Drew A. Larson, Margaret E. Staton, Beant Kapoor, Nurul Islam-Faridi, Tetyana Zhebentyayeva, Shenghua Fan, Jozsef Stork, Austin Thomas, Alaa S. Ahmed, Elizabeth C. Stanton, Allan Houston, Scott E. Schlarbaum, Matthew W. Hahn, John E. Carlson, Albert G. Abbott, Seth DeBolt, C. Dana Nelson
<h2> Introduction</h2> <p>Oaks (<i>Quercus</i> spp.) are important members of ecosystems throughout much of the world (Kremer & Hipp, <span>2020</span>). In eastern North America, white oak (<i>Quercus alba</i>) is a keystone species and is one of the most abundant forest trees across much of its range (Rogers, <span>1990</span>; Fralish, <span>2004</span>). In addition to its ecological and cultural importance (Abrams, <span>2003</span>; Bocsi <i>et al</i>., <span>2021a</span>,<span>b</span>; Stringer & Morris, <span>2022</span>), white oak has significant economic importance, including a number of high-value timber applications and as the primary species used to cooper barrels for aging distilled spirits (Stringer & Morris, <span>2022</span>; Dhungel <i>et al</i>., <span>2023</span>). However, few studies have addressed the genomic diversity of <i>Q. alba</i>, and a lack of available genetic and genomic resources currently presents barriers to furthering the understanding of white oak biology and evolutionary history.</p> <p><i>Quercus</i> (Fagaceae) comprises <i>c</i>. 500 species, often divided into two subgenera: <i>Cerris</i> and <i>Quercus</i> (Hipp <i>et al</i>., <span>2020</span>). The latter is typically further divided into the white oaks (section <i>Quercus</i>), to which <i>Q. alba</i> belongs, and the red oaks (section <i>Lobatae</i>). The phylogeny of oaks has been the focus of several recent studies utilizing reduced representation genome sequencing (Sork <i>et al</i>., <span>2016</span>; Hipp <i>et al</i>., <span>2020</span>; Manos & Hipp, <span>2021</span>), which have clarified some relationships within section <i>Quercus</i>. However, phylogenetic inference in oaks is likely complicated by the suggested prevalence of hybridization and introgression in the group (e.g. McVay <i>et al</i>., <span>2017</span>; Lazic <i>et al</i>., <span>2021</span>).</p> <p>The first published oak genome was that of <i>Quercus robur</i> L. (Plomion <i>et al</i>., <span>2016a</span>), the pedunculate oak, which is common throughout western Eurasia. To date, there have been at least 11 <i>Quercus</i> species with published chromosome-scale genomes, including four annotated genomes from the white oak clade (Plomion <i>et al</i>., <span>2016a</span>; Ai <i>et al</i>., <span>2022</span>; Han <i>et al</i>., <span>2022</span>; Liu <i>et al</i>., <span>2022</span>, <span>2024</span>; Sork <i>et al</i>., <span>2022</span>; Zhou <i>et al</i>., <span>2022</span>; Kapoor <i>et al</i>., <span>2023</span>; L. Wang <i>et al</i>., <span>2023</span>; W. Wang <i>et al</i>., <span>2023</span>). This growing number of annotated genomes allows for comparative analyses of gene content and inferences of genome evolution across the oak phylogeny.</p> <p>Disease resistance-related genes (R genes) have been a focus of genomic studies on oaks and other tree species because of their central role in plant immunity to pathogens (Plomion <i>et al</i>., <span>201
{"title":"A haplotype-resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks","authors":"Drew A. Larson, Margaret E. Staton, Beant Kapoor, Nurul Islam-Faridi, Tetyana Zhebentyayeva, Shenghua Fan, Jozsef Stork, Austin Thomas, Alaa S. Ahmed, Elizabeth C. Stanton, Allan Houston, Scott E. Schlarbaum, Matthew W. Hahn, John E. Carlson, Albert G. Abbott, Seth DeBolt, C. Dana Nelson","doi":"10.1111/nph.20463","DOIUrl":"https://doi.org/10.1111/nph.20463","url":null,"abstract":"<h2> Introduction</h2>\u0000<p>Oaks (<i>Quercus</i> spp.) are important members of ecosystems throughout much of the world (Kremer & Hipp, <span>2020</span>). In eastern North America, white oak (<i>Quercus alba</i>) is a keystone species and is one of the most abundant forest trees across much of its range (Rogers, <span>1990</span>; Fralish, <span>2004</span>). In addition to its ecological and cultural importance (Abrams, <span>2003</span>; Bocsi <i>et al</i>., <span>2021a</span>,<span>b</span>; Stringer & Morris, <span>2022</span>), white oak has significant economic importance, including a number of high-value timber applications and as the primary species used to cooper barrels for aging distilled spirits (Stringer & Morris, <span>2022</span>; Dhungel <i>et al</i>., <span>2023</span>). However, few studies have addressed the genomic diversity of <i>Q. alba</i>, and a lack of available genetic and genomic resources currently presents barriers to furthering the understanding of white oak biology and evolutionary history.</p>\u0000<p><i>Quercus</i> (Fagaceae) comprises <i>c</i>. 500 species, often divided into two subgenera: <i>Cerris</i> and <i>Quercus</i> (Hipp <i>et al</i>., <span>2020</span>). The latter is typically further divided into the white oaks (section <i>Quercus</i>), to which <i>Q. alba</i> belongs, and the red oaks (section <i>Lobatae</i>). The phylogeny of oaks has been the focus of several recent studies utilizing reduced representation genome sequencing (Sork <i>et al</i>., <span>2016</span>; Hipp <i>et al</i>., <span>2020</span>; Manos & Hipp, <span>2021</span>), which have clarified some relationships within section <i>Quercus</i>. However, phylogenetic inference in oaks is likely complicated by the suggested prevalence of hybridization and introgression in the group (e.g. McVay <i>et al</i>., <span>2017</span>; Lazic <i>et al</i>., <span>2021</span>).</p>\u0000<p>The first published oak genome was that of <i>Quercus robur</i> L. (Plomion <i>et al</i>., <span>2016a</span>), the pedunculate oak, which is common throughout western Eurasia. To date, there have been at least 11 <i>Quercus</i> species with published chromosome-scale genomes, including four annotated genomes from the white oak clade (Plomion <i>et al</i>., <span>2016a</span>; Ai <i>et al</i>., <span>2022</span>; Han <i>et al</i>., <span>2022</span>; Liu <i>et al</i>., <span>2022</span>, <span>2024</span>; Sork <i>et al</i>., <span>2022</span>; Zhou <i>et al</i>., <span>2022</span>; Kapoor <i>et al</i>., <span>2023</span>; L. Wang <i>et al</i>., <span>2023</span>; W. Wang <i>et al</i>., <span>2023</span>). This growing number of annotated genomes allows for comparative analyses of gene content and inferences of genome evolution across the oak phylogeny.</p>\u0000<p>Disease resistance-related genes (R genes) have been a focus of genomic studies on oaks and other tree species because of their central role in plant immunity to pathogens (Plomion <i>et al</i>., <span>201","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"37 6 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385824","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}
Wilhelm H. A. Osterman, James G. Hagan, Jeannette Whitton, Anne D. Bjorkman
The relationship between polyploid formation, triploid fitness and plant reproduction has been studied for over a century, and uniparental reproduction has long been recognized to play a crucial role in polyploid establishment. Yet, we lack a synthesized framework of how polyploid establishment is expected to be influenced by different reproductive modes among angiosperms. Here, we provide new perspectives on how uniparental reproduction, pollination ecology, triploid fitness and assortative mating can impact minority cytotype exclusion (MCE) and, thereby, the likelihood of polyploid establishment. We review the current state of knowledge of the reproductive mechanisms that impact polyploid establishment and discuss often overlooked aspects of these processes, such as the influence of pollinator communities on rates of self-pollination. We propose a framework for considering how variation in reproductive strategies and pollinator communities can impact the ability of a polyploid to overcome MCE. Finally, we propose links between patterns of variation in uniparental reproduction across plant communities and observed patterns in the distribution and abundance of polyploids.
{"title":"The ecology of polyploid establishment and exclusion, with implications for polyploid biogeography","authors":"Wilhelm H. A. Osterman, James G. Hagan, Jeannette Whitton, Anne D. Bjorkman","doi":"10.1111/nph.20451","DOIUrl":"https://doi.org/10.1111/nph.20451","url":null,"abstract":"The relationship between polyploid formation, triploid fitness and plant reproduction has been studied for over a century, and uniparental reproduction has long been recognized to play a crucial role in polyploid establishment. Yet, we lack a synthesized framework of how polyploid establishment is expected to be influenced by different reproductive modes among angiosperms. Here, we provide new perspectives on how uniparental reproduction, pollination ecology, triploid fitness and assortative mating can impact minority cytotype exclusion (MCE) and, thereby, the likelihood of polyploid establishment. We review the current state of knowledge of the reproductive mechanisms that impact polyploid establishment and discuss often overlooked aspects of these processes, such as the influence of pollinator communities on rates of self-pollination. We propose a framework for considering how variation in reproductive strategies and pollinator communities can impact the ability of a polyploid to overcome MCE. Finally, we propose links between patterns of variation in uniparental reproduction across plant communities and observed patterns in the distribution and abundance of polyploids.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"41 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375334","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}
Jonathan Levins, Łukasz Paukszto, Katarzyna Krawczyk, Mateusz Maździarz, Billie C. Arch, D. Christine Cargill, Eduardo Flores-Sandoval, Joanna Szablińska-Piernik, Paweł Sulima, Monika Szczecińska, Samarth Kulshrestha, Kevin M. Davies, Jakub Sawicki, John L. Bowman
<h2> Introduction</h2> <p>Organismal complexity is correlated with transcription factor (TF) diversity, and the origin of new TFs is often associated with developmental or physiological innovations (Lang <i>et al</i>., <span>2010</span>; Weirauch & Hughes, <span>2011</span>; Mendoza <i>et al</i>., <span>2013</span>; Catarino <i>et al</i>., <span>2016</span>; Wilhelmsson <i>et al</i>., <span>2017</span>). Conversely, the loss of transcription factor (TF) genes or <i>cis</i>-regulatory sequences through which TFs act has been correlated with the loss of developmental or physiological traits, a process commonly referred to as regressive evolution. For example, parallel reductions in vision have occurred among cave-dwelling animals (e.g. Jeffery, <span>2009</span>; Langille <i>et al</i>., <span>2022</span>), hindlimbs have been lost independently in snakes and cetaceans (e.g. Cohn & Tickle, <span>1999</span>; Thewissen <i>et al</i>., <span>2006</span>), and similar parallel reductions are observed in the ability of land plants to support mycorrhizal fungal interactions (e.g. Delaux <i>et al</i>., <span>2014</span>; Favre <i>et al</i>., <span>2014</span>; Bravo <i>et al</i>., <span>2016</span>). Many cases of regressive evolution have been correlated with the loss of regulatory sequences or losses of genes. For example, a characteristic suite of genes, including key TFs controlling the process, have been lost in species that no longer have the ability to form mycorrhizal fungal interactions (Delaux <i>et al</i>., <span>2014</span>; Favre <i>et al</i>., <span>2014</span>; Bravo <i>et al</i>., <span>2016</span>).</p> <p>Among the Marchantiopsida, a liverwort clade includes the complex thalloid liverworts (Crandall-Stotler <i>et al</i>., <span>2009</span>), by far the most speciose genus is <i>Riccia</i>, with well over 200 species (Schuster, <span>1992</span>; Cargill <i>et al</i>., <span>2016</span>). Phylogenetically, <i>Riccia</i> is nested within the other Marchantiopsida (Forrest <i>et al</i>., <span>2006</span>; He-Nygrén <i>et al</i>., <span>2006</span>; Villarreal <i>et al</i>., <span>2016</span>), lending support to Goebel's idea that the <i>Riccia</i> are highly reduced from a more complex Marchantiopsida ancestor (Goebel, <span>1930</span>). For example, oil bodies, a synapomorphy of liverworts, are lacking in <i>Riccia</i> gametophytes (Müller, <span>1939</span>; Jovet-Ast, <span>1986</span>). In contrast to the ancestral and majority of extant liverworts that are dioicous, most <i>Riccia</i> species are monoicous. The <i>Riccia</i> sporophyte is dramatically reduced, lacking an elaborate foot, seta elongation, any specialized mechanism for capsule rupture and elaters, all of which are ancestral characters in liverworts and the Marchantiopsida, with the latter three characters all linked to spore dispersal. Thus, in <i>Riccia</i>, the mature sporophyte is embedded in the gametophytic thallus (cleistocarpy), and spores are released on
{"title":"Evolution of sexual systems and regressive evolution in Riccia","authors":"Jonathan Levins, Łukasz Paukszto, Katarzyna Krawczyk, Mateusz Maździarz, Billie C. Arch, D. Christine Cargill, Eduardo Flores-Sandoval, Joanna Szablińska-Piernik, Paweł Sulima, Monika Szczecińska, Samarth Kulshrestha, Kevin M. Davies, Jakub Sawicki, John L. Bowman","doi":"10.1111/nph.20454","DOIUrl":"https://doi.org/10.1111/nph.20454","url":null,"abstract":"<h2> Introduction</h2>\u0000<p>Organismal complexity is correlated with transcription factor (TF) diversity, and the origin of new TFs is often associated with developmental or physiological innovations (Lang <i>et al</i>., <span>2010</span>; Weirauch & Hughes, <span>2011</span>; Mendoza <i>et al</i>., <span>2013</span>; Catarino <i>et al</i>., <span>2016</span>; Wilhelmsson <i>et al</i>., <span>2017</span>). Conversely, the loss of transcription factor (TF) genes or <i>cis</i>-regulatory sequences through which TFs act has been correlated with the loss of developmental or physiological traits, a process commonly referred to as regressive evolution. For example, parallel reductions in vision have occurred among cave-dwelling animals (e.g. Jeffery, <span>2009</span>; Langille <i>et al</i>., <span>2022</span>), hindlimbs have been lost independently in snakes and cetaceans (e.g. Cohn & Tickle, <span>1999</span>; Thewissen <i>et al</i>., <span>2006</span>), and similar parallel reductions are observed in the ability of land plants to support mycorrhizal fungal interactions (e.g. Delaux <i>et al</i>., <span>2014</span>; Favre <i>et al</i>., <span>2014</span>; Bravo <i>et al</i>., <span>2016</span>). Many cases of regressive evolution have been correlated with the loss of regulatory sequences or losses of genes. For example, a characteristic suite of genes, including key TFs controlling the process, have been lost in species that no longer have the ability to form mycorrhizal fungal interactions (Delaux <i>et al</i>., <span>2014</span>; Favre <i>et al</i>., <span>2014</span>; Bravo <i>et al</i>., <span>2016</span>).</p>\u0000<p>Among the Marchantiopsida, a liverwort clade includes the complex thalloid liverworts (Crandall-Stotler <i>et al</i>., <span>2009</span>), by far the most speciose genus is <i>Riccia</i>, with well over 200 species (Schuster, <span>1992</span>; Cargill <i>et al</i>., <span>2016</span>). Phylogenetically, <i>Riccia</i> is nested within the other Marchantiopsida (Forrest <i>et al</i>., <span>2006</span>; He-Nygrén <i>et al</i>., <span>2006</span>; Villarreal <i>et al</i>., <span>2016</span>), lending support to Goebel's idea that the <i>Riccia</i> are highly reduced from a more complex Marchantiopsida ancestor (Goebel, <span>1930</span>). For example, oil bodies, a synapomorphy of liverworts, are lacking in <i>Riccia</i> gametophytes (Müller, <span>1939</span>; Jovet-Ast, <span>1986</span>). In contrast to the ancestral and majority of extant liverworts that are dioicous, most <i>Riccia</i> species are monoicous. The <i>Riccia</i> sporophyte is dramatically reduced, lacking an elaborate foot, seta elongation, any specialized mechanism for capsule rupture and elaters, all of which are ancestral characters in liverworts and the Marchantiopsida, with the latter three characters all linked to spore dispersal. Thus, in <i>Riccia</i>, the mature sporophyte is embedded in the gametophytic thallus (cleistocarpy), and spores are released on","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"26 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375335","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}
<p>Although membrane-localized transport proteins can be easily identified in sequence datasets based on homology, their functional characterization remains a significant challenge. A key obstacle lies in the broad substrate specificity observed within transporter protein families, which complicates functional predictions based solely on sequence data (Thomas & Tampé, <span>2020</span>). Furthermore, the inherent instability and consequent loss of activity of these proteins upon isolation from membranes hinders their purification and <i>in vitro</i> analysis (Hardy <i>et al</i>., <span>2016</span>). As a result, functional annotations for these proteins often remain incomplete, as exemplified by the limited number of transporters explicitly associated with lignification. The first transporter identified in this context was ABCG29 in Arabidopsis, which mediates the transport of <i>p</i>-coumaryl alcohol (Alejandro <i>et al</i>., <span>2012</span>). More recently, the coniferyl alcohol transporters ABCG15 in bamboo (Li <i>et al</i>., <span>2024</span>) and ABCG36 in spruce (Sun <i>et al</i>., <span>2024</span>) have been characterized, with the latter also facilitating the transport of sinapyl alcohol.</p> <div> <blockquote><p>‘The dual capacity of these transporters to mitigate precursor toxicity while modulating lignin composition may indicate that lignification evolved as a detoxification strategy’</p> <div></div> </blockquote> </div> <p>To identify novel monolignol transporters, in a paper recently published in <i>New Phytologist</i>, Zhou <i>et al</i>. (<span>2024</span>; doi: 10.1111/nph.20325) refined the research focus by capitalizing on the structurally simple lignin synthesized in the seed coat of spider flower (<i>Cleome hassleriana</i>), an ornamental plant native to South America. This lignin is known as catechyl or C-lignin and is uniquely composed of units derived from caffeyl alcohol (Chen <i>et al</i>., <span>2012</span>; Fig. 1). By targeting tissues that produce this homopolymeric lignin, the authors hypothesized that genes coding for transporters specific to C-lignin biosynthesis would exhibit heightened expression in the seed coat, enabling their identification against the more complex background of heteropolymeric lignin-related transporters in other tissues. Integration of transcriptomic and proteomic data facilitated the identification of six candidate transporters potentially required for substrate delivery for C-lignin. These candidates underwent functional validation through yeast transport assays to evaluate their role in mediating the transmembrane movement of lignin precursors. Among the candidates, two transporters, ChSTP8 and ChSUC1, exhibited activity with caffeyl alcohol but not with the classical monolignols (i.e. <i>p</i>-coumaryl, coniferyl and sinapyl alcohol). Homology modeling and molecular docking analyses further elucidated the specificity of these transporters, revealing interactions between two conser
{"title":"Study of spider flower C-lignin reveals two novel monolignol transporters","authors":"Caroline Van Beirs, Bartel Vanholme","doi":"10.1111/nph.20447","DOIUrl":"https://doi.org/10.1111/nph.20447","url":null,"abstract":"<p>Although membrane-localized transport proteins can be easily identified in sequence datasets based on homology, their functional characterization remains a significant challenge. A key obstacle lies in the broad substrate specificity observed within transporter protein families, which complicates functional predictions based solely on sequence data (Thomas & Tampé, <span>2020</span>). Furthermore, the inherent instability and consequent loss of activity of these proteins upon isolation from membranes hinders their purification and <i>in vitro</i> analysis (Hardy <i>et al</i>., <span>2016</span>). As a result, functional annotations for these proteins often remain incomplete, as exemplified by the limited number of transporters explicitly associated with lignification. The first transporter identified in this context was ABCG29 in Arabidopsis, which mediates the transport of <i>p</i>-coumaryl alcohol (Alejandro <i>et al</i>., <span>2012</span>). More recently, the coniferyl alcohol transporters ABCG15 in bamboo (Li <i>et al</i>., <span>2024</span>) and ABCG36 in spruce (Sun <i>et al</i>., <span>2024</span>) have been characterized, with the latter also facilitating the transport of sinapyl alcohol.</p>\u0000<div>\u0000<blockquote><p>‘The dual capacity of these transporters to mitigate precursor toxicity while modulating lignin composition may indicate that lignification evolved as a detoxification strategy’</p>\u0000<div></div>\u0000</blockquote>\u0000</div>\u0000<p>To identify novel monolignol transporters, in a paper recently published in <i>New Phytologist</i>, Zhou <i>et al</i>. (<span>2024</span>; doi: 10.1111/nph.20325) refined the research focus by capitalizing on the structurally simple lignin synthesized in the seed coat of spider flower (<i>Cleome hassleriana</i>), an ornamental plant native to South America. This lignin is known as catechyl or C-lignin and is uniquely composed of units derived from caffeyl alcohol (Chen <i>et al</i>., <span>2012</span>; Fig. 1). By targeting tissues that produce this homopolymeric lignin, the authors hypothesized that genes coding for transporters specific to C-lignin biosynthesis would exhibit heightened expression in the seed coat, enabling their identification against the more complex background of heteropolymeric lignin-related transporters in other tissues. Integration of transcriptomic and proteomic data facilitated the identification of six candidate transporters potentially required for substrate delivery for C-lignin. These candidates underwent functional validation through yeast transport assays to evaluate their role in mediating the transmembrane movement of lignin precursors. Among the candidates, two transporters, ChSTP8 and ChSUC1, exhibited activity with caffeyl alcohol but not with the classical monolignols (i.e. <i>p</i>-coumaryl, coniferyl and sinapyl alcohol). Homology modeling and molecular docking analyses further elucidated the specificity of these transporters, revealing interactions between two conser","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"29 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375299","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}
High native species diversity generally suppresses non-native invasions, but many ecosystems are now characterized by non-native assemblages that vary in species diversity. How this non-native species diversity affects subsequent invaders and its environmental dependence remain unclear.
We conducted a plant–soil feedback experiment. In the conditioning phase, we created three diversity levels (1, 2, or 4 species) using six non-native species to condition the soil. In the responding phase, we planted these six species individually with soil inocula and exposed them to two watering treatments (well-watered vs drought).
Under well-watered conditions, the non-native biomass increased with soil inocula generated by different non-native diversity. This biomass pattern was mainly related to arbuscular mycorrhizal fungal richness which increased with non-native species diversity. However, under drought conditions, the non-native biomass did not depend on soil inocula generated by non-native diversity.
Our results reveal the crucial role of soil microbial legacies in driving the positive diversity–invasibility relationships of non-native communities and drought stress can eliminate these positive relationships. These findings provide an explanation for the commonly observed co-occurrence of multiple non-native species in nature, predicting an accelerating accumulation of non-native species in a benign environment, but not in a stressed environment.
{"title":"Soil microbial legacies and drought mediate diversity–invasibility relationships in non-native communities","authors":"Jiahui Yi, Zhibin Tao, Kaoping Zhang, Baoguo Nie, Evan Siemann, Wei Huang","doi":"10.1111/nph.20462","DOIUrl":"https://doi.org/10.1111/nph.20462","url":null,"abstract":"<p>\u0000</p><ul>\u0000<li>High native species diversity generally suppresses non-native invasions, but many ecosystems are now characterized by non-native assemblages that vary in species diversity. How this non-native species diversity affects subsequent invaders and its environmental dependence remain unclear.</li>\u0000<li>We conducted a plant–soil feedback experiment. In the conditioning phase, we created three diversity levels (1, 2, or 4 species) using six non-native species to condition the soil. In the responding phase, we planted these six species individually with soil inocula and exposed them to two watering treatments (well-watered vs drought).</li>\u0000<li>Under well-watered conditions, the non-native biomass increased with soil inocula generated by different non-native diversity. This biomass pattern was mainly related to arbuscular mycorrhizal fungal richness which increased with non-native species diversity. However, under drought conditions, the non-native biomass did not depend on soil inocula generated by non-native diversity.</li>\u0000<li>Our results reveal the crucial role of soil microbial legacies in driving the positive diversity–invasibility relationships of non-native communities and drought stress can eliminate these positive relationships. These findings provide an explanation for the commonly observed co-occurrence of multiple non-native species in nature, predicting an accelerating accumulation of non-native species in a benign environment, but not in a stressed environment.</li>\u0000</ul><p></p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"44 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375336","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}
SummaryMitochondria support plant growth and adaptation via energy production and signaling pathways. However, how mitochondria control the transition between growth and stress response is largely unknown in plants.Using molecular approaches, we identified the histone H3K4me3 demethylase JMJ15 and the transcription factor CRF6 as targets of SnRK1 in Arabidopsis. By analyzing antimycin A (AA)–triggered mitochondrial stress, we explored how SnRK1, JMJ15, and CRF6 form a regulatory module that gauges mitochondrial status to balance growth and the oxidative stress response.SnRK1a1, a catalytic α‐subunit of SnRK1, phosphorylates and destabilizes JMJ15 to inhibit its H3K4me3 demethylase activity. While SnRK1a1 does not phosphorylate CRF6, it promotes its degradation via the proteasome pathway. CRF6 interacts with JMJ15 and prevents its SnRK1a1 phosphorylation‐dependent degradation, forming an antagonistic feedback loop. SnRK1a1, JMJ15, and CRF6 are required for transcriptional reprogramming in response to AA stress. The transcriptome profiles of jmj15 and crf6 mutants were highly correlated with those of plants overexpressing SnRK1a1 under both normal and AA stress conditions. Genetic analysis revealed that CRF6 acts downstream of SnRK1 and JMJ15.Our findings identify the SnRK1‐JMJ15‐CRF6 module that integrates energy and mitochondrial signaling for the growth–defense trade‐off, highlighting an epigenetic mechanism underlying mitonuclear communication.
{"title":"The SnRK1‐JMJ15‐CRF6 module integrates energy and mitochondrial signaling to balance growth and the oxidative stress response in Arabidopsis","authors":"Yanming Zhao, Xinying Wang, Qianyan Lei, Xiaoyan Zhang, Yubei Wang, Huijia Ji, Chongyang Ma, Pengcheng Wang, Chun‐Peng Song, Xiaohong Zhu","doi":"10.1111/nph.20425","DOIUrl":"https://doi.org/10.1111/nph.20425","url":null,"abstract":"Summary<jats:list list-type=\"bullet\"> <jats:list-item>Mitochondria support plant growth and adaptation via energy production and signaling pathways. However, how mitochondria control the transition between growth and stress response is largely unknown in plants.</jats:list-item> <jats:list-item>Using molecular approaches, we identified the histone H3K4me3 demethylase JMJ15 and the transcription factor CRF6 as targets of SnRK1 in Arabidopsis. By analyzing antimycin A (AA)–triggered mitochondrial stress, we explored how SnRK1, JMJ15, and CRF6 form a regulatory module that gauges mitochondrial status to balance growth and the oxidative stress response.</jats:list-item> <jats:list-item>SnRK1a1, a catalytic α‐subunit of SnRK1, phosphorylates and destabilizes JMJ15 to inhibit its H3K4me3 demethylase activity. While SnRK1a1 does not phosphorylate CRF6, it promotes its degradation via the proteasome pathway. CRF6 interacts with JMJ15 and prevents its SnRK1a1 phosphorylation‐dependent degradation, forming an antagonistic feedback loop. SnRK1a1, JMJ15, and CRF6 are required for transcriptional reprogramming in response to AA stress. The transcriptome profiles of <jats:italic>jmj15</jats:italic> and <jats:italic>crf6</jats:italic> mutants were highly correlated with those of plants overexpressing <jats:italic>SnRK1a1</jats:italic> under both normal and AA stress conditions. Genetic analysis revealed that CRF6 acts downstream of SnRK1 and JMJ15.</jats:list-item> <jats:list-item>Our findings identify the SnRK1‐JMJ15‐CRF6 module that integrates energy and mitochondrial signaling for the growth–defense trade‐off, highlighting an epigenetic mechanism underlying mitonuclear communication.</jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"14 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143192104","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}
Seeds are the main dispersal and propagation units of angiosperms. Examining the relative allocation of seed reserves by quantifying the relative embryo size (ES) at dispersal (i.e. size of the embryo relative to the seed) across angiosperms, sets the basis to track the evolutionary history of this key reproductive trait related to germination timing and offspring survival.
We used a robust, dated phylogeny and sampling of ES for selected species across most angiosperm families to model the macroevolution of ES. Data on ES were collated from living specimens and primary literature.
Early angiosperms typically had a low ES, which is still reflected in contemporary magnoliids and ANA-grade species. The analysis of major evolutionary shifts in ES throughout angiosperm phylogeny revealed that these shifts were predominantly associated with the formation of the main angiosperm lineages. The tempo and mode of ES evolution were not constant over angiosperm history, paralleling major paleo-events.
This study provides crucial new insights in seed trait evolution, which contribute to understanding the diversification of reproductive strategies in angiosperms.
{"title":"Major shifts in embryo size occurred early in the evolutionary history of angiosperms","authors":"Filip Vandelook, Angelino Carta","doi":"10.1111/nph.20445","DOIUrl":"https://doi.org/10.1111/nph.20445","url":null,"abstract":"<p>\u0000</p><ul>\u0000<li>Seeds are the main dispersal and propagation units of angiosperms. Examining the relative allocation of seed reserves by quantifying the relative embryo size (ES) at dispersal (i.e. size of the embryo relative to the seed) across angiosperms, sets the basis to track the evolutionary history of this key reproductive trait related to germination timing and offspring survival.</li>\u0000<li>We used a robust, dated phylogeny and sampling of ES for selected species across most angiosperm families to model the macroevolution of ES. Data on ES were collated from living specimens and primary literature.</li>\u0000<li>Early angiosperms typically had a low ES, which is still reflected in contemporary magnoliids and ANA-grade species. The analysis of major evolutionary shifts in ES throughout angiosperm phylogeny revealed that these shifts were predominantly associated with the formation of the main angiosperm lineages. The tempo and mode of ES evolution were not constant over angiosperm history, paralleling major paleo-events.</li>\u0000<li>This study provides crucial new insights in seed trait evolution, which contribute to understanding the diversification of reproductive strategies in angiosperms.</li>\u0000</ul><p></p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"8 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083545","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}
Jessie A. Pelosi, Elissa S. Sorojsrisom, William Brad Barbazuk, Emily B. Sessa
How asexually reproducing organisms maintain genetic diversity and adaptive potential is a long-standing question in evolutionary biology. Asexual lineages have historically been thought of as evolutionary dead ends, yet some exhibit remarkable persistence through time.
The gametophyte-only fern Vittaria appalachiana is a clonal eukaryote, the focus of extensive study due to its peculiar habit and life history, and is an excellent system to explore the consequences of asexuality. Using reduced representation sequencing and life cycle simulations, we assess theoretical expectations for genomic consequences of long-term asexual reproduction and test hypotheses about its origin and demographic history.
We show that V. appalachiana colonies are not patches of single genotypes but are mosaics of genetic diversity, and the accumulation of mutations in the absence of recombination plays an important role in driving this diversity. We identify increased genomic variation, excess heterozygosity, decreased population differentiation, and increased effective population size, all of which are consistent with the expectations for prolonged clonality. Our analyses support the hypothesis that the loss of sexual reproduction in V. appalachiana occurred during the Last Glacial Maximum.
Our results from empirical and simulation-based analyses illuminate how an asexual eukaryote generates, retains, and partitions genomic diversity.
{"title":"Population genomics of the gametophyte-only fern Vittaria appalachiana provides insights into clonal plant evolution","authors":"Jessie A. Pelosi, Elissa S. Sorojsrisom, William Brad Barbazuk, Emily B. Sessa","doi":"10.1111/nph.20433","DOIUrl":"https://doi.org/10.1111/nph.20433","url":null,"abstract":"<p>\u0000</p><ul>\u0000<li>How asexually reproducing organisms maintain genetic diversity and adaptive potential is a long-standing question in evolutionary biology. Asexual lineages have historically been thought of as evolutionary dead ends, yet some exhibit remarkable persistence through time.</li>\u0000<li>The gametophyte-only fern <i>Vittaria appalachiana</i> is a clonal eukaryote, the focus of extensive study due to its peculiar habit and life history, and is an excellent system to explore the consequences of asexuality. Using reduced representation sequencing and life cycle simulations, we assess theoretical expectations for genomic consequences of long-term asexual reproduction and test hypotheses about its origin and demographic history.</li>\u0000<li>We show that <i>V. appalachiana</i> colonies are not patches of single genotypes but are mosaics of genetic diversity, and the accumulation of mutations in the absence of recombination plays an important role in driving this diversity. We identify increased genomic variation, excess heterozygosity, decreased population differentiation, and increased effective population size, all of which are consistent with the expectations for prolonged clonality. Our analyses support the hypothesis that the loss of sexual reproduction in <i>V. appalachiana</i> occurred during the Last Glacial Maximum.</li>\u0000<li>Our results from empirical and simulation-based analyses illuminate how an asexual eukaryote generates, retains, and partitions genomic diversity.</li>\u0000</ul><p></p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"37 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143084093","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}
Long-Can Mei, Fan Wang, Xin-He Yu, Li-Jun Chen, Jun-Hao Ma, Yu-Ting Xiang, Hong-Yan Lin, Guang-Fu Yang
<h2> Introduction</h2> <p>4-Hydroxyphenylpyruvate dioxygenase (HPPD) represents a pivotal enzyme in the metabolic processes of plants, exerting a decisive influence on the catabolism of the amino acid tyrosine. It is located within the plastids of plant cells, where it functions as a catalyst for the conversion of 4-hydroxyphenylpyruvate to homogentisate (HGA; Raspail <i>et al</i>., <span>2011</span>). This reaction represents the initial committed step in the biosynthetic pathway that culminates in the formation of plastoquinone and tocopherols (Ren <i>et al</i>., <span>2011</span>). These compounds are indispensable for the optimal functioning of photosynthesis and the protection of plants from oxidative stress. Given its pivotal function in these processes, the regulation of HPPD is rigorously controlled at the transcriptional, posttranscriptional, and posttranslational levels. The HPPD protein has become the subject of extensive research, with the aim of understanding its structure and function, its regulation in different plant species, and its evolutionary history. Furthermore, studies on HPPD contribute to the broader understanding of plant physiology, particularly with regard to the mechanisms of stress tolerance (Ji <i>et al</i>., <span>2016</span>; Frelin <i>et al</i>., <span>2017</span>), the regulation of secondary metabolism (Dreesen <i>et al</i>., <span>2018</span>; Y. Yang <i>et al</i>., <span>2024</span>), and the interplay between metabolic pathways that are essential for plant growth and survival (Diaz-Tielas <i>et al</i>., <span>2019</span>). Overall, HPPD represents a vital node in plant metabolic networks, with implications ranging from basic botanical research to practical applications in crop management and improvement.</p> <p>In recent years, research on the role of HPPD in plant metabolism and physiology has seen a notable expansion (Concepcion <i>et al</i>., <span>2021</span>; Kim <i>et al</i>., <span>2021</span>; Park <i>et al</i>., <span>2022</span>; Wang <i>et al</i>., <span>2025</span>). For example, the CRISPR-Cas9-mediated gene editing of the <i>Os</i>HPPD 3′ UTR resulted in the creation of new rice lines exhibiting resistance to HPPD-inhibiting herbicides (Wu <i>et al</i>., <span>2023</span>). A fluorescent biosensor targeting HPPD was developed for noninvasive and real-time imaging of plant abiotic stress responses, thereby facilitating the detection of HPPD expression in plants under various stresses, including drought, salinity, and extreme temperatures (Fu <i>et al</i>., <span>2022</span>). An efficient germline-specific evolution system was employed to generate herbicide-resistant HPPD variants, which could be utilized in crop breeding (Wang <i>et al</i>., <span>2024</span>). Despite recent advances, challenges remain in understanding the molecular mechanisms underlying HPPD in plant stress tolerance, as well as in developing artificial evolution and functional interpretation of HPPD. A specialized database o
{"title":"HTD: a targetome database for plant physiology and regulation in HPPD family","authors":"Long-Can Mei, Fan Wang, Xin-He Yu, Li-Jun Chen, Jun-Hao Ma, Yu-Ting Xiang, Hong-Yan Lin, Guang-Fu Yang","doi":"10.1111/nph.20439","DOIUrl":"https://doi.org/10.1111/nph.20439","url":null,"abstract":"<h2> Introduction</h2>\u0000<p>4-Hydroxyphenylpyruvate dioxygenase (HPPD) represents a pivotal enzyme in the metabolic processes of plants, exerting a decisive influence on the catabolism of the amino acid tyrosine. It is located within the plastids of plant cells, where it functions as a catalyst for the conversion of 4-hydroxyphenylpyruvate to homogentisate (HGA; Raspail <i>et al</i>., <span>2011</span>). This reaction represents the initial committed step in the biosynthetic pathway that culminates in the formation of plastoquinone and tocopherols (Ren <i>et al</i>., <span>2011</span>). These compounds are indispensable for the optimal functioning of photosynthesis and the protection of plants from oxidative stress. Given its pivotal function in these processes, the regulation of HPPD is rigorously controlled at the transcriptional, posttranscriptional, and posttranslational levels. The HPPD protein has become the subject of extensive research, with the aim of understanding its structure and function, its regulation in different plant species, and its evolutionary history. Furthermore, studies on HPPD contribute to the broader understanding of plant physiology, particularly with regard to the mechanisms of stress tolerance (Ji <i>et al</i>., <span>2016</span>; Frelin <i>et al</i>., <span>2017</span>), the regulation of secondary metabolism (Dreesen <i>et al</i>., <span>2018</span>; Y. Yang <i>et al</i>., <span>2024</span>), and the interplay between metabolic pathways that are essential for plant growth and survival (Diaz-Tielas <i>et al</i>., <span>2019</span>). Overall, HPPD represents a vital node in plant metabolic networks, with implications ranging from basic botanical research to practical applications in crop management and improvement.</p>\u0000<p>In recent years, research on the role of HPPD in plant metabolism and physiology has seen a notable expansion (Concepcion <i>et al</i>., <span>2021</span>; Kim <i>et al</i>., <span>2021</span>; Park <i>et al</i>., <span>2022</span>; Wang <i>et al</i>., <span>2025</span>). For example, the CRISPR-Cas9-mediated gene editing of the <i>Os</i>HPPD 3′ UTR resulted in the creation of new rice lines exhibiting resistance to HPPD-inhibiting herbicides (Wu <i>et al</i>., <span>2023</span>). A fluorescent biosensor targeting HPPD was developed for noninvasive and real-time imaging of plant abiotic stress responses, thereby facilitating the detection of HPPD expression in plants under various stresses, including drought, salinity, and extreme temperatures (Fu <i>et al</i>., <span>2022</span>). An efficient germline-specific evolution system was employed to generate herbicide-resistant HPPD variants, which could be utilized in crop breeding (Wang <i>et al</i>., <span>2024</span>). Despite recent advances, challenges remain in understanding the molecular mechanisms underlying HPPD in plant stress tolerance, as well as in developing artificial evolution and functional interpretation of HPPD. A specialized database o","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"1 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077384","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}
Si Jing, Han Zhang, Zidan Yang, Xin-Qiao Du, Yingying Hu, Shao-Shuai Wang, Shuwei Wang, Kaina Zhang, Zhen Li, Wei-Hua Wu, Jörg Kudla, Jigang Li, Yi Wang
Diurnal light–dark cycles regulate nutrient uptake and transport; however, the underlying molecular mechanisms remain largely unknown.
Transcription factor MYB59 and ion transporter NPF7.3 participate in root-to-shoot K+/NO3− translocation in Arabidopsis. In this study, transcriptional analyses and western blotting experiments revealed the diurnal expression of the MYB59-NPF7.3 module. ChIP-qPCR and EMSA showed that transcription factors HY5 and PIF directly bind to the MYB59 promoter. Phenotype analyses and ion content measurement indicated that HY5 and PIF antagonistically control root-to-shoot K+/NO3− translocation through the MYB59-NPF7.3 module.
We found HY5 proteins accumulate in roots and repress MYB59 transcription during daytime, while PIF proteins promote MYB59 transcription in the dark. The expression levels of the NPF7.3 transcript and protein are gradually decreased during daytime, but increased at night. The enhancement of K+/NO3− loading into the xylem mediated by NPF7.3 could increase root pressure at night, which maintained the root-to-shoot water/nutrient translocation.
This study reveals a synergistic mechanism between light signaling and nutrient transport in plants, and defines a diurnal molecular switch of driving forces for root-to-shoot water/nutrient translocation.
{"title":"Alternating inverse modulation of xylem K+/NO3− loading by HY5 and PIF facilitates diurnal regulation of root-to-shoot water and nutrient transport","authors":"Si Jing, Han Zhang, Zidan Yang, Xin-Qiao Du, Yingying Hu, Shao-Shuai Wang, Shuwei Wang, Kaina Zhang, Zhen Li, Wei-Hua Wu, Jörg Kudla, Jigang Li, Yi Wang","doi":"10.1111/nph.20319","DOIUrl":"https://doi.org/10.1111/nph.20319","url":null,"abstract":"<p>\u0000</p><ul>\u0000<li>Diurnal light–dark cycles regulate nutrient uptake and transport; however, the underlying molecular mechanisms remain largely unknown.</li>\u0000<li>Transcription factor MYB59 and ion transporter NPF7.3 participate in root-to-shoot K<sup>+</sup>/NO<sub>3</sub><sup>−</sup> translocation in <i>Arabidopsis</i>. In this study, transcriptional analyses and western blotting experiments revealed the diurnal expression of the <i>MYB59</i>-<i>NPF7.3</i> module. ChIP-qPCR and EMSA showed that transcription factors HY5 and PIF directly bind to the <i>MYB59</i> promoter. Phenotype analyses and ion content measurement indicated that HY5 and PIF antagonistically control root-to-shoot K<sup>+</sup>/NO<sub>3</sub><sup>−</sup> translocation through the <i>MYB59</i>-<i>NPF7.3</i> module.</li>\u0000<li>We found HY5 proteins accumulate in roots and repress <i>MYB59</i> transcription during daytime, while PIF proteins promote <i>MYB59</i> transcription in the dark. The expression levels of the <i>NPF7.3</i> transcript and protein are gradually decreased during daytime, but increased at night. The enhancement of K<sup>+</sup>/NO<sub>3</sub><sup>−</sup> loading into the xylem mediated by NPF7.3 could increase root pressure at night, which maintained the root-to-shoot water/nutrient translocation.</li>\u0000<li>This study reveals a synergistic mechanism between light signaling and nutrient transport in plants, and defines a diurnal molecular switch of driving forces for root-to-shoot water/nutrient translocation.</li>\u0000</ul><p></p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"37 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076900","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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