Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors(TFs)in intricate regulatory networks in a cell-type specific manner.Here we...Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors(TFs)in intricate regulatory networks in a cell-type specific manner.Here we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis seedlings.This atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets,addressing batch effects and conserving biological variance.This integration spans a broad spectrum of tissues,including both below-and above-ground parts.Utilizing a rigorous approach for cell type annotation,we identified 47 distinct cell types or states,largely expanding our current view of plant cell compositions.We systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene expression.Taken together,our study not only offers extensive plant cell atlas exploration that serves as a valuable resource,but also provides molecular insights into gene-regulatory programs that varies from different cell types.展开更多
Cornus wilsoniana W.is a woody oil plant with high oil content and strong hypolipidemic effects,making it a valuable species for medicinal,landscaping,and ecological purposes in China.To advance genetic research on th...Cornus wilsoniana W.is a woody oil plant with high oil content and strong hypolipidemic effects,making it a valuable species for medicinal,landscaping,and ecological purposes in China.To advance genetic research on this species,we employed PacBio together with Hi-C data to create a draft genome assembly for C.wilsoniana.Based on an 11-chromosome anchored chromosome-level assembly,the estimated genome size was determined to be 843.51 Mb.The N50 contig size and N50 scaffold size were calculated to be 4.49 and 78.00 Mb,respectively.Furthermore,30474 protein-coding genes were annotated.Comparative genomics analysis revealed that C.wilsoniana diverged from its closest species∼12.46 million years ago(Mya).Furthermore,the divergence between Cornaceae and Nyssaceae occurred>62.22 Mya.We also found evidence of whole-genome duplication events and whole-genome triplicationγ,occurring at∼44.90 and 115.86 Mya.We further inferred the origins of chromosomes,which sheds light on the complex evolutionary history of the karyotype of C.wilsoniana.Through transcriptional and metabolic analysis,we identified two FAD2 homologous genes that may play a crucial role in controlling the oleic to linoleic acid ratio.We further investigated the correlation between metabolites and genes and identified 33 MADS-TF homologous genes that may affect f lower morphology in C.wilsoniana.Overall,this study lays the groundwork for future research aimed at identifying the genetic basis of crucial traits in C.wilsoniana.展开更多
The plant genome produces an extremely large collection of long noncoding RNAs(lncRNAs)that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological processes.Her...The plant genome produces an extremely large collection of long noncoding RNAs(lncRNAs)that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological processes.Here,we mapped the transcriptional heterogeneity of lncRNAs and their associated gene reg-ulatory networks at single-cell resolution.We generated a comprehensive cell atlas at the whole-organism level by integrative analysis of 28 published single-cell RNA sequencing(scRNA-seq)datasets from juvenile Arabidopsis seedlings.We then provided an in-depth analysis of cell-type-related lncRNA signatures that show expression patterns consistent with canonical protein-coding gene markers.We further demon-strated that the cell-type-specific expression of lncRNAs largely explains their tissue specificity.In addi-tion,we predicted gene regulatory networks on the basis of motif enrichment and co-expression analysis of lncRNAs and mRNAs,and we identified putative transcription factors orchestrating cell-type-specific expression of lncRNAs.The analysis results are available at the single-cell-based plant lncRNA atlas data-base(scPLAD;https://biobigdata.nju.edu.cn/scPLAD/).Overall,this work demonstrates the power of inte-grative single-cell data analysis applied to plant lncRNA biology and provides fundamental insights into lncRNA expression specificity and associated gene regulation.展开更多
Spike architecture influences both grain weight and grain number per spike,which are the two major components of grain yield in bread wheat(Triticum aestivum L.).However,the complex wheat genome and the influence of var...Spike architecture influences both grain weight and grain number per spike,which are the two major components of grain yield in bread wheat(Triticum aestivum L.).However,the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits.Here,we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat.We identified 170 loci that are responsible for variations in spike length,spikelet number per spike,and grain number per spike through genome-wide association study and meta-QTL analyses.We constructed gene regulatory networks for young inflorescences at the double ridge stage and thefloret primordium stage,in which the spikelet meristem and thefloret meristem are predominant,respec-tively,by integrating transcriptome,histone modification,chromatin accessibility,eQTL,and protein–pro-tein interactome data.From these networks,we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits.The functions of TaZF-B1,VRT-B2,and TaSPL15-A/D in establishment of wheat spike architecture were verified.This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.展开更多
Single-cell transcriptomics has been fully embraced in plant biological research and is revolutionizing our understanding of plant growth,development,and responses to external stimuli.However,single-cell tran-scriptom...Single-cell transcriptomics has been fully embraced in plant biological research and is revolutionizing our understanding of plant growth,development,and responses to external stimuli.However,single-cell tran-scriptomic data analysis in plants is not trivial,given that there is currently no end-to-end solution and that integration of various bioinformatics tools involves a large number of required dependencies.Here,we pre-sent scPlant,a versatile framework for exploring plant single-cell atlases with minimuminput data provided by users.The scPlant pipeline is implemented with numerous functions for diverse analytical tasks,ranging from basic data processing to advanced demands such as cell-type annotation and deconvolution,trajec-tory inference,cross-species data integration,and cell-type-specific gene regulatory network construc-tion.In addition,a variety of visualization tools are bundled in a built-in Shiny application,enabling explo-ration of single-cell transcriptomic data on the fly.展开更多
A continuous-wave(CW)single-longitudinal-mode(SLM)Raman laser at 1240 nm with power of up to 20.6 W was demonstrated in a free-running diamond Raman oscillator without any axial-mode selection elements.The SLM operati...A continuous-wave(CW)single-longitudinal-mode(SLM)Raman laser at 1240 nm with power of up to 20.6 W was demonstrated in a free-running diamond Raman oscillator without any axial-mode selection elements.The SLM operation was achieved due to the spatial-hole-burning free nature of Raman gain and was maintained at the highest available pump power by suppressing the parasitic stimulated Brillouin scattering(SBS).A folded-cavity design was employed for reducing the perturbing effect of resonances at the pump frequency.At a pump power of 69 W,the maximum Stokes output reached 20.6 W,corresponding to a 30%optical-to-optical conversion efficiency from 1064to 1240 nm.The result shows that parasitic SBS is the main physical process disturbing the SLM operation of Raman oscillator at higher power.In addition,for the first time,the spectral linewidth of a CW SLM diamond Raman laser was resolved using the long-delayed self-heterodyne interferometric method,which is 105 kHz at 20 W.展开更多
Colorectal cancer(CRC), a malignant tumor worldwide consists of microsatellite instability(MSI) and stable(MSS) phenotypes. Although SHP2 is a hopeful target for cancer therapy, its relationship with innate immunosupp...Colorectal cancer(CRC), a malignant tumor worldwide consists of microsatellite instability(MSI) and stable(MSS) phenotypes. Although SHP2 is a hopeful target for cancer therapy, its relationship with innate immunosuppression remains elusive. To address that, single-cell RNA sequencing wasperformed to explore the role of SHP2 in all cell types of tumor microenvironment(TME) from murine MC38 xenografts. Intratumoral cells were found to be functionally heterogeneous and responded significantly to SHP099, a SHP2 allosteric inhibitor. The malignant evolution of tumor cells was remarkably arrested by SHP099. Mechanistically, STING-TBK1-IRF3-mediated type I interferon signaling was highly activated by SHP099 in infiltrated myeloid cells. Notably, CRC patients with MSS phenotype exhibited greater macrophage infiltration and more potent SHP2 phosphorylation in CD68;macrophages than MSI-high phenotypes, suggesting the potential role of macrophagic SHP2 in TME. Collectively,our data reveals a mechanism of innate immunosuppression mediated by SHP2, suggesting that SHP2 is a promising target for colon cancer immunotherapy.展开更多
Nucleotide-binding leucine-rich-repeat(NLR)genes comprise the largest family of plant disease-resis-tance genes.Angiosperm NLR genes are phylogenetically divided into the TNL,CNL,and RNL subclasses.NLR copy numbers an...Nucleotide-binding leucine-rich-repeat(NLR)genes comprise the largest family of plant disease-resis-tance genes.Angiosperm NLR genes are phylogenetically divided into the TNL,CNL,and RNL subclasses.NLR copy numbers and subclass composition vary tremendously across angiosperm genomes.However,the evolutionary associations between genomic NLR content and ecological adaptation,or between NLR content and signal transduction components,are poorly characterized because of limited genome avail-ability.In this study,we established an angiosperm NLR atlas(ANNA,https://biobigdata.nju.edu.cn/ANNA/)that includes NLR genes from over 300 angiosperm genomes.Using ANNA,we revealed that NLR copy numbers differ up to 66-fold among closely related species owing to rapid gene loss and gain.Interestingly,NLR contraction was associated with adaptations to aquatic,parasitic,and carnivorous life-styles.The convergent NLR reduction in aquatic plants resembles the lack of NLR expansion during the long-term evolution of green algae before the colonization of land.A co-evolutionary pattern between NLR subclasses and plant immune pathway components was also identified,suggesting that immune pathway deficiencies may drive TNL loss.Finally,we identified a conserved TNL lineage that may function independently of the EDS1-SAG101-NRG1 module.Collectively,these findings provide new insights into the evolution of NLR genes in the context of ecological adaptation and genome content variation.展开更多
Dear Editor,The recent outbreak of novel coronavirus disease 2019(COVID-19)has already become a global-scale epidemic.Since the case from China was reported on Dec 30th,2019(Huang et al.,2020;Li et al.,2020),the patho...Dear Editor,The recent outbreak of novel coronavirus disease 2019(COVID-19)has already become a global-scale epidemic.Since the case from China was reported on Dec 30th,2019(Huang et al.,2020;Li et al.,2020),the pathogen was soon identified as a new coronavirus on Jan 7th.展开更多
Plant genomes contain a large fraction of noncoding sequences.The discovery and annotation of conserved noncoding sequences(CNSs)in plants is an ongoing challenge.Here we report the application of comparative genomics...Plant genomes contain a large fraction of noncoding sequences.The discovery and annotation of conserved noncoding sequences(CNSs)in plants is an ongoing challenge.Here we report the application of comparative genomics to systematically identify CNSs in 50 well-annotated Gramineae genomes using rice(Oryza sativa)as the reference.We conduct multiple-way whole-genome alignments to the rice genome.The rice genome is annotated as 20 conservation states(CSs)at single-nucleotide resolution using a multivariate hidden Markov model(Cons HMM)based on the multiple-genome alignments.Different states show distinct enrichments for various genomic features,and the conservation scores of CSs are highly correlated with the level of associated chromatin accessibility.We find that at least 33.5%of the rice genome is highly under selection,with more than 70%of the sequence lying outside of coding regions.A catalog of 855,366 regulatory CNSs is generated,and they significantly overlapped with putative active regulatory elements such as promoters,enhancers,and transcription factor binding sites.Collectively,our study provides a resource for elucidating functional noncoding regions of the rice genome and an evolutionary aspect of regulatory sequences in higher plants.展开更多
基金supported by the National Natural Science Foundation of China (No.32070656)the Nanjing University Deng Feng Scholars Program+1 种基金the Priority Academic Program Development (PAPD) of Jiangsu Higher Education Institutions,China Postdoctoral Science Foundation funded project (No.2022M711563)Jiangsu Funding Program for Excellent Postdoctoral Talent (No.2022ZB50)
文摘Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors(TFs)in intricate regulatory networks in a cell-type specific manner.Here we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis seedlings.This atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets,addressing batch effects and conserving biological variance.This integration spans a broad spectrum of tissues,including both below-and above-ground parts.Utilizing a rigorous approach for cell type annotation,we identified 47 distinct cell types or states,largely expanding our current view of plant cell compositions.We systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene expression.Taken together,our study not only offers extensive plant cell atlas exploration that serves as a valuable resource,but also provides molecular insights into gene-regulatory programs that varies from different cell types.
基金supported by the National Natural Science Foundation of China(31770767,32070656,32070677 and 32270709)Foundation of State Key Laboratory of Utilization of Woody Oil Resource(GZKF202201)+1 种基金Hunan Province Key Research and Development Program Project(2018NK2044)Jiangsu Collaborative Innovation Center for Modern Crop Production and Collaborative Innovation Center for Modern Crop Production cosponsored by province and ministry.
文摘Cornus wilsoniana W.is a woody oil plant with high oil content and strong hypolipidemic effects,making it a valuable species for medicinal,landscaping,and ecological purposes in China.To advance genetic research on this species,we employed PacBio together with Hi-C data to create a draft genome assembly for C.wilsoniana.Based on an 11-chromosome anchored chromosome-level assembly,the estimated genome size was determined to be 843.51 Mb.The N50 contig size and N50 scaffold size were calculated to be 4.49 and 78.00 Mb,respectively.Furthermore,30474 protein-coding genes were annotated.Comparative genomics analysis revealed that C.wilsoniana diverged from its closest species∼12.46 million years ago(Mya).Furthermore,the divergence between Cornaceae and Nyssaceae occurred>62.22 Mya.We also found evidence of whole-genome duplication events and whole-genome triplicationγ,occurring at∼44.90 and 115.86 Mya.We further inferred the origins of chromosomes,which sheds light on the complex evolutionary history of the karyotype of C.wilsoniana.Through transcriptional and metabolic analysis,we identified two FAD2 homologous genes that may play a crucial role in controlling the oleic to linoleic acid ratio.We further investigated the correlation between metabolites and genes and identified 33 MADS-TF homologous genes that may affect f lower morphology in C.wilsoniana.Overall,this study lays the groundwork for future research aimed at identifying the genetic basis of crucial traits in C.wilsoniana.
基金supported by grants from the National Natural Science Foundation of China (grants 32070656,32270709,32070677,and 32000362)the Natural Science Foundation of Jiangsu Higher Education Institutions of China (grant 23KJA210002)+1 种基金the open funds of the Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding (grant PL202105),the Priority Academic Program Development of Jiangsu Higher Education Institutions of Jiangsu Higher Education Institutions (PAPD)the 2023 Postgraduate Research&Practice Innovation Program of Jiangsu Province (grant KYCX23_0131).
文摘The plant genome produces an extremely large collection of long noncoding RNAs(lncRNAs)that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological processes.Here,we mapped the transcriptional heterogeneity of lncRNAs and their associated gene reg-ulatory networks at single-cell resolution.We generated a comprehensive cell atlas at the whole-organism level by integrative analysis of 28 published single-cell RNA sequencing(scRNA-seq)datasets from juvenile Arabidopsis seedlings.We then provided an in-depth analysis of cell-type-related lncRNA signatures that show expression patterns consistent with canonical protein-coding gene markers.We further demon-strated that the cell-type-specific expression of lncRNAs largely explains their tissue specificity.In addi-tion,we predicted gene regulatory networks on the basis of motif enrichment and co-expression analysis of lncRNAs and mRNAs,and we identified putative transcription factors orchestrating cell-type-specific expression of lncRNAs.The analysis results are available at the single-cell-based plant lncRNA atlas data-base(scPLAD;https://biobigdata.nju.edu.cn/scPLAD/).Overall,this work demonstrates the power of inte-grative single-cell data analysis applied to plant lncRNA biology and provides fundamental insights into lncRNA expression specificity and associated gene regulation.
基金supported by STI2030-Major Projects (2023ZD0406802)the Fundamental Research Funds for the Central Universities (2662020ZKPY002)+1 种基金the National Key Laboratory of Crop Genetic Improvement Self-Research Program (ZW19A0201)the HZAUAGIS Cooperation Fund 869 (SZYJY2021006).
文摘Spike architecture influences both grain weight and grain number per spike,which are the two major components of grain yield in bread wheat(Triticum aestivum L.).However,the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits.Here,we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat.We identified 170 loci that are responsible for variations in spike length,spikelet number per spike,and grain number per spike through genome-wide association study and meta-QTL analyses.We constructed gene regulatory networks for young inflorescences at the double ridge stage and thefloret primordium stage,in which the spikelet meristem and thefloret meristem are predominant,respec-tively,by integrating transcriptome,histone modification,chromatin accessibility,eQTL,and protein–pro-tein interactome data.From these networks,we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits.The functions of TaZF-B1,VRT-B2,and TaSPL15-A/D in establishment of wheat spike architecture were verified.This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.
基金supported by the National Natural Science Foundation of China(no.32070656)the Nanjing University Deng Feng Scholars Program.
文摘Single-cell transcriptomics has been fully embraced in plant biological research and is revolutionizing our understanding of plant growth,development,and responses to external stimuli.However,single-cell tran-scriptomic data analysis in plants is not trivial,given that there is currently no end-to-end solution and that integration of various bioinformatics tools involves a large number of required dependencies.Here,we pre-sent scPlant,a versatile framework for exploring plant single-cell atlases with minimuminput data provided by users.The scPlant pipeline is implemented with numerous functions for diverse analytical tasks,ranging from basic data processing to advanced demands such as cell-type annotation and deconvolution,trajec-tory inference,cross-species data integration,and cell-type-specific gene regulatory network construc-tion.In addition,a variety of visualization tools are bundled in a built-in Shiny application,enabling explo-ration of single-cell transcriptomic data on the fly.
基金supported by the National Natural Science Foundation of China(No.62005073)the Program of the State Key Laboratory of Crystal Materials(No.KF2101)+3 种基金the National Key Research and Development Program of China(No.2020YFC2200300)the Program of the State Key Laboratory of Quantum Optics and Quantum Optics Devices(No.KF202207)the Research Funds of Hangzhou Institute for Advanced Study(No.2022ZZ01006)the Hangzhou Agricultural and Social Development initiative Design Project(No.2022ZDSJ0846).
文摘A continuous-wave(CW)single-longitudinal-mode(SLM)Raman laser at 1240 nm with power of up to 20.6 W was demonstrated in a free-running diamond Raman oscillator without any axial-mode selection elements.The SLM operation was achieved due to the spatial-hole-burning free nature of Raman gain and was maintained at the highest available pump power by suppressing the parasitic stimulated Brillouin scattering(SBS).A folded-cavity design was employed for reducing the perturbing effect of resonances at the pump frequency.At a pump power of 69 W,the maximum Stokes output reached 20.6 W,corresponding to a 30%optical-to-optical conversion efficiency from 1064to 1240 nm.The result shows that parasitic SBS is the main physical process disturbing the SLM operation of Raman oscillator at higher power.In addition,for the first time,the spectral linewidth of a CW SLM diamond Raman laser was resolved using the long-delayed self-heterodyne interferometric method,which is 105 kHz at 20 W.
基金supported by National Natural Science Foundation of China(Nos.91853109,81730100,81872877,and 81673436)Mountain-Climbing Talents Project of Nanjing University(China)。
文摘Colorectal cancer(CRC), a malignant tumor worldwide consists of microsatellite instability(MSI) and stable(MSS) phenotypes. Although SHP2 is a hopeful target for cancer therapy, its relationship with innate immunosuppression remains elusive. To address that, single-cell RNA sequencing wasperformed to explore the role of SHP2 in all cell types of tumor microenvironment(TME) from murine MC38 xenografts. Intratumoral cells were found to be functionally heterogeneous and responded significantly to SHP099, a SHP2 allosteric inhibitor. The malignant evolution of tumor cells was remarkably arrested by SHP099. Mechanistically, STING-TBK1-IRF3-mediated type I interferon signaling was highly activated by SHP099 in infiltrated myeloid cells. Notably, CRC patients with MSS phenotype exhibited greater macrophage infiltration and more potent SHP2 phosphorylation in CD68;macrophages than MSI-high phenotypes, suggesting the potential role of macrophagic SHP2 in TME. Collectively,our data reveals a mechanism of innate immunosuppression mediated by SHP2, suggesting that SHP2 is a promising target for colon cancer immunotherapy.
基金supported by the National Natural Science Foundation of China(32070243 to Z.Q.S.and 31770245 to J.Q.C.)the Fundamental Research Funds for the Central Universities(020814380169 to Z.Q.S.)。
文摘Nucleotide-binding leucine-rich-repeat(NLR)genes comprise the largest family of plant disease-resis-tance genes.Angiosperm NLR genes are phylogenetically divided into the TNL,CNL,and RNL subclasses.NLR copy numbers and subclass composition vary tremendously across angiosperm genomes.However,the evolutionary associations between genomic NLR content and ecological adaptation,or between NLR content and signal transduction components,are poorly characterized because of limited genome avail-ability.In this study,we established an angiosperm NLR atlas(ANNA,https://biobigdata.nju.edu.cn/ANNA/)that includes NLR genes from over 300 angiosperm genomes.Using ANNA,we revealed that NLR copy numbers differ up to 66-fold among closely related species owing to rapid gene loss and gain.Interestingly,NLR contraction was associated with adaptations to aquatic,parasitic,and carnivorous life-styles.The convergent NLR reduction in aquatic plants resembles the lack of NLR expansion during the long-term evolution of green algae before the colonization of land.A co-evolutionary pattern between NLR subclasses and plant immune pathway components was also identified,suggesting that immune pathway deficiencies may drive TNL loss.Finally,we identified a conserved TNL lineage that may function independently of the EDS1-SAG101-NRG1 module.Collectively,these findings provide new insights into the evolution of NLR genes in the context of ecological adaptation and genome content variation.
基金supported by the Fundamental Research Funds for the Central Universities(14380129)the National Natural Science Foundation of China(21877060)。
文摘Dear Editor,The recent outbreak of novel coronavirus disease 2019(COVID-19)has already become a global-scale epidemic.Since the case from China was reported on Dec 30th,2019(Huang et al.,2020;Li et al.,2020),the pathogen was soon identified as a new coronavirus on Jan 7th.
基金supported by the Nanjing University Deng Feng Scholars Programthe Priority Academic Program Development(PAPD)of Jiangsu Higher Education Institutionsthe National Natural Science Foundation of China(32070656)。
文摘Plant genomes contain a large fraction of noncoding sequences.The discovery and annotation of conserved noncoding sequences(CNSs)in plants is an ongoing challenge.Here we report the application of comparative genomics to systematically identify CNSs in 50 well-annotated Gramineae genomes using rice(Oryza sativa)as the reference.We conduct multiple-way whole-genome alignments to the rice genome.The rice genome is annotated as 20 conservation states(CSs)at single-nucleotide resolution using a multivariate hidden Markov model(Cons HMM)based on the multiple-genome alignments.Different states show distinct enrichments for various genomic features,and the conservation scores of CSs are highly correlated with the level of associated chromatin accessibility.We find that at least 33.5%of the rice genome is highly under selection,with more than 70%of the sequence lying outside of coding regions.A catalog of 855,366 regulatory CNSs is generated,and they significantly overlapped with putative active regulatory elements such as promoters,enhancers,and transcription factor binding sites.Collectively,our study provides a resource for elucidating functional noncoding regions of the rice genome and an evolutionary aspect of regulatory sequences in higher plants.
