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
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
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
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
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
Genomics is a biology term appeared ten years ago, used todescribe the researches of genomic mapping, sequencing,and structure analysis, etc. Genomics, the first journal forpublishing papers on genomics research was b...Genomics is a biology term appeared ten years ago, used todescribe the researches of genomic mapping, sequencing,and structure analysis, etc. Genomics, the first journal forpublishing papers on genomics research was born in 1986.In the past decade, the concept of genomics has beenwidely accepted by scientists who are engaging in biologyresearch. Meanwhile, the research scope of genomics hasbeen extended continuously, from simple gene mappingand sequencing to function genomics study. To reflect thechange, genomics is divided into two parts now, thestructure genomics and the function genomics.Structure genomics retains the primary research con-tent of genomics, such as constructing high density genetic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
Soybean,the fourth most important crop in the world,uniquely serves as a source of both plant oil and plant protein for the world’s food and animal feed.Although soybean production has increased approximately 13-fold...Soybean,the fourth most important crop in the world,uniquely serves as a source of both plant oil and plant protein for the world’s food and animal feed.Although soybean production has increased approximately 13-fold over the past 60 years,the continually growing global population necessitates further increases in soybean production.In the past,especially in the last decade,significant progress has been made in both functional genomics and molecular breeding.However,many more challenges should be overcome to meet the anticipated future demand.Here,we summarize past achievements in the areas of soybean omics,functional genomics,and molecular breeding.Furthermore,we analyze trends in these areas,including shortages and challenges,and propose new directions,potential approaches,and possible outputs toward 2035.Our views and perspectives provide insight into accelerating the development of elite soybean varieties to meet the increasing demands of soybean production.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
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
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
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
Maize(Zea mays L.)is not only an important cereal crop,but also a model plant species for genetic,cytologic,genomic,and molecular studies.Maize possesses tremendous phenotypic and genetic diversity.During the past few...Maize(Zea mays L.)is not only an important cereal crop,but also a model plant species for genetic,cytologic,genomic,and molecular studies.Maize possesses tremendous phenotypic and genetic diversity.During the past few decades,researchers have made significant advances in multiple areas,including the genomic compositions and variations of maize and its ancestors,the genetic and genomic bases of maize domestication and evolution,the genetic architecture of various agronomic traits(yield,quality,biotic and abiotic stress responses,nutrient use efficiency,fertility and heterosis),and the development of novel molecular breeding technologies.In this review,we summarize these research achievements and provide a perspective for future maize research and breeding.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
The recent publication by Mollaoglu et al.1 in Cell reveals an unexpected role for tumor derived IL4 in driving immunotherapy resistance in ovarian cancer(OvCa).This finding nominates the combination of immunotherapy ...The recent publication by Mollaoglu et al.1 in Cell reveals an unexpected role for tumor derived IL4 in driving immunotherapy resistance in ovarian cancer(OvCa).This finding nominates the combination of immunotherapy and IL4-signaling targeting strategies as a promising new approach for the treatment of advanced OvCa.Ovarian Cancer(OvCa)is the third most common gynecological malignant disease affecting women.2 It is often diagnosed at late stages and is characterized by heterogenous features with limited treatment options.Initial response to standard of care platinumbased chemotherapy combined with surgery is often followed by disease relapse and subsequent death of patients.Despite the recent success of immune checkpoint inhibition in different cancer entities,most OvCa patients do not benefit from immunotherapy-based treatment approaches.The responsiveness of ovarian tumors to immune checkpoint blockade(ICB)is thereby hindered by weak immunogenicity due to low mutational burden and an immune suppressive tumor microenvironment(TME)characterized by heterogenous immune cell infiltration.3 Still,functional evidence for key factors that govern cancer cellimmune cell interaction and drive immunotherapy resistance in OvCa remains limited.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 （Oryza sativa） is a major staple food crop for more than 3.5 billion people worldwide. Under- standing the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is...Rice （Oryza sativa） is a major staple food crop for more than 3.5 billion people worldwide. Under- standing the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is also a model plant for genomics research of monocotyledonso Thanks to the rapid development of functional genomic technologies, over 2000 genes controlling important agronomic traits have been cloned, and their molecular biological mechanisms have also been partially char- acterized. Here, we briefly review the advances in rice functional genomics research during the past 10 years, including a summary of functional genomics platforms, genes and molecular regulatory networks that regulate important agronomic traits, and newly developed tools for gene identification. These achievements made in functional genomics research will greatly facilitate the development of green super rice. We also discuss future challenges and prospects of rice functional genomics research.展开更多
Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge.Here,we review the concept and practices of Gree...Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge.Here,we review the concept and practices of Green Super Rice(GSR)that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture.The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources,functional gene discoveries,and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving,environmentally friendly crop production systems.We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agricul-ture and better nourish the world population.展开更多
Rose has emerged as a model ornamental plant for studies of flower development, senescence, and morphology, as well as the metabolism of floral fragrances and colors.Virus-induced gene silencing(VIGS) has long been us...Rose has emerged as a model ornamental plant for studies of flower development, senescence, and morphology, as well as the metabolism of floral fragrances and colors.Virus-induced gene silencing(VIGS) has long been used in functional genomics studies of rose by vacuum infiltration of cuttings or seedlings with an Agrobacterium suspension carrying TRV-derived vectors. However, VIGS in rose flowers remains a challenge because of its low efficiency and long time to establish silencing. Here we present a novel and rapid VIGS method that can be used to analyze gene function in rose,called ‘graft-accelerated VIGS’, where axil ary sprouts are cut from the rose plant and vacuum infiltrated with Agrobacterium. The inoculated scions are then grafted back onto the plants to flower and silencing phenotypes can be observed within 5 weeks, post-infiltration. Using this new method, we successfully silenced expression of the RhDFR, RhA G, and RhNUDXin rose flowers, and affected their color, petal number, as well as fragrance, respectively. This grafting method will facilitate high-throughput functional analysis of genes in rose flowers. Importantly, it may also be applied to other woody species that are not currently amenable to VIGS by conventional leaf or plantlet/seedling infiltration methods.展开更多
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.
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.
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 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.
文摘Genomics is a biology term appeared ten years ago, used todescribe the researches of genomic mapping, sequencing,and structure analysis, etc. Genomics, the first journal forpublishing papers on genomics research was born in 1986.In the past decade, the concept of genomics has beenwidely accepted by scientists who are engaging in biologyresearch. Meanwhile, the research scope of genomics hasbeen extended continuously, from simple gene mappingand sequencing to function genomics study. To reflect thechange, genomics is divided into two parts now, thestructure genomics and the function genomics.Structure genomics retains the primary research con-tent of genomics, such as constructing high density genetic
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 the National Natural Science Foundation of China(grant nos.32388201 and 32372126)Fundamental Research Funds for the Central Universities(YDZX2024041).
文摘Soybean,the fourth most important crop in the world,uniquely serves as a source of both plant oil and plant protein for the world’s food and animal feed.Although soybean production has increased approximately 13-fold over the past 60 years,the continually growing global population necessitates further increases in soybean production.In the past,especially in the last decade,significant progress has been made in both functional genomics and molecular breeding.However,many more challenges should be overcome to meet the anticipated future demand.Here,we summarize past achievements in the areas of soybean omics,functional genomics,and molecular breeding.Furthermore,we analyze trends in these areas,including shortages and challenges,and propose new directions,potential approaches,and possible outputs toward 2035.Our views and perspectives provide insight into accelerating the development of elite soybean varieties to meet the increasing demands of soybean production.
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 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 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 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.
基金supported by the National Natural Science Foundation of China(32321005).
文摘Maize(Zea mays L.)is not only an important cereal crop,but also a model plant species for genetic,cytologic,genomic,and molecular studies.Maize possesses tremendous phenotypic and genetic diversity.During the past few decades,researchers have made significant advances in multiple areas,including the genomic compositions and variations of maize and its ancestors,the genetic and genomic bases of maize domestication and evolution,the genetic architecture of various agronomic traits(yield,quality,biotic and abiotic stress responses,nutrient use efficiency,fertility and heterosis),and the development of novel molecular breeding technologies.In this review,we summarize these research achievements and provide a perspective for future maize research and breeding.
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funded by the Deutsche Forschungsgemeinschaft(DFG,German Research Foundation,LE 3613/3-1).
文摘The recent publication by Mollaoglu et al.1 in Cell reveals an unexpected role for tumor derived IL4 in driving immunotherapy resistance in ovarian cancer(OvCa).This finding nominates the combination of immunotherapy and IL4-signaling targeting strategies as a promising new approach for the treatment of advanced OvCa.Ovarian Cancer(OvCa)is the third most common gynecological malignant disease affecting women.2 It is often diagnosed at late stages and is characterized by heterogenous features with limited treatment options.Initial response to standard of care platinumbased chemotherapy combined with surgery is often followed by disease relapse and subsequent death of patients.Despite the recent success of immune checkpoint inhibition in different cancer entities,most OvCa patients do not benefit from immunotherapy-based treatment approaches.The responsiveness of ovarian tumors to immune checkpoint blockade(ICB)is thereby hindered by weak immunogenicity due to low mutational burden and an immune suppressive tumor microenvironment(TME)characterized by heterogenous immune cell infiltration.3 Still,functional evidence for key factors that govern cancer cellimmune cell interaction and drive immunotherapy resistance in OvCa remains limited.
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.
文摘Rice （Oryza sativa） is a major staple food crop for more than 3.5 billion people worldwide. Under- standing the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is also a model plant for genomics research of monocotyledonso Thanks to the rapid development of functional genomic technologies, over 2000 genes controlling important agronomic traits have been cloned, and their molecular biological mechanisms have also been partially char- acterized. Here, we briefly review the advances in rice functional genomics research during the past 10 years, including a summary of functional genomics platforms, genes and molecular regulatory networks that regulate important agronomic traits, and newly developed tools for gene identification. These achievements made in functional genomics research will greatly facilitate the development of green super rice. We also discuss future challenges and prospects of rice functional genomics research.
基金the National High Technology Research and Development Program of China(2014AA10A604)the Bill&Melinda Gates Foundation(OPP1130530)+1 种基金the Earmarked Fund for the China Agricultural Research System of China(CARS-01-06)Hubei Special Major Projects for Technological Innovation(2019ABA104,2020ABA016).
文摘Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge.Here,we review the concept and practices of Green Super Rice(GSR)that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture.The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources,functional gene discoveries,and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving,environmentally friendly crop production systems.We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agricul-ture and better nourish the world population.
基金supported by the National Natural Science Foundation of China (31501791, 31660579, and 31360492)Leading talents in science and technology (2016HA005)funded in part by Beijing Natural Science Foundation (6162017)
文摘Rose has emerged as a model ornamental plant for studies of flower development, senescence, and morphology, as well as the metabolism of floral fragrances and colors.Virus-induced gene silencing(VIGS) has long been used in functional genomics studies of rose by vacuum infiltration of cuttings or seedlings with an Agrobacterium suspension carrying TRV-derived vectors. However, VIGS in rose flowers remains a challenge because of its low efficiency and long time to establish silencing. Here we present a novel and rapid VIGS method that can be used to analyze gene function in rose,called ‘graft-accelerated VIGS’, where axil ary sprouts are cut from the rose plant and vacuum infiltrated with Agrobacterium. The inoculated scions are then grafted back onto the plants to flower and silencing phenotypes can be observed within 5 weeks, post-infiltration. Using this new method, we successfully silenced expression of the RhDFR, RhA G, and RhNUDXin rose flowers, and affected their color, petal number, as well as fragrance, respectively. This grafting method will facilitate high-throughput functional analysis of genes in rose flowers. Importantly, it may also be applied to other woody species that are not currently amenable to VIGS by conventional leaf or plantlet/seedling infiltration methods.
