New Phytologist最新文献

{"title":"Autophagy restricts tomato fruit ripening via a general role in ethylene repression","authors":"Girishkumar Kumaran, Pradeep Kumar Pathak, Ebenezer Quandoh, Jyoti Devi, Sergey Mursalimov, Sharon Alkalai-Tuvia, Jia Xuan Leong, Kyrylo Schenstnyi, Elena Levin, Suayib Üstün, Simon Michaeli","doi":"10.1111/nph.70127","DOIUrl":"10.1111/nph.70127","url":null,"abstract":"<p>Ripening involves complex biochemical and molecular reprogramming, resulting in color, texture, aroma, and flavor changes to attract humans and other animals (Giovannoni <i>et al</i>., <span>2017</span>). In climacteric fruits, this process is controlled by a myriad of phytohormones, predominantly ethylene (Li <i>et al</i>., <span>2021</span>; Huang <i>et al</i>., <span>2022</span>). To allow these changes, fruits constantly reshape their cellular proteome by fine-tuning protein degradation and synthesis (Szymanski <i>et al</i>., <span>2017</span>). While the ubiquitin–proteasome system was shown to be critical in ethylene signaling and ripening (Fenn & Giovannoni, <span>2021</span>; Jia <i>et al</i>., <span>2023</span>), knowledge of the impact of autophagy, another central degradation system, is rather limited.</p><p>Autophagy delivers cytosolic components to the vacuole for degradation and recycling. Double-membrane vesicles, termed autophagosomes, are generated around the cellular cargo destined for degradation. The autophagosome then fuses with the tonoplast to release a single membrane structure, termed autophagic body. Inside of the vacuole, the autophagic body degrades along with its cargo, and its constituents are recycled to replenish cellular energy. Autophagy is executed via the function of > 30 autophagy-related (ATG) proteins (Ding <i>et al</i>., <span>2018</span>; Marshall & Vierstra, <span>2018</span>). Notably, ATG proteins annotated with different numbers are not related and have distinct roles in autophagy. Among these, the ubiquitin-like ATG8 proteins are important for autophagosome biogenesis, fusion with the vacuole, and selective recognition of the cargo to be degraded. They are found conjugated either to phosphatidylethanolamine (PE) lipids (lipidated) or in a nonactive (nonlipidated) free form (Kellner <i>et al</i>., <span>2017</span>). The ATG8 family consists of nine members in <i>Arabidopsis thaliana</i> (<i>Arabidopsis</i>; AtATG8a to AtATG8i). When conjugated to a fluorescent protein, ATG8 family proteins are considered optimal markers for autophagy activity (or flux) assessment, as the stability of the fluorescent protein moiety allows for the estimation of the amount of autophagic material that was delivered to the vacuole. While assessing the ATG8 lipidation status (ATG8-PE : ATG8 ratio) provides a measure of autophagic membrane levels in the cytosol, it does not necessarily reflect autophagy activity (Qi <i>et al</i>., <span>2023</span>). Due to some level of redundancy (Del Chiaro <i>et al</i>., <span>2024</span>), <i>ATG8</i> family members are not used for functional analysis. Alternatively, the downregulation of other essential (and usually single-copy) <i>ATG</i> genes, such as <i>ATG2</i>, <i>ATG5</i>, or <i>ATG7</i>, each independently, can serve for functional analysis (Marshall & Vierstra, <span>2018</span>). Each of these genes has a critical role in autophagy, rendering the respective","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"246 6","pages":"2392-2404"},"PeriodicalIF":8.3,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.70127","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143931015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The OST1-HOS1-HAT1 module regulates cold response in Arabidopsis thaliana","authors":"Xinke Kang, Fan Wei, Shuli Chai, Sihan Peng, Bingyao Huang, Qing Han, Tianyue Zhao, Peiyi Zhang, Yuang Tian, Ran Xia, Honghui Lin, Dawei Zhang","doi":"10.1111/nph.70189","DOIUrl":"https://doi.org/10.1111/nph.70189","url":null,"abstract":"<p>\u0000</p><ul>\u0000<li>Plants have evolved sophisticated strategies to cope with various environmental stresses. Recent studies have provided insights into the mechanisms of rapid cold stress response through key components including OST1, ICE1, HOS1, and CBFs. However, the mechanisms by which plants modulate the intensity of their cold tolerance in response to fluctuating temperatures remain largely unexplored.</li>\u0000<li>In this study, we employed a multidisciplinary approach integrating molecular biology, plant physiology, and genetic methodologies to comprehensively decipher the molecular mechanisms by which HAT1 regulates cold stress responses in plants and further unraveled its cold-dependent posttranslational modification network.</li>\u0000<li>We found that under normal conditions, HAT1 acts as a repressor of cold-induced expression of <i>CBF</i> and <i>COR</i> genes, attenuating the cold response. When plants are exposed to cold stress, cold triggers OST1 to phosphorylate HAT1 and facilitates its interaction with HOS1, which subsequently induces ubiquitination and degradation of HAT1. This process alleviates repression of the <i>CBF</i> and <i>COR</i> genes by HAT1 and activates the cold stress response.</li>\u0000<li>Thus, our results reveal that HAT1 acts as a brake to prevent excessive cold stress response. The OST1-HOS1 module regulates HAT1 protein stability, allowing plants to dynamically balance growth and cold tolerance in response to environmental signals.</li>\u0000</ul><p></p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"36 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143927209","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":"Looking back to look ahead: the temporal dimension of conservation seed bank collections.","authors":"Efisio Mattana,Sandrine Godefroid,Stephanie Miles,Angelino Carta,Andreas Ensslin,Ted Chapman,Juan Viruel","doi":"10.1111/nph.70187","DOIUrl":"https://doi.org/10.1111/nph.70187","url":null,"abstract":"A wealth of plant material and data is stored globally in conservation seed banks. This material represents not only a repository of plant genetic resources but also an asset for nature-based solutions (NbS), such as ecological restoration and reforestation, and research in plant science. Here, we explore the temporal and spatial dimensions of seed collections and the challenges limiting their use in NbS and research, while highlighting how they could be a source of material for adaptation and evolution studies. However, existing seed lots originally collected for conservation purposes will not be sufficient to support NbS and research on their own. We propose a long-term experimental approach that, together with new targeted collecting programmes, can leverage the temporal dimension of seed collections by carrying out repeated sampling from the same population. At the same time, we stress how these approaches will benefit from new dedicated collections holding seeds from each maternal line separately. By moving towards a bidimensional (space and time) collecting approach, conservation seed banks can go beyond long-term conservation per se and transform their collections into dynamic repositories capable of addressing pressing ecological, evolutionary, and conservation questions and help to understand and shape plant communities of the future.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"39 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143914949","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":"Recent advances in proteomic workflows to interrogate the SUMOylome in plants.","authors":"Kishor D Ingole,Elizaveta Alekseeva,Kathryn S Lilley,Ari Sadanandom","doi":"10.1111/nph.70176","DOIUrl":"https://doi.org/10.1111/nph.70176","url":null,"abstract":"Protein posttranslational modifications (PTMs) are vital for regulating protein functions. SUMOylation, a PTM essential for plant survival, involves attaching a Small Ubiquitin-like MOdifier (SUMO) to lysine residues of target proteins. SUMOylation influences stress tolerance, cell proliferation, protein stability, and gene expression. While well studied in mammals and yeast, SUMOylation studies in plants are scarce, as the identification of SUMOylated proteins and the specific modification sites is challenging. Deciphering the plant SUMOylome is essential for understanding stress response mechanisms. Advanced proteomic techniques are necessary to map these complex protein modifications. This article offers insights into the workflows employed for probing the SUMOylome. We analyze how current technological approaches have advanced our understanding of SUMOylation and highlight limitations that currently impede comprehensive mapping of SUMO signaling pathways.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"2 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143914948","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":"Diversification of CLE expression patterns and nonmeristematic roles for CLAVATA receptor-like kinases in a moss.","authors":"Zoe Nemec-Venza,George R L Greiff,C Jill Harrison","doi":"10.1111/nph.70170","DOIUrl":"https://doi.org/10.1111/nph.70170","url":null,"abstract":"The CLAVATA pathway controls meristematic cell proliferation and multiple nonmeristematic processes in Arabidopsis development. While CLAVATA ancestrally regulates meristematic proliferation in nonseed plant gametophytes, ancestral sporophytic and nonmeristematic functions in land plants are unknown. Here, we analysed the promoter activities of all peptide (PpCLE) and receptor-encoding (PpCLV1a, PpCLV1b and PpRPK2) genes throughout the moss (Physcomitrium patens) life cycle and validated our expression analyses using mutant phenotype data. In gametophore apices, PpCLE3 expression marked apical cells, and PpCLV1b and PpRPK2 overlapped. In nonmeristematic tissues, gametophytes showed highly focal PpCLE but broader receptor-encoding gene expression, and many genes were co-expressed. Mutant phenotype analysis revealed roles for PpCLV1a, PpCLV1b and PpRPK2 in fertility and male and female reproductive development. In sporophytes, no PpCLE expression specifically marked the apical cells, and PpCLV1b and PpRPK2 expression initially marked distinct apical and basal domains, but later overlapped at the intercalary meristem. Overall, fewer genes were co-expressed in sporophytes than in gametophytes, but all genes were co-expressed in guard cells. Our data indicate that nonmeristematic CLAVATA functions in gametangium development and stomatal development may be ancestral within land plants. Peptide encoding (CLE) gene copy numbers amplified in mosses, and promoter evolution was a likely driver of cell type diversification during moss evolution.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"3 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143914950","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":"Protection of naringenin chalcone by a pathogenesis-related 10 protein promotes flavonoid biosynthesis in Marchantia polymorpha","authors":"Yanfei Zhou, Cyril Hamiaux, Christelle M. Andre, Janine M. Cooney, Kathy E. Schwinn, John W. van Klink, John L. Bowman, Kevin M. Davies, Nick W. Albert","doi":"10.1111/nph.70194","DOIUrl":"https://doi.org/10.1111/nph.70194","url":null,"abstract":"&lt;h2&gt; Introduction&lt;/h2&gt;\u0000&lt;p&gt;Flavonoid biosynthesis, a branch of the phenylpropanoid pathway, is a central specialised metabolite pathway of land plants. Flavonoids are key to how plants interact with the terrestrial environment, helping in tolerance of diverse abiotic stresses and attacks from pests and pathogens and providing pigmentation to flowers, fruit, seeds and vegetative tissues (Agati &amp; Tattini, &lt;span&gt;2010&lt;/span&gt;; Cheynier &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2013&lt;/span&gt;; Landi &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2015&lt;/span&gt;; Davies &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2018&lt;/span&gt;). The flavonoid pathway commences with the production of chalcones by the polyketide synthase (PKS) enzyme CHALCONE SYNTHASE (CHS). The subsequent pathway steps lead to diverse, distinct flavonoid classes, including flavones, flavonols, isoflavonoids, aurones, auronidins, anthocyanins and proanthocyanidins (condensed tannin). The core biosynthesis genes for the major flavonoid classes have been extensively characterized across many plant species (Yonekura-Sakakibara &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2019&lt;/span&gt;; Ferreyra &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2021&lt;/span&gt;; Davies &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2022&lt;/span&gt;). However, recent studies have brought to light possible important roles in flavonoid production for additional nonenzymatic proteins, the modes of action of which are generally not understood. The best studied is CHALCONE ISOMERASE-LIKE (CHIL), which is necessary for efficient flavonoid biosynthesis in diverse land plant lineages (Morita &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2014&lt;/span&gt;; Berland &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2019&lt;/span&gt;). CHIL can bind with and alter the specificity of CHS and at least some other PKS enzymes, notably STILBENE SYNTHASE (Waki &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2020&lt;/span&gt;). As the PKSs direct substrate flow into the alternative phenylpropanoid pathway sections, such as flavonoids, stilbenes, dihydrochalcones and bibenzyls, CHIL acts at a key biosynthetic step where enzyme specificity and efficacy are particularly important.&lt;/p&gt;\u0000&lt;p&gt;Relatively unexamined candidates for other nonenzymatic proteins involved in flavonoid biosynthesis are some members of the pathogenesis-related 10 (PR10) sub-class of pathogenesis-related proteins (PR proteins). Pathogenesis-related proteins represent diverse protein families, often with unknown functions, whose corresponding genes are induced in response to pathogen attacks, environmental stresses or certain physiological processes (van Loon, &lt;span&gt;1985&lt;/span&gt;). Following identification of PR10 in parsley (PcPR10 of &lt;i&gt;Petroselinum crispum&lt;/i&gt;; Somssich &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;1986&lt;/span&gt;) and as the major allergen present in birch pollen (Bet v1 of &lt;i&gt;Betula&lt;/i&gt; spp.; Breiteneder &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;1989&lt;/span&gt;), PR10 genes have been identified in various gymnosperm and angiosperm species (Liu &amp; Ekramoddoullah, &lt;span&gt;2006&lt;/span&gt;). Yet, no conserved role for PR10 family members has been identified, although they have commonly been linked to defence against pathogens (Park &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2004&lt;/span&gt;;","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"26 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143910860","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":"Many non‐native plant species are threatened in parts of their native range","authors":"Ingmar R. Staude, Matthias Grenié, Chris D. Thomas, Ingolf Kühn, Alexander Zizka, Marina Golivets, Sophie E. H. Ledger, Laura Méndez","doi":"10.1111/nph.70193","DOIUrl":"https://doi.org/10.1111/nph.70193","url":null,"abstract":"","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"15 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143910423","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":"Acclimation to white light in a far-red light specialist: insights from Acaryochloris marina MBIC11017","authors":"Thomas J. Oliver, Eduard Elias, Roberta Croce","doi":"10.1111/nph.70188","DOIUrl":"https://doi.org/10.1111/nph.70188","url":null,"abstract":"&lt;h2&gt; Introduction&lt;/h2&gt;\u0000&lt;p&gt;Oxygenic photosynthesis converts solar energy into chemical energy using two protein–pigment complexes, Photosystem I (PSI) and Photosystem II (PSII). In most oxygenic phototrophs, these photosystems use Chl&lt;i&gt;a&lt;/i&gt; as a light-harvesting pigment and a redox-active molecule, absorbing light and performing charge separation, so the photosystems can perform their catalytic functions. For many years, it was thought that this process was constrained by the energy of the first singlet excited state of Chl&lt;i&gt;a&lt;/i&gt;, a constraint widely known as the ‘red-limit’ (Bjorn &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2009&lt;/span&gt;). However, subsequent discoveries have unearthed oxygenic phototrophs that use different, red-shifted Chl molecules (Miyashita &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;1996&lt;/span&gt;; Chen &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2010&lt;/span&gt;; Gan &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2014&lt;/span&gt;; Antonaru &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2020&lt;/span&gt;), with less energy in their excited state, to catalyse the light reactions of oxygenic photosynthesis. The marine cyanobacterium &lt;i&gt;Acaryochloris marina&lt;/i&gt; is one among them. More than 90% of the Chls within &lt;i&gt;A. marina&lt;/i&gt; are Chl&lt;i&gt;d&lt;/i&gt; (Miyashita &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;1996&lt;/span&gt;, &lt;span&gt;1997&lt;/span&gt;), a pigment whose &lt;i&gt;Q&lt;/i&gt;&lt;sub&gt;Y&lt;/sub&gt; absorption maximum is red-shifted by &lt;i&gt;c&lt;/i&gt;. 30 nm, relative to Chl&lt;i&gt;a&lt;/i&gt;. The near ubiquity of Chl&lt;i&gt;d&lt;/i&gt; in &lt;i&gt;A. marina&lt;/i&gt; means that the cyanobacterium is well-suited to living in shaded environments, in which visible light is filtered and far-red light (FRL, 700–800 nm) is abundant (Kuhl &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2005&lt;/span&gt;). Strains of &lt;i&gt;A. marina&lt;/i&gt; have been found in a variety of shaded marine environments, including the underside of ascidians (Kuhl &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2005&lt;/span&gt;; Lopez-Legentil &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2011&lt;/span&gt;; Ohkubo &amp; Miyashita, &lt;span&gt;2012&lt;/span&gt;) and within stromatolites (Johnson &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2022&lt;/span&gt;).&lt;/p&gt;\u0000&lt;p&gt;The red-shifted nature of Chl&lt;i&gt;d&lt;/i&gt; results in a &lt;i&gt;c&lt;/i&gt;. 100-meV loss of energy in its excited state compared with that of Chl&lt;i&gt;a&lt;/i&gt;. Therefore, to efficiently make use of Chl&lt;i&gt;d&lt;/i&gt;, the photosynthetic machinery of &lt;i&gt;A. marina&lt;/i&gt; differs from that found in Chl&lt;i&gt;a&lt;/i&gt;-containing phototrophs (Elias &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;). Differences are found in both its light-harvesting antenna and its photosystems. Both PSI and PSII in &lt;i&gt;A. marina&lt;/i&gt; use Chl&lt;i&gt;d&lt;/i&gt; as their primary donors, which has implications for their ability to perform their catalytic chemistry. The primary donor of PSI, the Chl&lt;i&gt;d&lt;/i&gt;/Chl&lt;i&gt;d&lt;/i&gt;′ dimer, &lt;i&gt;P&lt;/i&gt;&lt;sub&gt;740&lt;/sub&gt;, is red-shifted by 40 nm compared with that of the &lt;i&gt;P&lt;/i&gt;&lt;sub&gt;700&lt;/sub&gt; dimer found in Chl&lt;i&gt;a&lt;/i&gt;-containing PSI of most cyanobacteria and plants (Hu &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;1998&lt;/span&gt;). However, the midpoint potential of the &lt;i&gt;P&lt;/i&gt;&lt;sub&gt;740&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;/&lt;i&gt;P&lt;/i&gt;&lt;sub&gt;740&lt;/sub&gt; couple (425–440 mV) is essentially identical to that of the &lt;i&gt;P&lt;/i&gt;&lt;sub&gt;700&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;/&lt;i&gt;P&lt;/i&gt;&lt;sub&gt;700&lt;/sub&gt; couple (Bail","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"53 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143910862","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":"Multiple transitions to high l-DOPA 4,5-dioxygenase activity reveal molecular pathways to convergent betalain pigmentation in Caryophyllales","authors":"Nathanael Walker-Hale, M. Alejandra Guerrero-Rubio, Samuel F. Brockington","doi":"10.1111/nph.70177","DOIUrl":"https://doi.org/10.1111/nph.70177","url":null,"abstract":"&lt;h2&gt; Introduction&lt;/h2&gt;\u0000&lt;p&gt;Life is replete with examples of similar traits that have evolved in disparate lineages through convergent evolution (Losos, &lt;span&gt;2011&lt;/span&gt;; Foote &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2015&lt;/span&gt;; Heyduk &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2019&lt;/span&gt;). Widespread phenotypic convergence has been interpreted either as evidence that evolution responds predictably to similar selection pressures, or that evolution is highly constrained in the generation of new variation, or a combination of the two (Losos, &lt;span&gt;2011&lt;/span&gt;). Convergence can therefore be interpreted as evidence of adaptation but also as the result of chance variation which is then fixed by drift (Stayton, &lt;span&gt;2008&lt;/span&gt;, &lt;span&gt;2015&lt;/span&gt;). Investigating the molecular basis of phenotypic convergence offers a powerful framework for exploring the variation and processes driving the iterative evolution of phenotypes (Zhang &amp; Kumar, &lt;span&gt;1997&lt;/span&gt;; Foote &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2015&lt;/span&gt;; Sackton &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2019&lt;/span&gt;). Even distantly related lineages can reuse homologous variation in the evolution of convergent traits, via the reoccurrence of identical or similar mutations, or through different mutations with comparable effects in homologous loci (Christin &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2010&lt;/span&gt;; Stern, &lt;span&gt;2013&lt;/span&gt;; Storz, &lt;span&gt;2016&lt;/span&gt;). By contrast, other studies have revealed convergent phenotypes with a divergent genetic basis, suggesting that either molecular convergence or divergence can be involved in the evolution of convergent traits, or a combination of the two (Hoekstra &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2006&lt;/span&gt;; Natarajan &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2016&lt;/span&gt;; Van Belleghem &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2023&lt;/span&gt;).&lt;/p&gt;\u0000&lt;p&gt;Multiple methods have been deployed to distinguish convergence at the molecular level. One approach uses ancestral sequence reconstruction to search for repeated amino acid substitutions at homologous sites, between lineages with convergent phenotypes (Zhang &amp; Kumar, &lt;span&gt;1997&lt;/span&gt;; Castoe &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2009&lt;/span&gt;; Foote &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2015&lt;/span&gt;). Ancestral sequence reconstruction infers all substitutions between parent and descendant states, with repeated amino-acid substitutions at the same site categorized according to the amino-acid identity of the parent and descendant states: convergent (if identical descendent states result from parent states that are different), parallel (if identical descendent states result from parent states that are the same), and divergent (if repeated substitutions in the same site result in different descendent states) (Zhang &amp; Kumar, &lt;span&gt;1997&lt;/span&gt;; Castoe &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2009&lt;/span&gt;). Meanwhile, alternative model-based methods have sought to relax the constraint of amino acid identity to infer adaptive convergence, acknowledging that different states might have similar fitness in the environments of convergent phenotypes (Tamuri &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2009&lt;/span&gt;; Parto &amp; Lartillot, &lt;span","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"15 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143910859","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":"Wild Cicer species exhibit superior leaf photosynthetic phosphorus- and water-use efficiencies compared with cultivated chickpea under low-phosphorus conditions","authors":"Jiayin Pang, Simiao Li, Ulrike Mathesius, Jens Berger, Weina Zhang, Komal D. Sawant, Rajeev K. Varshney, Kadambot H. M. Siddique, Hans Lambers","doi":"10.1111/nph.70185","DOIUrl":"https://doi.org/10.1111/nph.70185","url":null,"abstract":"&lt;h2&gt; Introduction&lt;/h2&gt;\u0000&lt;p&gt;Chickpea (&lt;i&gt;Cicer arietinum&lt;/i&gt;) is a vital legume crop for food and feed in developing countries (Foyer &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2016&lt;/span&gt;). However, domestication has significantly narrowed its genetic diversity (Abbo &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2003&lt;/span&gt;; Varshney &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2013&lt;/span&gt;, &lt;span&gt;2021&lt;/span&gt;; Marques &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2020&lt;/span&gt;; Khan &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;). To address this limitation, the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) developed a chickpea reference set of 300 accessions from 29 countries, representing diverse genetic backgrounds (Upadhyaya &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2008&lt;/span&gt;). Studies on this set revealed significant genotypic variation in plant growth, shoot phosphorus (P) content, physiological P-use efficiency (PUE), leaf photosynthetic characteristics, photosynthetic PUE (PPUE), root morphology, carboxylate exudation, and arbuscular mycorrhizal fungal colonisation (Pang &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2018a&lt;/span&gt;,&lt;span&gt;b&lt;/span&gt;, &lt;span&gt;2023&lt;/span&gt;; Wen &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2020&lt;/span&gt;, &lt;span&gt;2022&lt;/span&gt;). However, this reference set included only seven wild &lt;i&gt;Cicer&lt;/i&gt; accessions due to the limited global collections available at the time (Berger &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2003&lt;/span&gt;; Coyne &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2020&lt;/span&gt;). Wild species are typically genetically much more diverse than their domesticated counterparts due to the domestication bottleneck (Tanksley &amp; McCouch, &lt;span&gt;1997&lt;/span&gt;; Purugganan &amp; Fuller, &lt;span&gt;2009&lt;/span&gt;). While crops are weak competitors in managed systems that minimize stress, wild progenitors such as wild &lt;i&gt;Cicer&lt;/i&gt; thrive in unregulated low-fertility environments (Renzi &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2022&lt;/span&gt;). Therefore, screening wild germplasm for nutrient acquisition capacity is crucial. Recent international collaborations have expanded wild &lt;i&gt;Cicer&lt;/i&gt; collections (von Wettberg &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2018&lt;/span&gt;), enabling exploration of their genetic diversity for abiotic stress tolerance, including low P availability.&lt;/p&gt;\u0000&lt;p&gt;&lt;i&gt;Cicer reticulatum&lt;/i&gt;, the primary gene pool of cultivated chickpea, is fully compatible with domesticated &lt;i&gt;C. arietinum&lt;/i&gt; (Coyne &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2020&lt;/span&gt;). The secondary gene pool, &lt;i&gt;C. echinospermum&lt;/i&gt;, exhibits variable compatibility with cultivated chickpea depending on the population (Kahraman &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2017&lt;/span&gt;). Both wild species are restricted to south-eastern Anatolia, Türkiye, where they inhabit distinct ecological niches shaped by diverse soil substrates and a steep elevational gradient exceeding 1000 m (von Wettberg &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2018&lt;/span&gt;). Therefore, localized adaptation underscores their potential for broadening the genetic base of chickpea and introducing adaptive traits lost during domestication (Croser &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2003&lt;/span&gt;; von Wettberg &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2018&lt;/span&gt;).&lt;/p&gt;\u0000&lt;p&gt;Recent studies have explored wild &lt;i&gt;Cicer&lt;/i&gt; sp","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"5 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143910861","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}