inherent defects in HTS and coupled bioinformatics analysis,such as challenges with sequence assembly and the detection of viral dark matter,require improvement to enhance practical efficiency.In addition,the utilization of HTS for the systematic management of citrus viral diseases remains limited,and drawing insights from other virus-plant pathosystems while integrating emerging compatible techniques and ideas may broaden its specific applications.
文摘RNA interference （RNAi）, caused by endogenous or exogenous double- stranded RNA （dsRNA） homologous with target genes, refers to gene silencing widely existing in animals and plants. It was first found in plants, and now it has developed into a kind of biotechnology as well as an important approach in post- genome era. This paper is to summarize the achievements of studies on RNAi tech- nology in basic biology, medicine, pharmacy, botany and other fields.
基金supported by the National Natural Science Foundation of China(Grant Nos.81702460 and 81802994)
文摘Gliomas are the most common and malignant intracranial tumors in adults.Recent studies have revealed the significance of functional genomics for glioma pathophysiological studies and treatments.However,access to comprehensive genomic data and analytical platforms is often limited.Here,we developed the Chinese Glioma Genome Atlas(CGGA),a user-friendly data portal for the storage and interactive exploration of cross-omics data,including nearly 2000 primary and recurrent glioma samples from Chinese cohort.Currently,open access is provided to whole-exome sequencing data(286 samples),mRNA sequencing(1018 samples)and microarray data(301 samples),DNA methylation microarray data(159 samples),and microRNA microarray data(198 samples),and to detailed clinical information(age,gender,chemoradiotherapy status,WHO grade,histological type,critical molecular pathological information,and survival data).In addition,we have developed several tools for users to analyze the mutation profiles,mRNA/microRNA expression,and DNA methylation profiles,and to perform survival and gene correlation analyses of specific glioma subtypes.This database removes the barriers for researchers,providing rapid and convenient access to high-quality functional genomic data resources for biological studies and clinical applications.CGGA is available at http://www.cgga.org.cn.
基金This work was supported （2012AA10A304） the Nationa by the 863 Project Grant Natural Science Foundation of China （31171441） and the Program for New Century Excellent Talents in University.We thank Ying Yang, Xingwang Li, Yuxiao Chang, Jian Zhang, Dong Guo, Xiaoxia Dai, and Changjun You for their contributions of flanking sequence in the Rice Mutant Database. No conflict of interest declared.
文摘Rice is one of the most important crops worldwide, both as a staple food and as a model system for genomic research. In order to systematically assign functions to all predicted genes in the rice genome, a large number of rice mutant lines, including those created by T-DNA insertion, Ds/dSpm tagging, Tos17 tagging, and chemical/irradiation mutagenesis, have been generated by groups around the world. In this study, we have reviewed the current status of mutant resources for functional analysis of the rice genome. A total of 246 566 flanking sequence tags from rice mutant libraries with T-DNA, Ds/dSpm, or Tos17 insertion have been collected and analyzed. The results show that, among 211 470 unique hits, inserts located in the genic region account for 68.16%, and 60.49% of nuclear genes contain at least one insertion. Currently, 57% of non-transposable-element-related genes in rice have insertional tags. In addition, chemical/irradiation-induced rice mutant libraries have contributed a lot to both gene identification and new technology for the identification of mutant sites. In this review, we summarize how these tools have been used to generate a large collection of mutants. In addition, we discuss the merits of classic mutation strategies. In order to achieve saturation of mutagenesis in rice, DNA targeting, and new resources like RiceFox for gene functional identification are reviewed from a perspective of the future generation of rice mutant resources.
基金financially supported by the National Key Research and Development Program of China(2017YFD0101001)the Beijing Municipal Government Science Foundation,China(IDHT20170513)the Starting Grant from Hebei Agricultural University,China(YJ201958)。
文摘The characterization of agronomically important genes has great potential for the improvement of wheat.However,progress in wheat genetics and functional genomics has been impeded by the high complexity and enormous size of the wheat genome.Recent advances in genome sequencing and sequence assembly have produced a high-quality genome sequence for wheat.Here,we suggest that the strategies used to characterize biological mechanisms in model species,including mutant preparation and characterization,gene cloning methods,and improved transgenic technology,can be applied to wheat biology.These strategies will accelerate progress in wheat biology and promote wheat breeding program development.We also outline recent advances in wheat functional genomics.Finally,we discuss the future of wheat functional genomics and the rational design-based molecular breeding of new wheat varieties to contribute to world food security.
基金supported by the Natural Science Foundation of Guangdong Province, China (Grant No. 7118123).
文摘RNA interference （RNAi）, a process that inhibits gene expression by the double-stranded RNA （dsRNA）, causes the degradation of target messenger RNA molecules. RNAi exists in almost all organisms. We review the recent history of RNAi studies, RNAi molecular mechanisms, characteristics and RNAi applications in higher plants. At the same time, the prospect of RNAi applications in functional genomics and genetic improvement of higher plants and possible future problems and possibilities are also discussed.
