SummaryForest trees are foundation species of many ecosystems and are challenged by global environmental changes. We assemble genetic facts and arguments supporting or undermining resilient responses of forest trees to those changes. Genetic resilience is understood here as the capacity of a species to restore its adaptive potential following environmental changes and disturbances. Importantly, the data come primarily from European temperate tree species with large distributions and consider only marginally species with small distributions. We first examine historical trajectories of trees during repeated climatic changes. Species that survived the Pliocene–Pleistocene transition and underwent the oscillations of glacial and interglacial periods were equipped with life history traits enhancing persistence and resilience. Evidence of their resilience also comes from the maintenance of large effective population sizes across time and rapid microevolutionary responses to recent climatic events. We then review genetic mechanisms and attributes shaping resilient responses. Usually, invoked constraints to resilience, such as genetic load or generation time and overlap, have limited consequences or are offset by positive impacts. Conversely, genetic plasticity, gene flow, introgression, genetic architecture of fitness‐related traits and demographic dynamics strengthen resilience by accelerating adaptive responses. Finally, we address the limitations of this review and highlight critical research gaps.
{"title":"‘Chimes of resilience’: what makes forest trees genetically resilient?","authors":"Antoine Kremer, Jun Chen, Martin Lascoux","doi":"10.1111/nph.70108","DOIUrl":"https://doi.org/10.1111/nph.70108","url":null,"abstract":"SummaryForest trees are foundation species of many ecosystems and are challenged by global environmental changes. We assemble genetic facts and arguments supporting or undermining resilient responses of forest trees to those changes. Genetic resilience is understood here as the capacity of a species to restore its adaptive potential following environmental changes and disturbances. Importantly, the data come primarily from European temperate tree species with large distributions and consider only marginally species with small distributions. We first examine historical trajectories of trees during repeated climatic changes. Species that survived the Pliocene–Pleistocene transition and underwent the oscillations of glacial and interglacial periods were equipped with life history traits enhancing persistence and resilience. Evidence of their resilience also comes from the maintenance of large effective population sizes across time and rapid microevolutionary responses to recent climatic events. We then review genetic mechanisms and attributes shaping resilient responses. Usually, invoked constraints to resilience, such as genetic load or generation time and overlap, have limited consequences or are offset by positive impacts. Conversely, genetic plasticity, gene flow, introgression, genetic architecture of fitness‐related traits and demographic dynamics strengthen resilience by accelerating adaptive responses. Finally, we address the limitations of this review and highlight critical research gaps.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"227 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789759","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}
Thomas Sibret, Marc Peaucelle, Kristine Y. Crous, Félicien Meunier, Marijn Bauters, David S. Ellsworth, Ivan A. Janssens, Pascal Boeckx, Hans Verbeeck
Understanding leaf photosynthetic traits and their variation in tropical forests is crucial for improving model predictions of forest productivity, and accurately representing the high functional diversity in these forests remains a challenge. Moreover, leaf photosynthesis data are lacking for the tropical forest of the Congo basin.
We observed photosynthetic, chemical and structural leaf traits of 24 woody species in a Congolese tropical forest and studied their variance across functional guilds, within-tree crown positions and overall canopy positions defined by their relative height within the canopy.
Guild and crown position jointly influenced leaf traits, with a significant effect observed (marginal R2 > 0.43). The traditional guild classification explained a significant portion of the observed interspecies variation, revealing a clear gradient from shade-tolerant to light-demanding species. Crown position significantly affected intraindividual leaf trait variability, with bottom crown leaves exhibiting trait values at least 19.3% lower than top leaves. Importantly, the linear relationship between relative canopy height and leaf traits emerged as a robust and continuous metric, effectively integrating both inter- and intraspecific variability.
We conclude that while guild-based classifications provide a useful framework for identifying plant functional groups, relative canopy height offers a robust and quantitative approach for capturing overall canopy trait variation, valuable for modeling canopy processes.
{"title":"Photosynthetic traits scale linearly with relative height within the canopy in an African tropical forest","authors":"Thomas Sibret, Marc Peaucelle, Kristine Y. Crous, Félicien Meunier, Marijn Bauters, David S. Ellsworth, Ivan A. Janssens, Pascal Boeckx, Hans Verbeeck","doi":"10.1111/nph.70076","DOIUrl":"https://doi.org/10.1111/nph.70076","url":null,"abstract":"<p>\u0000</p><ul>\u0000<li>Understanding leaf photosynthetic traits and their variation in tropical forests is crucial for improving model predictions of forest productivity, and accurately representing the high functional diversity in these forests remains a challenge. Moreover, leaf photosynthesis data are lacking for the tropical forest of the Congo basin.</li>\u0000<li>We observed photosynthetic, chemical and structural leaf traits of 24 woody species in a Congolese tropical forest and studied their variance across functional guilds, within-tree crown positions and overall canopy positions defined by their relative height within the canopy.</li>\u0000<li>Guild and crown position jointly influenced leaf traits, with a significant effect observed (marginal <i>R</i><sup>2</sup> > 0.43). The traditional guild classification explained a significant portion of the observed interspecies variation, revealing a clear gradient from shade-tolerant to light-demanding species. Crown position significantly affected intraindividual leaf trait variability, with bottom crown leaves exhibiting trait values at least 19.3% lower than top leaves. Importantly, the linear relationship between relative canopy height and leaf traits emerged as a robust and continuous metric, effectively integrating both inter- and intraspecific variability.</li>\u0000<li>We conclude that while guild-based classifications provide a useful framework for identifying plant functional groups, relative canopy height offers a robust and quantitative approach for capturing overall canopy trait variation, valuable for modeling canopy processes.</li>\u0000</ul><p></p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"58 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143798384","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}
Xiangrong Yang, Yaya Chen, Tianwu Zhang, Panhong Zhang, Zengpeng Guo, Li Huang, Guorui Hu, Hui Zhang, Miaojun Ma
SummaryPhenology is a sensitive indicator of plant responses to environmental changes, and its shifts could impact community structure and function. However, the effects of phenological shifts on community stability are poorly understood.We conducted a 4‐yr N enrichment and precipitation change experiment to assess their effects on community stability through phenological responses. To do so, we measured phenological duration and overlap (based on leaf‐out and flowering phenology of 55 species) in an alpine meadow on the Tibetan Plateau.N enrichment extended the vegetative stage of grasses, sedges, and community by 4.62, 4.72, and 11.74 d, respectively, but shortened that of forbs by 6.14 d and increased the overlap of flowering among individuals within the community. Meanwhile, N enrichment decreased species richness, asynchrony, and stability of sedges. Furthermore, N enrichment decreased community stability by decreasing asynchrony but was not associated with richness. Interestingly, N enrichment also decreased sedges stability by extending their vegetative stage and increasing the overlap of flowering, consequently reducing community stability.Our findings imply that N enrichment reduces phenological compensation and thus threatens grassland stability, which highlights the importance of phenological niches in understanding the maintenance of grassland stability under ongoing climate change.
{"title":"Plant phenology response to nitrogen addition decreases community biomass stability in an alpine meadow","authors":"Xiangrong Yang, Yaya Chen, Tianwu Zhang, Panhong Zhang, Zengpeng Guo, Li Huang, Guorui Hu, Hui Zhang, Miaojun Ma","doi":"10.1111/nph.70132","DOIUrl":"https://doi.org/10.1111/nph.70132","url":null,"abstract":"Summary<jats:list list-type=\"bullet\"> <jats:list-item>Phenology is a sensitive indicator of plant responses to environmental changes, and its shifts could impact community structure and function. However, the effects of phenological shifts on community stability are poorly understood.</jats:list-item> <jats:list-item>We conducted a 4‐yr N enrichment and precipitation change experiment to assess their effects on community stability through phenological responses. To do so, we measured phenological duration and overlap (based on leaf‐out and flowering phenology of 55 species) in an alpine meadow on the Tibetan Plateau.</jats:list-item> <jats:list-item>N enrichment extended the vegetative stage of grasses, sedges, and community by 4.62, 4.72, and 11.74 d, respectively, but shortened that of forbs by 6.14 d and increased the overlap of flowering among individuals within the community. Meanwhile, N enrichment decreased species richness, asynchrony, and stability of sedges. Furthermore, N enrichment decreased community stability by decreasing asynchrony but was not associated with richness. Interestingly, N enrichment also decreased sedges stability by extending their vegetative stage and increasing the overlap of flowering, consequently reducing community stability.</jats:list-item> <jats:list-item>Our findings imply that N enrichment reduces phenological compensation and thus threatens grassland stability, which highlights the importance of phenological niches in understanding the maintenance of grassland stability under ongoing climate change.</jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"37 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143784674","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}
Karolina Jörgensen, Karina E. Clemmensen, Petra Fransson, Stefano Manzoni, Håkan Wallander, Björn D. Lindahl
Trait spectra have been used in various branches of ecology to explain and predict patterns of species distributions. Several categorical and continuous traits have been proposed as relevant for ectomycorrhizal fungi, but a spectrum that unifies co-varying traits remains to be established and tested. Here, we propose a nitrogen acquisition and carbon use trait spectrum for ectomycorrhizal fungi in nitrogen-limited forests, which encompasses several morphological, physiological, and metabolic traits. Using a simple stoichiometric model, the trait spectrum is linked to the concept of apparent carbon use efficiency and resolves the contradiction that species with high supply of host carbon can maintain nitrogen transfer despite building large mycelial biomass. We suggest that ectomycorrhizal fungal species are distributed along this spectrum, with lifestyles ranging from ‘absorbers’ with a niche in high productive forests with high availability of soluble nitrogen to ‘miners’ with the ability to exploit organic matter in forests with low nitrogen availability. Further, we propose ways to test the outlined trait spectrum empirically.
{"title":"A trait spectrum linking nitrogen acquisition and carbon use of ectomycorrhizal fungi","authors":"Karolina Jörgensen, Karina E. Clemmensen, Petra Fransson, Stefano Manzoni, Håkan Wallander, Björn D. Lindahl","doi":"10.1111/nph.70129","DOIUrl":"https://doi.org/10.1111/nph.70129","url":null,"abstract":"Trait spectra have been used in various branches of ecology to explain and predict patterns of species distributions. Several categorical and continuous traits have been proposed as relevant for ectomycorrhizal fungi, but a spectrum that unifies co-varying traits remains to be established and tested. Here, we propose a nitrogen acquisition and carbon use trait spectrum for ectomycorrhizal fungi in nitrogen-limited forests, which encompasses several morphological, physiological, and metabolic traits. Using a simple stoichiometric model, the trait spectrum is linked to the concept of apparent carbon use efficiency and resolves the contradiction that species with high supply of host carbon can maintain nitrogen transfer despite building large mycelial biomass. We suggest that ectomycorrhizal fungal species are distributed along this spectrum, with lifestyles ranging from ‘absorbers’ with a niche in high productive forests with high availability of soluble nitrogen to ‘miners’ with the ability to exploit organic matter in forests with low nitrogen availability. Further, we propose ways to test the outlined trait spectrum empirically.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"1 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143784732","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}
Jie Cao, Qi Yang, Yaning Zhao, Shuya Tan, Shichun Li, Dawei Cheng, Ruxue Zhang, Murao Zhang, Zhonghai Li
SummaryLeaf senescence is a complex genetic process intricately regulated by multiple layers of control. Transcription factors, as master regulators of gene expression, play crucial roles in initiating and progressing leaf senescence.Through screening an activation‐tagged mutant library, we identified MYB47 as a negative regulator of leaf senescence. Constitutive or inducible overexpression of MYB47 significantly delays leaf senescence, while loss‐of‐function mutants exhibit accelerated senescence. Transcriptome analysis revealed a marked suppression of jasmonic acid (JA) signaling in MYB47 overexpression lines. Conversely, the myb47 mutants display elevated JA levels and reduced expression of JA catabolic genes, CYP94B3 and CYP94C1.Biochemical evidence demonstrated that MYB47 directly binds to the promoters of CYP94B3 and CYP94C1, upregulating their expression. Consequently, JA contents are significantly reduced in MYB47 overexpression lines. Overexpressing CYP94B3 or CYP94C1 in myb47 mutants alleviates their early senescence phenotype. Furthermore, JA induces MYB47 expression, forming a negative feedback loop (JA‐MYB47‐CYP94B3/C1‐JA) that fine‐tunes leaf senescence.Our findings reveal a novel regulatory module involving MYB47 and JA signaling that governs leaf senescence. By stimulating JA catabolism and attenuating JA signaling, MYB47 plays a crucial role in delaying leaf senescence.
{"title":"MYB47 delays leaf senescence by modulating jasmonate pathway via direct regulation of CYP94B3/CYP94C1 expression in Arabidopsis","authors":"Jie Cao, Qi Yang, Yaning Zhao, Shuya Tan, Shichun Li, Dawei Cheng, Ruxue Zhang, Murao Zhang, Zhonghai Li","doi":"10.1111/nph.70133","DOIUrl":"https://doi.org/10.1111/nph.70133","url":null,"abstract":"Summary<jats:list list-type=\"bullet\"> <jats:list-item>Leaf senescence is a complex genetic process intricately regulated by multiple layers of control. Transcription factors, as master regulators of gene expression, play crucial roles in initiating and progressing leaf senescence.</jats:list-item> <jats:list-item>Through screening an activation‐tagged mutant library, we identified MYB47 as a negative regulator of leaf senescence. Constitutive or inducible overexpression of <jats:italic>MYB47</jats:italic> significantly delays leaf senescence, while loss‐of‐function mutants exhibit accelerated senescence. Transcriptome analysis revealed a marked suppression of jasmonic acid (JA) signaling in <jats:italic>MYB47</jats:italic> overexpression lines. Conversely, the <jats:italic>myb47</jats:italic> mutants display elevated JA levels and reduced expression of JA catabolic genes, <jats:italic>CYP94B3</jats:italic> and <jats:italic>CYP94C1</jats:italic>.</jats:list-item> <jats:list-item>Biochemical evidence demonstrated that MYB47 directly binds to the promoters of <jats:italic>CYP94B3</jats:italic> and <jats:italic>CYP94C1</jats:italic>, upregulating their expression. Consequently, JA contents are significantly reduced in <jats:italic>MYB47</jats:italic> overexpression lines. Overexpressing <jats:italic>CYP94B3</jats:italic> or <jats:italic>CYP94C1</jats:italic> in <jats:italic>myb47</jats:italic> mutants alleviates their early senescence phenotype. Furthermore, JA induces <jats:italic>MYB47</jats:italic> expression, forming a negative feedback loop (JA‐MYB47‐CYP94B3/C1‐JA) that fine‐tunes leaf senescence.</jats:list-item> <jats:list-item>Our findings reveal a novel regulatory module involving MYB47 and JA signaling that governs leaf senescence. By stimulating JA catabolism and attenuating JA signaling, MYB47 plays a crucial role in delaying leaf senescence.</jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"20 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143784675","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}
SummaryPlant photosynthesis is highly responsive to fluctuations in environmental cues. To achieve optimal photosynthetic performance, plants must accurately regulate light absorption, maintaining a dynamic balance between energy supply and consumption in the field. Understanding the potential damage and imbalances caused by excessive light during photosynthesis necessitates a comprehensive insight into the protective role of non‐photochemical quenching (NPQ). This rapid photoprotective mechanism dissipates excess excitation energy as heat and is ubiquitous throughout the plant kingdom. Previous reviews have primarily focused on the regulation of NPQ amplitude, often overlooking its efficiency in photoprotection. This review outlines the significance, components, and mechanisms of NPQ, presenting fundamental equations that quantitatively describe both NPQ amplitude and its protective functions. I highlight the methodological approaches to quantify the NPQ levels necessary to prevent photoinactivation and photoinhibition, respectively. I conclude by identifying key open questions regarding NPQ and suggesting directions for future research.
{"title":"Non‐photochemical quenching (NPQ) in photoprotection: insights into NPQ levels required to avoid photoinactivation and photoinhibition","authors":"Guanqiang Zuo","doi":"10.1111/nph.70121","DOIUrl":"https://doi.org/10.1111/nph.70121","url":null,"abstract":"SummaryPlant photosynthesis is highly responsive to fluctuations in environmental cues. To achieve optimal photosynthetic performance, plants must accurately regulate light absorption, maintaining a dynamic balance between energy supply and consumption in the field. Understanding the potential damage and imbalances caused by excessive light during photosynthesis necessitates a comprehensive insight into the protective role of non‐photochemical quenching (NPQ). This rapid photoprotective mechanism dissipates excess excitation energy as heat and is ubiquitous throughout the plant kingdom. Previous reviews have primarily focused on the regulation of NPQ amplitude, often overlooking its efficiency in photoprotection. This review outlines the significance, components, and mechanisms of NPQ, presenting fundamental equations that quantitatively describe both NPQ amplitude and its protective functions. I highlight the methodological approaches to quantify the NPQ levels necessary to prevent photoinactivation and photoinhibition, respectively. I conclude by identifying key open questions regarding NPQ and suggesting directions for future research.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"183 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143782638","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}
François Orange, Sophie Pagnotta, Olivier Pierre, Janice de Almeida Engler
Plant-parasitic nematodes like root-knot nematodes (RKN; Meloidogyne spp.) cause great losses in agriculture by inducing root swellings, named galls, in host roots disturbing plant growth and development. Previous two-dimensional studies using different microscopy techniques revealed the presence of numerous nuclear clusters in nematode-induced giant cells within galls.
Here, we show in three dimensions (3D) that nuclear clustering occurring in giant cells is revealed to be much more complex, illustrating subclusters built of multiple nuclear lobes. These nuclear subclusters are unveiled to be interconnected and likely communicate via nucleotubes, highlighting the potential relevance of this nuclear transfer for disease. In addition, microtubules and microtubule organizing centers are profusely present between the densely packed nuclear lobes, suggesting that the cytoskeleton might be involved in anchoring nuclear clusters in giant cells.
This study illustrates that it is possible to apply volume electron microscopy (EM) approaches such as array tomography (AT) to roots infected by nematodes using basic equipment found in most EM facilities. The application of AT was valuable to observe the cellular ultrastructure in 3D, revealing the remarkable nuclear architecture of giant cells in the model host Arabidopsis thaliana.
The discovery of nucleotubes, as a unique component of nuclear clusters present in giant cells, can be potentially exploited as a novel strategy to develop alternative approaches for RKN control in crop species.
{"title":"Application of array tomography to elucidate nuclear clustering architecture in giant-feeding cells induced by root-knot nematodes","authors":"François Orange, Sophie Pagnotta, Olivier Pierre, Janice de Almeida Engler","doi":"10.1111/nph.70066","DOIUrl":"https://doi.org/10.1111/nph.70066","url":null,"abstract":"<p>\u0000</p><ul>\u0000<li>Plant-parasitic nematodes like root-knot nematodes (RKN; <i>Meloidogyne</i> spp.) cause great losses in agriculture by inducing root swellings, named galls, in host roots disturbing plant growth and development. Previous two-dimensional studies using different microscopy techniques revealed the presence of numerous nuclear clusters in nematode-induced giant cells within galls.</li>\u0000<li>Here, we show in three dimensions (3D) that nuclear clustering occurring in giant cells is revealed to be much more complex, illustrating subclusters built of multiple nuclear lobes. These nuclear subclusters are unveiled to be interconnected and likely communicate via nucleotubes, highlighting the potential relevance of this nuclear transfer for disease. In addition, microtubules and microtubule organizing centers are profusely present between the densely packed nuclear lobes, suggesting that the cytoskeleton might be involved in anchoring nuclear clusters in giant cells.</li>\u0000<li>This study illustrates that it is possible to apply volume electron microscopy (EM) approaches such as array tomography (AT) to roots infected by nematodes using basic equipment found in most EM facilities. The application of AT was valuable to observe the cellular ultrastructure in 3D, revealing the remarkable nuclear architecture of giant cells in the model host <i>Arabidopsis thaliana</i>.</li>\u0000<li>The discovery of nucleotubes, as a unique component of nuclear clusters present in giant cells, can be potentially exploited as a novel strategy to develop alternative approaches for RKN control in crop species.</li>\u0000</ul><p></p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"23 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143784730","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}
{"title":"Out of site, out of mind? Considering pesticide drift and plant mutualisms","authors":"Charlie C. Nicholson","doi":"10.1111/nph.70135","DOIUrl":"https://doi.org/10.1111/nph.70135","url":null,"abstract":"","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"29 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143782637","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}
<h2> Introduction</h2><p>The chloroplast genomic (i.e. plastomic) sequences have long been used for inferring phylogenetic relationships of green plants. Current major plant classifications (e.g. Angiosperm Phylogeny Group classification, APG IV, <span>2016</span>; Pteridophyte Phylogeny Group classification, PPG I, <span>2016</span>) are predominantly based on the plastid phylogenies (Stull <i>et al</i>., <span>2023</span>). Due to the rapid progress in DNA sequencing technologies along with decreasing costs, phylogenetic analyses using whole plastomes have become a routine practice (Wang <i>et al</i>., <span>2024</span>). Plastomes have been presumed to be single double-stranded circular DNA molecules that are inherited uniparentally, with maternal inheritance in most angiosperms and paternal inheritance in gymnosperms (Birky, <span>1995</span>; Dong <i>et al</i>., <span>2012</span>; Greiner <i>et al</i>., <span>2015</span>). These characteristics led to the general belief that plastomes are free from or less likely to undergo intermolecular recombination (Walker <i>et al</i>., <span>2019</span>). Therefore, different plastomic genes or regions, which are assumed to share the same evolutionary trajectory, are often concatenated directly for phylogenetic analyses (Jansen <i>et al</i>., <span>2007</span>; Moore <i>et al</i>., <span>2010</span>; Li <i>et al</i>., <span>2021</span>).</p><p>Despite the widespread use of plastomes in phylogenetics, both biparental inheritance and recombination of plastomes – processes that could inadvertently affect inference – have been increasingly detected. The mechanisms that maintain uniparental inheritance, including elimination or degradation of the organelle during male gametophyte development or after pollen mitosis or fertilization, may break down and lead to biparental inheritance (Nagata, <span>2010</span>). Biparental inheritance of plastomes has been reported in some plant groups, such as <i>Passiflora</i> (Passifloraceae; Hansen <i>et al</i>., <span>2007</span>; Shrestha <i>et al</i>., <span>2021</span>), <i>Cicer arietinum</i> (Fabaceae; Kumari <i>et al</i>., <span>2011</span>), and <i>Actinidia</i> (Actinidiaceae; Li <i>et al</i>., <span>2013</span>). It is believed that heteroplasmy, that is the mixture of different organelle genomes within a cell or individual, is widespread in both animals and plants (Nagata, <span>2010</span>; Ramsey & Mandel, <span>2019</span>; Camus <i>et al</i>., <span>2022</span>), and <i>c</i>. 20% of angiosperm genera may have undergone biparental inheritance (Zhang & Sodmergen., <span>2010</span>; Sakamoto & Takami, <span>2024</span>). The biparental inheritance allows the coexistence of both maternal and paternal plastids in the same offspring cell, creating opportunities for interplastomic recombination. Interspecific plastomic recombination has been created and detected in experimental studies (Medgyesy <i>et al</i>., <span>1985</span>). However, unlike in
{"title":"Sliding-window phylogenetic analyses uncover complex interplastomic recombination in the tropical Asian–American disjunct plant genus Hedyosmum (Chloranthaceae)","authors":"Peng-Wei Li, Yong-Bin Lu, Alexandre Antonelli, Zheng-Juan Zhu, Wei Wang, Xin-Mei Qin, Xue-Rong Yang, Qiang Zhang","doi":"10.1111/nph.70120","DOIUrl":"https://doi.org/10.1111/nph.70120","url":null,"abstract":"<h2> Introduction</h2>\u0000<p>The chloroplast genomic (i.e. plastomic) sequences have long been used for inferring phylogenetic relationships of green plants. Current major plant classifications (e.g. Angiosperm Phylogeny Group classification, APG IV, <span>2016</span>; Pteridophyte Phylogeny Group classification, PPG I, <span>2016</span>) are predominantly based on the plastid phylogenies (Stull <i>et al</i>., <span>2023</span>). Due to the rapid progress in DNA sequencing technologies along with decreasing costs, phylogenetic analyses using whole plastomes have become a routine practice (Wang <i>et al</i>., <span>2024</span>). Plastomes have been presumed to be single double-stranded circular DNA molecules that are inherited uniparentally, with maternal inheritance in most angiosperms and paternal inheritance in gymnosperms (Birky, <span>1995</span>; Dong <i>et al</i>., <span>2012</span>; Greiner <i>et al</i>., <span>2015</span>). These characteristics led to the general belief that plastomes are free from or less likely to undergo intermolecular recombination (Walker <i>et al</i>., <span>2019</span>). Therefore, different plastomic genes or regions, which are assumed to share the same evolutionary trajectory, are often concatenated directly for phylogenetic analyses (Jansen <i>et al</i>., <span>2007</span>; Moore <i>et al</i>., <span>2010</span>; Li <i>et al</i>., <span>2021</span>).</p>\u0000<p>Despite the widespread use of plastomes in phylogenetics, both biparental inheritance and recombination of plastomes – processes that could inadvertently affect inference – have been increasingly detected. The mechanisms that maintain uniparental inheritance, including elimination or degradation of the organelle during male gametophyte development or after pollen mitosis or fertilization, may break down and lead to biparental inheritance (Nagata, <span>2010</span>). Biparental inheritance of plastomes has been reported in some plant groups, such as <i>Passiflora</i> (Passifloraceae; Hansen <i>et al</i>., <span>2007</span>; Shrestha <i>et al</i>., <span>2021</span>), <i>Cicer arietinum</i> (Fabaceae; Kumari <i>et al</i>., <span>2011</span>), and <i>Actinidia</i> (Actinidiaceae; Li <i>et al</i>., <span>2013</span>). It is believed that heteroplasmy, that is the mixture of different organelle genomes within a cell or individual, is widespread in both animals and plants (Nagata, <span>2010</span>; Ramsey & Mandel, <span>2019</span>; Camus <i>et al</i>., <span>2022</span>), and <i>c</i>. 20% of angiosperm genera may have undergone biparental inheritance (Zhang & Sodmergen., <span>2010</span>; Sakamoto & Takami, <span>2024</span>). The biparental inheritance allows the coexistence of both maternal and paternal plastids in the same offspring cell, creating opportunities for interplastomic recombination. Interspecific plastomic recombination has been created and detected in experimental studies (Medgyesy <i>et al</i>., <span>1985</span>). However, unlike in","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"58 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143745309","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}
<h2> Introduction</h2><p>Rice (<i>Oryza sativa</i>) is a typical accumulating plant of silicon (Si), which is able to accumulate Si in the shoots up to 10% of dry weight (Ma & Takahashi, <span>2002</span>). This increase in accumulation is essential for high and stable production of rice (Tamai & Ma, <span>2008</span>). Silicon is actively absorbed by the roots in the form of silicic acid, a noncharged molecule (Ma & Takahashi, <span>2002</span>). After that, > 95% of Si absorbed is immediately translocated to the aboveground parts, including the leaf sheath and blade, and husk. In these tissues, silicic acid is polymerized to silica via transpiration, which is deposited beneath the cuticle of leaves and inside particular cells of leaf epidermis, forming silica cells and silica bodies or silica bulliform cells (motor cells; Ma & Takahashi, <span>2002</span>). This deposition forms a mechanical barrier, which is important in protecting the plants from various stresses, such as pathogens, insect pests, drought, high salinity, metal toxicity, lodging, and nutrient imbalance stresses (Ma & Takahashi, <span>2002</span>).</p><p>To transport Si from soil solution to different organs and tissues, different transporters involved in uptake, root-to-shoot translocation, and distribution, at least, are required. During the last two decades, transporters involved in different transport steps have been identified in rice (Huang & Ma, <span>2024</span>). In terms of uptake, two transporters, including OsLsi1 and OsLsi2, have been identified. OsLsi1 belongs to the Nod26-like major intrinsic protein (NIP) subfamily of aquaporin-like proteins and functions as an influx transporter of Si (Ma <i>et al</i>., <span>2006</span>), while OsLsi2 belongs to a putative anion transporter family without any similarity to OsLsi1 (Ma <i>et al</i>., <span>2007</span>) and functions as an efflux transporter of Si. Both OsLsi1 and OsLsi2 are localized at the exodermis and endodermis in the mature root regions but show different polar localization. OsLsi1 is localized at the distal side, while OsLsi2 is localized at the proximal side (Ma <i>et al</i>., <span>2006</span>; Yamaji & Ma, <span>2007</span>), forming an efficient uptake system for Si (Huang & Ma, <span>2024</span>). After uptake, Si as silicic acid is loaded into the root xylem by OsLsi3 (Huang <i>et al</i>., <span>2022</span>), while it is unloaded from the xylem by OsLsi6 (Yamaji <i>et al</i>., <span>2008</span>). OsLsi3, a homolog of OsLsi2, is localized at the root pericycle cells without polarity, while OsLsi6, a homolog of OsLsi1, is polarly localized at the adaxial side of the xylem parenchyma cells in leaf sheaths and leaf blades (Yamaji <i>et al</i>., <span>2008</span>). Finally, the preferential distribution of Si to the husk is mediated by three different Si transporters: OsLsi6, OsLsi2, and OsLsi3, which are highly expressed in the nodes, especially in the node I (Yamaji &
{"title":"Symplastic and apoplastic pathways for local distribution of silicon in rice leaves","authors":"Sheng Huang, Naoki Yamaji, Noriyuki Konishi, Namiki Mitani-Ueno, Jian Feng Ma","doi":"10.1111/nph.70110","DOIUrl":"https://doi.org/10.1111/nph.70110","url":null,"abstract":"<h2> Introduction</h2>\u0000<p>Rice (<i>Oryza sativa</i>) is a typical accumulating plant of silicon (Si), which is able to accumulate Si in the shoots up to 10% of dry weight (Ma & Takahashi, <span>2002</span>). This increase in accumulation is essential for high and stable production of rice (Tamai & Ma, <span>2008</span>). Silicon is actively absorbed by the roots in the form of silicic acid, a noncharged molecule (Ma & Takahashi, <span>2002</span>). After that, > 95% of Si absorbed is immediately translocated to the aboveground parts, including the leaf sheath and blade, and husk. In these tissues, silicic acid is polymerized to silica via transpiration, which is deposited beneath the cuticle of leaves and inside particular cells of leaf epidermis, forming silica cells and silica bodies or silica bulliform cells (motor cells; Ma & Takahashi, <span>2002</span>). This deposition forms a mechanical barrier, which is important in protecting the plants from various stresses, such as pathogens, insect pests, drought, high salinity, metal toxicity, lodging, and nutrient imbalance stresses (Ma & Takahashi, <span>2002</span>).</p>\u0000<p>To transport Si from soil solution to different organs and tissues, different transporters involved in uptake, root-to-shoot translocation, and distribution, at least, are required. During the last two decades, transporters involved in different transport steps have been identified in rice (Huang & Ma, <span>2024</span>). In terms of uptake, two transporters, including OsLsi1 and OsLsi2, have been identified. OsLsi1 belongs to the Nod26-like major intrinsic protein (NIP) subfamily of aquaporin-like proteins and functions as an influx transporter of Si (Ma <i>et al</i>., <span>2006</span>), while OsLsi2 belongs to a putative anion transporter family without any similarity to OsLsi1 (Ma <i>et al</i>., <span>2007</span>) and functions as an efflux transporter of Si. Both OsLsi1 and OsLsi2 are localized at the exodermis and endodermis in the mature root regions but show different polar localization. OsLsi1 is localized at the distal side, while OsLsi2 is localized at the proximal side (Ma <i>et al</i>., <span>2006</span>; Yamaji & Ma, <span>2007</span>), forming an efficient uptake system for Si (Huang & Ma, <span>2024</span>). After uptake, Si as silicic acid is loaded into the root xylem by OsLsi3 (Huang <i>et al</i>., <span>2022</span>), while it is unloaded from the xylem by OsLsi6 (Yamaji <i>et al</i>., <span>2008</span>). OsLsi3, a homolog of OsLsi2, is localized at the root pericycle cells without polarity, while OsLsi6, a homolog of OsLsi1, is polarly localized at the adaxial side of the xylem parenchyma cells in leaf sheaths and leaf blades (Yamaji <i>et al</i>., <span>2008</span>). Finally, the preferential distribution of Si to the husk is mediated by three different Si transporters: OsLsi6, OsLsi2, and OsLsi3, which are highly expressed in the nodes, especially in the node I (Yamaji &","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"20 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143745308","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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