Pub Date : 2026-01-15DOI: 10.1038/s41477-025-02194-4
Tian Zhang, Lu Yu, Yueyuan Wang, Pan Li, Xiaoyan Feng, Guoliang Jian, Fengqi Zhao, Xuejiao Liu, Zhen Yang, Xiaoqian Sha, Yongqi Wang, Lingyu Mi, Wan Sun, Tingting Wei, Siyi Guo, Changqing Zhang, Zhi Li, Chun-Peng Song
Stomata are pivotal for gas exchange during photosynthesis and transpiration and are therefore critical in plant growth and global water cycles. However, the mechanistic role of cell wall architecture in grass stomatal function remains elusive. Here immunolabelling and mechanical mapping revealed local distribution of methylesterified pectin at the stiffer polar ends of maize stomata. Expression-knockdown maize with reduced pectin labelling showed decreased polar stiffness and increased stomatal aperture. Finite element modelling corroborated these findings, suggesting that in contrast to non-grass stomata, the size and modulus of the polar materials limit maize stomatal opening. Surveys from various plant species suggest that polar-enriched methylesterified pectin is a unique feature of grass stomata. Xylanase pretreatment diminished pectin labelling at the polar ends, implying associations between pectin and xylan. Our multi-scale research uncovers a pectin–xylan–cellulose composite mediating polar fixation during maize stomatal movement, unveiling new targets for stomata engineering and crop breeding.
{"title":"Esterified-pectin-coupled polar stiffening controls grass stomatal opening","authors":"Tian Zhang, Lu Yu, Yueyuan Wang, Pan Li, Xiaoyan Feng, Guoliang Jian, Fengqi Zhao, Xuejiao Liu, Zhen Yang, Xiaoqian Sha, Yongqi Wang, Lingyu Mi, Wan Sun, Tingting Wei, Siyi Guo, Changqing Zhang, Zhi Li, Chun-Peng Song","doi":"10.1038/s41477-025-02194-4","DOIUrl":"https://doi.org/10.1038/s41477-025-02194-4","url":null,"abstract":"Stomata are pivotal for gas exchange during photosynthesis and transpiration and are therefore critical in plant growth and global water cycles. However, the mechanistic role of cell wall architecture in grass stomatal function remains elusive. Here immunolabelling and mechanical mapping revealed local distribution of methylesterified pectin at the stiffer polar ends of maize stomata. Expression-knockdown maize with reduced pectin labelling showed decreased polar stiffness and increased stomatal aperture. Finite element modelling corroborated these findings, suggesting that in contrast to non-grass stomata, the size and modulus of the polar materials limit maize stomatal opening. Surveys from various plant species suggest that polar-enriched methylesterified pectin is a unique feature of grass stomata. Xylanase pretreatment diminished pectin labelling at the polar ends, implying associations between pectin and xylan. Our multi-scale research uncovers a pectin–xylan–cellulose composite mediating polar fixation during maize stomatal movement, unveiling new targets for stomata engineering and crop breeding.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"45 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145968790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-12DOI: 10.1038/s41477-025-02180-w
Zoe Bernasconi, Aline G. Herger, Maria Del Pilar Caro, Lukas Kunz, Marion C. Müller, Ursin Stirnemann, Megan A. Outram, Victoria Widrig, Matthias Neidhart, Jonatan Isaksson, Seraina Schudel, Sebastian Rösli, Thomas Wicker, Kyle W. Bender, Cyril Zipfel, Peter N. Dodds, Melania Figueroa, Javier Sánchez-Martín, Beat Keller
The wheat resistance gene Pm4 encodes a kinase fusion protein and has gained particular attention as it confers race-specific resistance against two major wheat pathogens: powdery mildew and blast. Here we describe the identification of AvrPm4, the mildew avirulence effector recognized by Pm4, using UV mutagenesis, and its functional validation in wheat protoplasts. We show that AvrPm4 directly interacts with and is phosphorylated by Pm4. Using genetic association and quantitative trait locus mapping, we further demonstrate that the evasion of Pm4 resistance by virulent mildew isolates relies on a second fungal component, SvrPm4, which suppresses AvrPm4-induced cell death. Surprisingly, SvrPm4 was previously described as AvrPm1a. We show that SvrPm4, but not its inactive variant svrPm4, is recognized by the nucleotide-binding leucine-rich repeat immune receptor Pm1a. These multiple roles of a single effector provide a new perspective on fungal (a)virulence proteins and their combinatorial interactions with different types of immune receptors.
{"title":"Virulence on Pm4 kinase-based resistance is determined by two divergent wheat powdery mildew effectors","authors":"Zoe Bernasconi, Aline G. Herger, Maria Del Pilar Caro, Lukas Kunz, Marion C. Müller, Ursin Stirnemann, Megan A. Outram, Victoria Widrig, Matthias Neidhart, Jonatan Isaksson, Seraina Schudel, Sebastian Rösli, Thomas Wicker, Kyle W. Bender, Cyril Zipfel, Peter N. Dodds, Melania Figueroa, Javier Sánchez-Martín, Beat Keller","doi":"10.1038/s41477-025-02180-w","DOIUrl":"https://doi.org/10.1038/s41477-025-02180-w","url":null,"abstract":"The wheat resistance gene Pm4 encodes a kinase fusion protein and has gained particular attention as it confers race-specific resistance against two major wheat pathogens: powdery mildew and blast. Here we describe the identification of AvrPm4, the mildew avirulence effector recognized by Pm4, using UV mutagenesis, and its functional validation in wheat protoplasts. We show that AvrPm4 directly interacts with and is phosphorylated by Pm4. Using genetic association and quantitative trait locus mapping, we further demonstrate that the evasion of Pm4 resistance by virulent mildew isolates relies on a second fungal component, SvrPm4, which suppresses AvrPm4-induced cell death. Surprisingly, SvrPm4 was previously described as AvrPm1a. We show that SvrPm4, but not its inactive variant svrPm4, is recognized by the nucleotide-binding leucine-rich repeat immune receptor Pm1a. These multiple roles of a single effector provide a new perspective on fungal (a)virulence proteins and their combinatorial interactions with different types of immune receptors.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"83 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145956331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plants have evolved intricate mechanisms to adapt to tissue damage from environmental and biological factors, enhancing survival strategies. However, the link and mechanisms between wounding and dormancy traits remain unclear. Here we discovered that wounding dramatically accelerates bud-growth transition (BGT) in gladiolus and other horticultural geophytes, including Allium sativum and Allium cepa. Wounding induced jasmonic acid (JA) accumulation in gladiolus corms, promoting sucrose transport to dormant buds via the apoplastic pathway, supplying energy for cell division and facilitating BGT. Furthermore, we characterized a zinc finger transcription factor, ZINC FINGER OF ARABIDOPSIS THALIANA 11 (GhZAT11), responsive to both wounding and JA. GhZAT11 directly upregulated SUCROSE TRANSPORTER4 (GhSUT4) and CYCLIN D2;1 (GhCYCD2;1), enhancing sucrose transport and cell division in the shoot apical meristem. In addition, ZAT11, SUT4 and CYCD2;1 can act as markers for wound-induced BGT in geophytes. Our findings reveal that injuries trigger BGT via JA-regulated sucrose transport and cell division, offering novel insights into JA's role in wound-induced responses.
{"title":"GhZAT11 triggers wound-activated bud growth by accelerating sugar transport and cell division.","authors":"Jingru Li,Chang Liu,Jingwei Wei,Dong Jing,Junwei Tang,Yajie Zhao,Li Cao,Lin Wu,Chenglong Yang,Shaozhong Fang,Lianwei Qu,Yingdong Yang,Tibor Janda,Mingfang Yi,Jian Wu","doi":"10.1038/s41477-025-02206-3","DOIUrl":"https://doi.org/10.1038/s41477-025-02206-3","url":null,"abstract":"Plants have evolved intricate mechanisms to adapt to tissue damage from environmental and biological factors, enhancing survival strategies. However, the link and mechanisms between wounding and dormancy traits remain unclear. Here we discovered that wounding dramatically accelerates bud-growth transition (BGT) in gladiolus and other horticultural geophytes, including Allium sativum and Allium cepa. Wounding induced jasmonic acid (JA) accumulation in gladiolus corms, promoting sucrose transport to dormant buds via the apoplastic pathway, supplying energy for cell division and facilitating BGT. Furthermore, we characterized a zinc finger transcription factor, ZINC FINGER OF ARABIDOPSIS THALIANA 11 (GhZAT11), responsive to both wounding and JA. GhZAT11 directly upregulated SUCROSE TRANSPORTER4 (GhSUT4) and CYCLIN D2;1 (GhCYCD2;1), enhancing sucrose transport and cell division in the shoot apical meristem. In addition, ZAT11, SUT4 and CYCD2;1 can act as markers for wound-induced BGT in geophytes. Our findings reveal that injuries trigger BGT via JA-regulated sucrose transport and cell division, offering novel insights into JA's role in wound-induced responses.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"185 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145955964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-09DOI: 10.1038/s41477-025-02192-6
Samuel F Brockington,Patricia Malcolm,Anthony S Aiello,Thaís H Almeida,Margeaux Apple,Sandra Aragón-Rodríguez,Thomas P Arbour,Graciela Barreiro,Juan Fernando Phillips-Bernal,Thomas Borsch,Angela Cano,Thereis Choo,Emily E D Coffey,Dan Crowley,Richard Deverell,Sebsebe Demissew,Hannes Dempewolf,Mauricio Diazgranados,Banessa Falcón-Hidalgo,Jean Franczyk,Thomas Freeth,Ethan Freid,Stephan W Gale,M Patrick Griffith,Anton Güntsch,Clare Hart,James Hearsum,Peter M Hollingsworth,Douglas Justice,Donovan Kirkwood,Colin K Khoury,Wesley M Knapp,Anneleen Kool,Jill Koski,Tessa Kum,Yang Niu,Cornelia Löhne,Darach A Lupton,Zacharia Magombo,Esteban Manrique,María P Martín,Gustavo Martinelli,Donna McGinnis,Jennifer R Neale,Patrick Newman,Ari Novy,Tim Park,Susan Pell,Michael D Pirie,Raul Puente-Martinez,Hai Ren,Marc Reynders,Nicolás Rodríguez-Cerón,Nina Rønsted,Nicola Schoenenberger,Anna Maria Senekal,Rebecca Sucher,Brett Summerell,Alex Summers,Puay Y Tan,Hanna Tornevall,Seana K Walsh,Chad Washburn,Justyna Wiland-Szymańska,Qing-Feng Wang,Christopher Willis,Andrew Wyatt,Peter Wyse Jackson,Wen-Bin Yu,Paul Smith
Documented living plant collections distinguish botanic gardens from other green spaces and horticultural landscapes. With more than 3,500 collections worldwide, these institutions steward at least 105,634 species-around 30% of all land plant diversity-while fulfilling amenity, educational, scientific and conservation roles. However, twenty-first-century challenges demand a re-evaluation of how these collections are documented and managed. We argue that meeting these emerging needs requires higher standards of coordinated information management and innovation in data infrastructures across the global network. This Perspective critically examines data management practices of living collections supporting scientific research and conservation, from institutional to global levels. We identify the renewed demands on living collections, highlight exemplar global data infrastructures, define data challenges inherent to living collections and explore how current systems fall short in enabling a connected global system. Finally, we outline a vision for high-performance collections, fully integrated into a robust global data ecosystem.
{"title":"High-performance living plant collections require a globally integrated data ecosystem to meet twenty-first-century challenges.","authors":"Samuel F Brockington,Patricia Malcolm,Anthony S Aiello,Thaís H Almeida,Margeaux Apple,Sandra Aragón-Rodríguez,Thomas P Arbour,Graciela Barreiro,Juan Fernando Phillips-Bernal,Thomas Borsch,Angela Cano,Thereis Choo,Emily E D Coffey,Dan Crowley,Richard Deverell,Sebsebe Demissew,Hannes Dempewolf,Mauricio Diazgranados,Banessa Falcón-Hidalgo,Jean Franczyk,Thomas Freeth,Ethan Freid,Stephan W Gale,M Patrick Griffith,Anton Güntsch,Clare Hart,James Hearsum,Peter M Hollingsworth,Douglas Justice,Donovan Kirkwood,Colin K Khoury,Wesley M Knapp,Anneleen Kool,Jill Koski,Tessa Kum,Yang Niu,Cornelia Löhne,Darach A Lupton,Zacharia Magombo,Esteban Manrique,María P Martín,Gustavo Martinelli,Donna McGinnis,Jennifer R Neale,Patrick Newman,Ari Novy,Tim Park,Susan Pell,Michael D Pirie,Raul Puente-Martinez,Hai Ren,Marc Reynders,Nicolás Rodríguez-Cerón,Nina Rønsted,Nicola Schoenenberger,Anna Maria Senekal,Rebecca Sucher,Brett Summerell,Alex Summers,Puay Y Tan,Hanna Tornevall,Seana K Walsh,Chad Washburn,Justyna Wiland-Szymańska,Qing-Feng Wang,Christopher Willis,Andrew Wyatt,Peter Wyse Jackson,Wen-Bin Yu,Paul Smith","doi":"10.1038/s41477-025-02192-6","DOIUrl":"https://doi.org/10.1038/s41477-025-02192-6","url":null,"abstract":"Documented living plant collections distinguish botanic gardens from other green spaces and horticultural landscapes. With more than 3,500 collections worldwide, these institutions steward at least 105,634 species-around 30% of all land plant diversity-while fulfilling amenity, educational, scientific and conservation roles. However, twenty-first-century challenges demand a re-evaluation of how these collections are documented and managed. We argue that meeting these emerging needs requires higher standards of coordinated information management and innovation in data infrastructures across the global network. This Perspective critically examines data management practices of living collections supporting scientific research and conservation, from institutional to global levels. We identify the renewed demands on living collections, highlight exemplar global data infrastructures, define data challenges inherent to living collections and explore how current systems fall short in enabling a connected global system. Finally, we outline a vision for high-performance collections, fully integrated into a robust global data ecosystem.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"264 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-09DOI: 10.1038/s41477-025-02183-7
Hong Su,Yan Li,Yonghe Chen,Hengyun Lu,Rui Zhang,Wentao Dong,Bin Han,Qiang Zhao,Peng Wang
C4 plants operate a highly efficient photosynthetic CO2 concentrating mechanism. However, C4 photosynthesis represented by maize is based on the typical Kranz-type leaf anatomy, which involves complex regulation of vascular development coupling with metabolic distribution. To explore the possibility of using alternative C4 leaf anatomy as reference for engineering C3 crops, we sequenced, assembled and annotated the genome of Arundinella anomala, a C4 grass with variant Kranz anatomy and interveinal distinctive cells (DC). Following single-cell level transcriptomes for comparative analyses between C4 bundle sheath and DC cells, genetic and metabolic support for the intensified C4 function of DC cells were observed, including increased cyclic photosynthetic electron transport, carbon fixation and starch synthesis. Further, the mechanism involving SHORT-ROOT (SHR) and auxin to trigger independent development or proliferation of DC cells was explored. Notably, spaced distribution of DC-like cells can be achieved in rice leaves by inducing the expression of ZmSHR1. This work laid a foundation for introducing functional DC-like cells among the intervascular mesophyll cells of C3 grass leaves, and provided resources and strategies for engineering C4 traits into C3 crops.
{"title":"Assembly of Arundinella anomala genome to facilitate single-cell resolved functional and developmental characterization of C4 distinctive cells.","authors":"Hong Su,Yan Li,Yonghe Chen,Hengyun Lu,Rui Zhang,Wentao Dong,Bin Han,Qiang Zhao,Peng Wang","doi":"10.1038/s41477-025-02183-7","DOIUrl":"https://doi.org/10.1038/s41477-025-02183-7","url":null,"abstract":"C4 plants operate a highly efficient photosynthetic CO2 concentrating mechanism. However, C4 photosynthesis represented by maize is based on the typical Kranz-type leaf anatomy, which involves complex regulation of vascular development coupling with metabolic distribution. To explore the possibility of using alternative C4 leaf anatomy as reference for engineering C3 crops, we sequenced, assembled and annotated the genome of Arundinella anomala, a C4 grass with variant Kranz anatomy and interveinal distinctive cells (DC). Following single-cell level transcriptomes for comparative analyses between C4 bundle sheath and DC cells, genetic and metabolic support for the intensified C4 function of DC cells were observed, including increased cyclic photosynthetic electron transport, carbon fixation and starch synthesis. Further, the mechanism involving SHORT-ROOT (SHR) and auxin to trigger independent development or proliferation of DC cells was explored. Notably, spaced distribution of DC-like cells can be achieved in rice leaves by inducing the expression of ZmSHR1. This work laid a foundation for introducing functional DC-like cells among the intervascular mesophyll cells of C3 grass leaves, and provided resources and strategies for engineering C4 traits into C3 crops.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"1 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Engineering functional CO2-concentrating mechanisms into C3 crops holds great potential for enhancing photosynthetic efficiency. Limited CO2-inducible A (LciA), a chloroplast envelope bicarbonate channel belonging to the formate/nitrite transporter (FNT) family, is a key algal CO2-concentrating mechanism component and has been considered as a prime candidate for introduction into C3 plants. However, its application has been hindered by an incomplete mechanistic understanding. Here we report the cryogenic electron microscopy structure of Chlamydomonas reinhardtii LciA. Combining structural analysis and growth assays, we determined key residues governing substrate access and permeation, and identified two substitutions (K136A/A114F) that enhance LciA activity. We found that bicarbonate selectivity is governed by electrostatic coordination mediated by Lys220 and steric constraint imposed by Ala117 and Val267 within the selectivity filter. Leveraging these insights, we successfully engineered the bacterial FNT family nitrite channel NirC through site-directed mutagenesis to gain bicarbonate transport activity, and we characterized the bicarbonate transport capacity of the Chlamydomonas nitrite channels NAR1.1/NAR1.5, which were amenable to further enhancement. Taken together, our study establishes LciA as a fundamental template for engineering and identifying FNT proteins with bicarbonate transport capability, thereby greatly expanding the molecular toolkit for synthetic biology approaches aimed at boosting photosynthetic efficiency in both algae and crops.
{"title":"Structure of Chlamydomonas reinhardtii LciA guided the engineering of FNT family proteins to gain bicarbonate transport activity","authors":"Jiaxin Guo, Zhao Yang, Xue Zhang, Feifan Liu, Miaolian Ma, Fang Yu, Jirong Huang, Peng Zhang","doi":"10.1038/s41477-025-02200-9","DOIUrl":"https://doi.org/10.1038/s41477-025-02200-9","url":null,"abstract":"Engineering functional CO2-concentrating mechanisms into C3 crops holds great potential for enhancing photosynthetic efficiency. Limited CO2-inducible A (LciA), a chloroplast envelope bicarbonate channel belonging to the formate/nitrite transporter (FNT) family, is a key algal CO2-concentrating mechanism component and has been considered as a prime candidate for introduction into C3 plants. However, its application has been hindered by an incomplete mechanistic understanding. Here we report the cryogenic electron microscopy structure of Chlamydomonas reinhardtii LciA. Combining structural analysis and growth assays, we determined key residues governing substrate access and permeation, and identified two substitutions (K136A/A114F) that enhance LciA activity. We found that bicarbonate selectivity is governed by electrostatic coordination mediated by Lys220 and steric constraint imposed by Ala117 and Val267 within the selectivity filter. Leveraging these insights, we successfully engineered the bacterial FNT family nitrite channel NirC through site-directed mutagenesis to gain bicarbonate transport activity, and we characterized the bicarbonate transport capacity of the Chlamydomonas nitrite channels NAR1.1/NAR1.5, which were amenable to further enhancement. Taken together, our study establishes LciA as a fundamental template for engineering and identifying FNT proteins with bicarbonate transport capability, thereby greatly expanding the molecular toolkit for synthetic biology approaches aimed at boosting photosynthetic efficiency in both algae and crops.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"4 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145919980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-08DOI: 10.1038/s41477-025-02208-1
{"title":"Structure-based engineering of bicarbonate transport activity unlocks the CO<sub>2</sub>-concentrating mechanism.","authors":"","doi":"10.1038/s41477-025-02208-1","DOIUrl":"https://doi.org/10.1038/s41477-025-02208-1","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145934346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-07DOI: 10.1038/s41477-025-02176-6
Edgar Demesa-Arevalo, Hannah Dӧrpholz, Isaia Vardanega, Jan Eric Maika, Itzel Pineda-Valentino, Stella Eggels, Tobias Lautwein, Karl Kӧhrer, Thorsten Schnurbusch, Maria von Korff, Bjӧrn Usadel, Rüdiger Simon
Grass inflorescences are composite structures, featuring complex sets of meristems as stem cell niches that are initiated in a repetitive manner. Meristems differ in identity and longevity, generate branches or split to form flower meristems that finally produce seeds. Within meristems, distinct cell types are determined by positional information and the regional activity of gene regulatory networks. Understanding these local microenvironments requires precise spatio-temporal information on gene expression profiles, which current technology cannot achieve. Here we investigate transcriptional changes during barley development, from the specification of meristem and organ founder cells to the initiation of distinct floral organs, on the basis of an imputation approach integrating deep single-cell RNA sequencing with spatial gene expression data. The expression profiles of more than 40,000 genes can now be analysed at cellular resolution in multiple barley tissues using the new web-based graphical interface BARVISTA, which enables precise virtual microdissection to analyse any sub-ensemble of cells. Our study pinpoints previously inaccessible key transcriptional events in founder cells during primordia initiation and specification, characterizes complex branching mutant phenotypes by barcoding gene expression profiles, and defines spatio-temporal trajectories during flower development. We thus uncover the genetic basis of complex developmental processes, providing novel opportunities for precisely targeted manipulation of barley traits.
{"title":"Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development","authors":"Edgar Demesa-Arevalo, Hannah Dӧrpholz, Isaia Vardanega, Jan Eric Maika, Itzel Pineda-Valentino, Stella Eggels, Tobias Lautwein, Karl Kӧhrer, Thorsten Schnurbusch, Maria von Korff, Bjӧrn Usadel, Rüdiger Simon","doi":"10.1038/s41477-025-02176-6","DOIUrl":"https://doi.org/10.1038/s41477-025-02176-6","url":null,"abstract":"Grass inflorescences are composite structures, featuring complex sets of meristems as stem cell niches that are initiated in a repetitive manner. Meristems differ in identity and longevity, generate branches or split to form flower meristems that finally produce seeds. Within meristems, distinct cell types are determined by positional information and the regional activity of gene regulatory networks. Understanding these local microenvironments requires precise spatio-temporal information on gene expression profiles, which current technology cannot achieve. Here we investigate transcriptional changes during barley development, from the specification of meristem and organ founder cells to the initiation of distinct floral organs, on the basis of an imputation approach integrating deep single-cell RNA sequencing with spatial gene expression data. The expression profiles of more than 40,000 genes can now be analysed at cellular resolution in multiple barley tissues using the new web-based graphical interface BARVISTA, which enables precise virtual microdissection to analyse any sub-ensemble of cells. Our study pinpoints previously inaccessible key transcriptional events in founder cells during primordia initiation and specification, characterizes complex branching mutant phenotypes by barcoding gene expression profiles, and defines spatio-temporal trajectories during flower development. We thus uncover the genetic basis of complex developmental processes, providing novel opportunities for precisely targeted manipulation of barley traits.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"43 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145907936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-07DOI: 10.1038/s41477-025-02187-3
Beibei Song, Sera Choi, Liang Kong, Sung-Il Kim, Judith Fliegmann, Xiuming Li, Yong Gao, Thomas A. DeFalco, Meijuan Hu, Meng Li, Yan Zhao, Hongze Wang, Shengwei Ma, Libo Shan, Thorsten Nürnberger, Ping He, Cyril Zipfel, Jian-Min Zhou
{"title":"New alleles of Arabidopsis BIK1 reinforce its predominant role in pattern-triggered immunity and caution interpretations of other reported functions","authors":"Beibei Song, Sera Choi, Liang Kong, Sung-Il Kim, Judith Fliegmann, Xiuming Li, Yong Gao, Thomas A. DeFalco, Meijuan Hu, Meng Li, Yan Zhao, Hongze Wang, Shengwei Ma, Libo Shan, Thorsten Nürnberger, Ping He, Cyril Zipfel, Jian-Min Zhou","doi":"10.1038/s41477-025-02187-3","DOIUrl":"https://doi.org/10.1038/s41477-025-02187-3","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"43 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145908394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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