Ginger(Zingiber officinale),the type species of Zingiberaceae,is one of the most widespread medicinal plants and spices.Here,we report a high-quality,chromosome-scale reference genome of ginger‘Zhugen’,a traditional...Ginger(Zingiber officinale),the type species of Zingiberaceae,is one of the most widespread medicinal plants and spices.Here,we report a high-quality,chromosome-scale reference genome of ginger‘Zhugen’,a traditionally cultivated ginger in Southwest China used as a fresh vegetable,assembled from PacBio long reads,Illumina short reads,and high-throughput chromosome conformation capture(Hi-C)reads.The ginger genome was phased into two haplotypes,haplotype 1(1.53 Gb with a contig N50 of 4.68 M)and haplotype 0(1.51 Gb with a contig N50 of 5.28 M).Homologous ginger chromosomes maintained excellent gene pair collinearity.In 17,226 pairs of allelic genes,11.9%exhibited differential expression between alleles.Based on the results of ginger genome sequencing,transcriptome analysis,and metabolomic analysis,we proposed a backbone biosynthetic pathway of gingerol analogs,which consists of 12 enzymatic gene families,PAL,C4H,4CL,CST,C3’H,C3OMT,CCOMT,CSE,PKS,AOR,DHN,and DHT.These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs.Overall,this study serves as an excellent resource for further research on ginger biology and breeding,lays a foundation for a better understanding of ginger evolution,and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.展开更多
After online publication of the article 1,the authors noticed the affiliation“College of Landscape Architecture and Life Science/Institute of Special Plants,Chongqing University of Arts and Sciences,Yongchuan,Chongqi...After online publication of the article 1,the authors noticed the affiliation“College of Landscape Architecture and Life Science/Institute of Special Plants,Chongqing University of Arts and Sciences,Yongchuan,Chongqing,China”for author Yiqing Liu was missing.展开更多
Nicotine is widely recognized as the primary contributor to tobacco dependence.Previous studies have indicated that molecular and behavioral responses to nicotine are primarily mediated by ventral tegmental area(VTA)n...Nicotine is widely recognized as the primary contributor to tobacco dependence.Previous studies have indicated that molecular and behavioral responses to nicotine are primarily mediated by ventral tegmental area(VTA)neurons,and accumulating evidence suggests that glia play prominent roles in nicotine addiction.However,VTA neurons and glia have yet to be characterized at the transcriptional level during the progression of nicotine self-administration.Here,a male mouse model of nicotine self-administration is established and the timing of three critical phases(pre-addiction,addicting,and post-addiction phase)is characterized.Single-nucleus RNA sequencing in the VTA at each phase is performed to comprehensively classify specific cell subtypes.Adaptive changes occurred during the addicting and post-addiction phases,with the addicting phase displaying highly dynamic neuroplasticity that profoundly impacts the transcription in each cell subtype.Furthermore,significant transcriptional changes in energy metabolism-related genes are observed,accompanied by notable structural alterations in neuronal mitochondria during the progression of nicotine self-administration.The results provide insights into mechanisms underlying the progression of nicotine addiction,serving as an important resource for identifying potential molecular targets for nicotine cessation.展开更多
During the early systemic infection of plant pathogens,individual cells can harbor pathogens at various stages of infection,ranging from absent to abundant.Consequently,gene expression levels within these cells in res...During the early systemic infection of plant pathogens,individual cells can harbor pathogens at various stages of infection,ranging from absent to abundant.Consequently,gene expression levels within these cells in response to the pathogens exhibit significant variability.These variations are pivotal in determining pathogenicity or susceptibility,yet they remain largely unexplored and poorly understood.Sugarcane mosaic virus(SCMV)is a representative member of the monocot-infecting potyviruses with a polyadeny-lated RNA genome,which can be captured by single-cell RNA sequencing(scRNA-seq).Here,we per-formed scRNA-seq on SCMV-infected maize leaves during early systemic infection(prior to symptom mani-festation)to investigate the co-variation patterns between viral accumulation and intracellular gene expression alterations.We identifiedfive cell types and found that mesophyll-4(MS4)cells exhibited the highest levels of viral accumulation in most cells.Early systemic infection of SCMV resulted in a greater up-regulation of differentially expressed genes,which were mainly enriched in biological processes related to translation,peptide biosynthesis,and metabolism.Co-variation analysis of the altered maize gene expres-sion and viral accumulation levels in MS1,2,and 4 revealed several patterns,and the co-expression rela-tionships between them were mainly positive.Furthermore,functional studies identified several potential anti-or pro-viral factors that may play crucial roles during the early stage of SCMV systemic infection.These results not only provide new insights into plant gene regulation during viral infection but also offer a foundation for future investigations of host–virus interactions across molecular,cellular,and physiolog-ical scales.展开更多
There are two main types of root systems in flowering plants,namely taproot systems of dicots and fibrous root systems found in monocots.Despite this fundamental split,our current knowledge of cellular and molecular m...There are two main types of root systems in flowering plants,namely taproot systems of dicots and fibrous root systems found in monocots.Despite this fundamental split,our current knowledge of cellular and molecular mechanism driving root development is mainly based on studies of the dicot model Arabidopsis.However,the world major crops are monocots and little is known about the transcriptional programs underlying cell-type specification in this clade.Here,we report the transcriptomes of more than 20000 single cells derived from root tips of two agronomically important rice cultivars.Using combined computational and experimental analyses we were able to robustly identify most of the major cell types and define novel cell-type-specific marker genes for both cultivars.Importantly,we found divergent cell types associated with specific regulatory programs,including phytohormone biosynthesis,signaling,and response,which were well conserved between the two rice cultivars.In addition,we detected substantial differences between the cell-type transcript profiles of Arabidopsis and rice.These species-specific features emphasize the importance of analyzing tissues across diverse model species,including rice.Taken together,our study provides insight into the transcriptomic landscape of major cell types of rice root tip at single-cell resolution and opens new avenues to study cell-type specification,function,and evolution in plants.展开更多
The brain of the domestic pig(Sus scrofa domesticus)has drawn considerable attention due to its high similarities to that of humans.However,the cellular compositions of the pig brain(PB)remain elusive.Here we investig...The brain of the domestic pig(Sus scrofa domesticus)has drawn considerable attention due to its high similarities to that of humans.However,the cellular compositions of the pig brain(PB)remain elusive.Here we investigated the single-nucleus transcriptomic profiles of five regions of the PB(frontal lobe,parietal lobe,temporal lobe,occipital lobe,and hypothalamus)and identified 21 cell subpopulations.The cross-species comparison of mouse and pig hypothalamus revealed the shared and specific gene expression patterns at the single-cell resolution.Furthermore,we identified cell types and molecular pathways closely associated with neurological disorders,bridging the gap between gene mutations and pathogenesis.We reported,to our knowledge,the first single-cell atlas of domestic pig cerebral cortex and hypothalamus combined with a comprehensive analysis across species,providing extensive resources for future research regarding neural science,evolutionary developmental biology,and regenerative medicine.展开更多
The roots of legume plant play a crucial role in nitrogen fixation. However, the transcriptomes of different cell types of legume root and their functions remain largely unknown. Here, we performed single-cell RNA seq...The roots of legume plant play a crucial role in nitrogen fixation. However, the transcriptomes of different cell types of legume root and their functions remain largely unknown. Here, we performed single-cell RNA sequencing and profiled more than 22,000 single cells from root tips of Lotus japonicus, a model species of legume.We identified seven clusters corresponding to seven major cell types, which were validated by in situ hybridization. Further analysis revealed regulatory programs including phytohormone and nodulation associated with specific cell types, and revealed conserved and diverged features for the cell types. Our results represent the first single-cell resolution transcriptome for legume root tips and a valuable resource for studying the developmental and physiological functions of various cell types in legumes.展开更多
基金This work was supported by funding from the Ginger Genome Project of Chongqing University of Arts and Sciences(2018)the Natural Science Foundation of Chongqing(cstc2019jcyj-msxmX0300,cstc2019jcyj-msxmX0697,CQYC201903201,cstc2019jscx-dxwtBX0028)+4 种基金the Foundation for High-level Talents of Chongqing University of Arts and Science(2017RTZ21,P2018TZ05)the Scientific and Technological Research Program of Chongqing Municipal Education Commission(KJZD-K202001304,KJQN201801339,KJQN201801330,KJQN201801335)the Foundation of Hubei Rural Science and Technology(2020BBA037)the State Key Research and Development Program of Hubei(2020BBA037)the Foundation of Laiwu Experimental Station of the National Characteristic Vegetable Industry System.
文摘Ginger(Zingiber officinale),the type species of Zingiberaceae,is one of the most widespread medicinal plants and spices.Here,we report a high-quality,chromosome-scale reference genome of ginger‘Zhugen’,a traditionally cultivated ginger in Southwest China used as a fresh vegetable,assembled from PacBio long reads,Illumina short reads,and high-throughput chromosome conformation capture(Hi-C)reads.The ginger genome was phased into two haplotypes,haplotype 1(1.53 Gb with a contig N50 of 4.68 M)and haplotype 0(1.51 Gb with a contig N50 of 5.28 M).Homologous ginger chromosomes maintained excellent gene pair collinearity.In 17,226 pairs of allelic genes,11.9%exhibited differential expression between alleles.Based on the results of ginger genome sequencing,transcriptome analysis,and metabolomic analysis,we proposed a backbone biosynthetic pathway of gingerol analogs,which consists of 12 enzymatic gene families,PAL,C4H,4CL,CST,C3’H,C3OMT,CCOMT,CSE,PKS,AOR,DHN,and DHT.These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs.Overall,this study serves as an excellent resource for further research on ginger biology and breeding,lays a foundation for a better understanding of ginger evolution,and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.
文摘After online publication of the article 1,the authors noticed the affiliation“College of Landscape Architecture and Life Science/Institute of Special Plants,Chongqing University of Arts and Sciences,Yongchuan,Chongqing,China”for author Yiqing Liu was missing.
基金supported by the Major Project of Tobacco Biological Effects(552022AK0070,110202102014)。
文摘Nicotine is widely recognized as the primary contributor to tobacco dependence.Previous studies have indicated that molecular and behavioral responses to nicotine are primarily mediated by ventral tegmental area(VTA)neurons,and accumulating evidence suggests that glia play prominent roles in nicotine addiction.However,VTA neurons and glia have yet to be characterized at the transcriptional level during the progression of nicotine self-administration.Here,a male mouse model of nicotine self-administration is established and the timing of three critical phases(pre-addiction,addicting,and post-addiction phase)is characterized.Single-nucleus RNA sequencing in the VTA at each phase is performed to comprehensively classify specific cell subtypes.Adaptive changes occurred during the addicting and post-addiction phases,with the addicting phase displaying highly dynamic neuroplasticity that profoundly impacts the transcription in each cell subtype.Furthermore,significant transcriptional changes in energy metabolism-related genes are observed,accompanied by notable structural alterations in neuronal mitochondria during the progression of nicotine self-administration.The results provide insights into mechanisms underlying the progression of nicotine addiction,serving as an important resource for identifying potential molecular targets for nicotine cessation.
基金supported by grants from the National Natural Science Foundation of China(grant 32072384,W2412104)the China Agriculture Research System of MOF and MARA(CARS-02)+2 种基金This study was also supported by the Ministry of Agriculture and Rural Affairs of China(NK2023070202)S.C.G.is supported by startup funds from the University of California,Riversideby a grant from the National Institute of General Medical Sciences of the National Institutes of Health(award no.R35GM151194).
文摘During the early systemic infection of plant pathogens,individual cells can harbor pathogens at various stages of infection,ranging from absent to abundant.Consequently,gene expression levels within these cells in response to the pathogens exhibit significant variability.These variations are pivotal in determining pathogenicity or susceptibility,yet they remain largely unexplored and poorly understood.Sugarcane mosaic virus(SCMV)is a representative member of the monocot-infecting potyviruses with a polyadeny-lated RNA genome,which can be captured by single-cell RNA sequencing(scRNA-seq).Here,we per-formed scRNA-seq on SCMV-infected maize leaves during early systemic infection(prior to symptom mani-festation)to investigate the co-variation patterns between viral accumulation and intracellular gene expression alterations.We identifiedfive cell types and found that mesophyll-4(MS4)cells exhibited the highest levels of viral accumulation in most cells.Early systemic infection of SCMV resulted in a greater up-regulation of differentially expressed genes,which were mainly enriched in biological processes related to translation,peptide biosynthesis,and metabolism.Co-variation analysis of the altered maize gene expres-sion and viral accumulation levels in MS1,2,and 4 revealed several patterns,and the co-expression rela-tionships between them were mainly positive.Furthermore,functional studies identified several potential anti-or pro-viral factors that may play crucial roles during the early stage of SCMV systemic infection.These results not only provide new insights into plant gene regulation during viral infection but also offer a foundation for future investigations of host–virus interactions across molecular,cellular,and physiolog-ical scales.
基金This work was supported by National Transgenic Major Program(2019ZX08010-002)(to X.G.)Central Public-interest Scientific Institution Basal Research Fund(no.Y2020PT06 to X.G.)+1 种基金the DECODE ERC Synergy grant(to J.U.L.)the intramural research support from Chinese Academy of Agricultural Sciences,Centre for Organismal Studies,Heidelberg University.
文摘There are two main types of root systems in flowering plants,namely taproot systems of dicots and fibrous root systems found in monocots.Despite this fundamental split,our current knowledge of cellular and molecular mechanism driving root development is mainly based on studies of the dicot model Arabidopsis.However,the world major crops are monocots and little is known about the transcriptional programs underlying cell-type specification in this clade.Here,we report the transcriptomes of more than 20000 single cells derived from root tips of two agronomically important rice cultivars.Using combined computational and experimental analyses we were able to robustly identify most of the major cell types and define novel cell-type-specific marker genes for both cultivars.Importantly,we found divergent cell types associated with specific regulatory programs,including phytohormone biosynthesis,signaling,and response,which were well conserved between the two rice cultivars.In addition,we detected substantial differences between the cell-type transcript profiles of Arabidopsis and rice.These species-specific features emphasize the importance of analyzing tissues across diverse model species,including rice.Taken together,our study provides insight into the transcriptomic landscape of major cell types of rice root tip at single-cell resolution and opens new avenues to study cell-type specification,function,and evolution in plants.
基金the China Postdoctoral Science Foundation(2017M622795)the Science,Technology and Innovation Commission of Shenzhen Municipality(JCYJ20180507183628543)the Fundamental Research Funds for the Central Universities(2662018PY025 and 2662017PY105)。
文摘The brain of the domestic pig(Sus scrofa domesticus)has drawn considerable attention due to its high similarities to that of humans.However,the cellular compositions of the pig brain(PB)remain elusive.Here we investigated the single-nucleus transcriptomic profiles of five regions of the PB(frontal lobe,parietal lobe,temporal lobe,occipital lobe,and hypothalamus)and identified 21 cell subpopulations.The cross-species comparison of mouse and pig hypothalamus revealed the shared and specific gene expression patterns at the single-cell resolution.Furthermore,we identified cell types and molecular pathways closely associated with neurological disorders,bridging the gap between gene mutations and pathogenesis.We reported,to our knowledge,the first single-cell atlas of domestic pig cerebral cortex and hypothalamus combined with a comprehensive analysis across species,providing extensive resources for future research regarding neural science,evolutionary developmental biology,and regenerative medicine.
基金supported by a survey on Central China grassland forage germplasm resources (2017FY100604)National Natural Science Foundation of China (32001395)+1 种基金Chongqing Natural Science Foundation (stc2020jcyjmsxmX0626)The Agricultural Science and Technology Innovation Program (ASTIP) (to Z.L.)。
文摘The roots of legume plant play a crucial role in nitrogen fixation. However, the transcriptomes of different cell types of legume root and their functions remain largely unknown. Here, we performed single-cell RNA sequencing and profiled more than 22,000 single cells from root tips of Lotus japonicus, a model species of legume.We identified seven clusters corresponding to seven major cell types, which were validated by in situ hybridization. Further analysis revealed regulatory programs including phytohormone and nodulation associated with specific cell types, and revealed conserved and diverged features for the cell types. Our results represent the first single-cell resolution transcriptome for legume root tips and a valuable resource for studying the developmental and physiological functions of various cell types in legumes.
