Dear Editor,DNA modifications,including 5-methylcytosine(5m C),5-hydroxymethylcytosine(5hmC),5-carboxylcytosine(5caC),and 6-methyadenine(6mA),play crucial regulatory roles in diverse biological processes(Raiber et al....Dear Editor,DNA modifications,including 5-methylcytosine(5m C),5-hydroxymethylcytosine(5hmC),5-carboxylcytosine(5caC),and 6-methyadenine(6mA),play crucial regulatory roles in diverse biological processes(Raiber et al.,2017).Recently,4-acetyldeoxycytosine(4acC)was identified in plant genomes and was found to enrich around transcription start sites(TSSs)(Wang et al.,2022).However,the comprehensive mapping of multifactorial DNA modifications in plants remains a challenge.展开更多
Drought severely threatens food security, and its detrimental effects will be exacerbated by climate change in many parts of the world. Rice production is water-consuming and particularly vulnerable to drought stress....Drought severely threatens food security, and its detrimental effects will be exacerbated by climate change in many parts of the world. Rice production is water-consuming and particularly vulnerable to drought stress. Upland rice is a special rice ecotype that specifically adapts to dryland mainly due to its robust root system. However, the molecular and developmental mechanism underlying this adaption has remained elusive. In this study, by comparing the root development between upland and irrigated rice phenotypically and cytologically, we identified key developmental phenotypes that distinguish upland rice from irrigated rice. We further generated spatial transcriptomic atlases for coleoptilar nodes and root tips to explore their molecular differences in crown root formation and development, uncovering promising genes for enhancing rice drought resistance. Among the identified genes, HMGB1, a transcriptional regulator, functions as a key factor that facilitates root elongation and thickening in upland rice and thereby enhances drought resistance. In summary, our study uncovers spatially resolved transcriptomic features in roots of upland rice that contribute to its adaptation to dryland conditions, providing valuable genetic resources for breeding drought-resilient rice.展开更多
Marchantia polymorpha,a model liverwort,provides a valuable system for investigating the evolution of plant sexual reproduction.To explore the cellular landscape of its reproductive structures,we generate a single-nuc...Marchantia polymorpha,a model liverwort,provides a valuable system for investigating the evolution of plant sexual reproduction.To explore the cellular landscape of its reproductive structures,we generate a single-nucleus transcriptomic atlas of the antheridiophore,archegoniophore,and sporophyte.Using singlenucleus RNA sequencing(snRNA-seq),we capture over 30,000 high-quality nuclei and identify distinct cel populations.In the male organ,we characterize stages of spermatogenesis from early antheridium cells to mature sperm,revealing dynamic transcriptional programs including cell cycle regulation,chromatin remodeling,and calcium signaling.In the female organ,we define cell types including archegonial layers and secondary central cells.Sporophyte clusters are annotated as spores,elaters,capsule wall,foot,and seta cells,with transcriptional signatures related to structural support,stress response,and reproductive functions.Cross-species analysis indicates that capsule wall cells in liverworts are similar to tapetum cells.Notably,foot cells exhibit high expression of genes involved in sporopollenin biosynthesis and signaling pathways,serving as a central hub that mediates communication between the maternal gametophyte and the developing sporophyte.This study provides a comprehensive cellular and molecular map of M.polymorpha reproductive organs and sporophyte,establishing a framework for investigating the development and evolution of sexual reproduction in early land plants.展开更多
Potato is an important crop for ensuring global food and nutritional security.The metabolic transitions and underlying genetic mechanisms that occurred during potato domestication from wild progenitors remain not full...Potato is an important crop for ensuring global food and nutritional security.The metabolic transitions and underlying genetic mechanisms that occurred during potato domestication from wild progenitors remain not fully understood.In this study,we used a multi-omics approach to decipher its domestication footprint.The metabolomic remodeling of potato tubers featured a decrease in diversity and content of bitter steroidal glycoalkaloids(SGAs)and an increase in nutritional flavonoid content.Two biosynthesis genes affecting the structural divergence of SGAs and two transcription factors that regulate SGA content in potato were characterized.Two tandem MYB transcription factors were shown to modulate the phenylpropanoid flux between phenolic acids and flavonoids.Furthermore,we uncovered that selection of coding and cis-regulatory variations has substantially reshaped tuber metabolite diversity and content,respectively.Through dissection of the genetic architecture of 2046 loci for 568 metabolites,we identified 2745 epistatic interactions and 268 pleiotropic effects,providing a roadmap for metabolic manipulation in tubers.Taken together,these findings deepen our understanding of potato domestication and offer genetic strategies for developing cultivars with improved quality.展开更多
基金supported by the National Key Research and Development Program of China(2021YFF1000600)Basic Research Center for Agricultural Frontiers and Interdisciplinary Sciences(BRC-AFIS)+2 种基金Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-BRC-AFIS-202502)the Youth Innovation Program of Chinese Academy of Agricultural Sciences(Y2022QC33)the National Natural Science Foundation of China(32071437)。
文摘Dear Editor,DNA modifications,including 5-methylcytosine(5m C),5-hydroxymethylcytosine(5hmC),5-carboxylcytosine(5caC),and 6-methyadenine(6mA),play crucial regulatory roles in diverse biological processes(Raiber et al.,2017).Recently,4-acetyldeoxycytosine(4acC)was identified in plant genomes and was found to enrich around transcription start sites(TSSs)(Wang et al.,2022).However,the comprehensive mapping of multifactorial DNA modifications in plants remains a challenge.
基金supported by Biological Breeding-National Scinece and Tecnology Major Project(2023ZD04073)the National Natural Science Foundation of China(32070563 and 32470307)+3 种基金the Shenzhen Science and Technology Program(KQTD20230301092839007,KJZD20230921114607016)the Guangdong Laboratory of Lingnan Morden Agriculture(AGIS-ZDXM202203)the Fundamental Research Funds for the Central Universities(2662023SKPY002)Guangdong Provincial Key Laboratory of core collection of crop genetic resources research and application,BGl-Shenzhen,Shenzhen 518120,China(NO.2011A091000047).
文摘Drought severely threatens food security, and its detrimental effects will be exacerbated by climate change in many parts of the world. Rice production is water-consuming and particularly vulnerable to drought stress. Upland rice is a special rice ecotype that specifically adapts to dryland mainly due to its robust root system. However, the molecular and developmental mechanism underlying this adaption has remained elusive. In this study, by comparing the root development between upland and irrigated rice phenotypically and cytologically, we identified key developmental phenotypes that distinguish upland rice from irrigated rice. We further generated spatial transcriptomic atlases for coleoptilar nodes and root tips to explore their molecular differences in crown root formation and development, uncovering promising genes for enhancing rice drought resistance. Among the identified genes, HMGB1, a transcriptional regulator, functions as a key factor that facilitates root elongation and thickening in upland rice and thereby enhances drought resistance. In summary, our study uncovers spatially resolved transcriptomic features in roots of upland rice that contribute to its adaptation to dryland conditions, providing valuable genetic resources for breeding drought-resilient rice.
基金supported by the 10 KP project(https://db.cngb.org/1Okp/)and the Scientific Foundation of the Urban Management Bureau of Shenzhen(202403).
文摘Marchantia polymorpha,a model liverwort,provides a valuable system for investigating the evolution of plant sexual reproduction.To explore the cellular landscape of its reproductive structures,we generate a single-nucleus transcriptomic atlas of the antheridiophore,archegoniophore,and sporophyte.Using singlenucleus RNA sequencing(snRNA-seq),we capture over 30,000 high-quality nuclei and identify distinct cel populations.In the male organ,we characterize stages of spermatogenesis from early antheridium cells to mature sperm,revealing dynamic transcriptional programs including cell cycle regulation,chromatin remodeling,and calcium signaling.In the female organ,we define cell types including archegonial layers and secondary central cells.Sporophyte clusters are annotated as spores,elaters,capsule wall,foot,and seta cells,with transcriptional signatures related to structural support,stress response,and reproductive functions.Cross-species analysis indicates that capsule wall cells in liverworts are similar to tapetum cells.Notably,foot cells exhibit high expression of genes involved in sporopollenin biosynthesis and signaling pathways,serving as a central hub that mediates communication between the maternal gametophyte and the developing sporophyte.This study provides a comprehensive cellular and molecular map of M.polymorpha reproductive organs and sporophyte,establishing a framework for investigating the development and evolution of sexual reproduction in early land plants.
基金funded by the National Key Research and Development Program of China(2022YFF1002500)the National Natural Science Foundation of China(32272725 and 32488302)+1 种基金the Guangdong Major Project of Basic and Applied Basic Research(2021B0301030004)the China Postdoctoral Science Foundation(2022M723463).
文摘Potato is an important crop for ensuring global food and nutritional security.The metabolic transitions and underlying genetic mechanisms that occurred during potato domestication from wild progenitors remain not fully understood.In this study,we used a multi-omics approach to decipher its domestication footprint.The metabolomic remodeling of potato tubers featured a decrease in diversity and content of bitter steroidal glycoalkaloids(SGAs)and an increase in nutritional flavonoid content.Two biosynthesis genes affecting the structural divergence of SGAs and two transcription factors that regulate SGA content in potato were characterized.Two tandem MYB transcription factors were shown to modulate the phenylpropanoid flux between phenolic acids and flavonoids.Furthermore,we uncovered that selection of coding and cis-regulatory variations has substantially reshaped tuber metabolite diversity and content,respectively.Through dissection of the genetic architecture of 2046 loci for 568 metabolites,we identified 2745 epistatic interactions and 268 pleiotropic effects,providing a roadmap for metabolic manipulation in tubers.Taken together,these findings deepen our understanding of potato domestication and offer genetic strategies for developing cultivars with improved quality.
