New Phytologist最新文献

{"title":"Decline of seagrass (Posidonia oceanica) production over two decades in the face of warming of the Eastern Mediterranean Sea","authors":"Victoria Litsi-Mizan,&nbsp;Pavlos T. Efthymiadis,&nbsp;Vasilis Gerakaris,&nbsp;Oscar Serrano,&nbsp;Manolis Tsapakis,&nbsp;Eugenia T. Apostolaki","doi":"10.1111/nph.19084","DOIUrl":"https://doi.org/10.1111/nph.19084","url":null,"abstract":"<p>\u0000 </p>","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":"239 6","pages":"2126-2137"},"PeriodicalIF":9.4,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.19084","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5880933","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":"A vacuolar transporter plays important roles in zinc and cadmium accumulation in rice grain","authors":"Min Ning,&nbsp;Shi Jia Liu,&nbsp;Fenglin Deng,&nbsp;Liyu Huang,&nbsp;Hu Li,&nbsp;Jing Che,&nbsp;Naoki Yamaji,&nbsp;Fengyi Hu,&nbsp;Gui Jie Lei","doi":"10.1111/nph.19070","DOIUrl":"https://doi.org/10.1111/nph.19070","url":null,"abstract":"<div>\u0000 \u0000 <p>\u0000 \u0000 </p><ul>\u0000 \u0000 \u0000 <li>Rice grain is a poor dietary source of zinc (Zn) but the primary source of cadmium (Cd) for humans; however, the molecular mechanisms for their accumulation in rice grain remain incompletely understood.</li>\u0000 \u0000 \u0000 <li>This study functionally characterized a tonoplast-localized transporter, OsMTP1. <i>OsMTP1</i> was preferentially expressed in the roots, aleurone layer, and embryo of seeds. <i>OsMTP1</i> knockout decreased Zn concentration in the root cell sap, roots, aleurone layer and embryo, and subsequently increased Zn concentration in shoots and polished rice (endosperm) without yield penalty. <i>OsMTP1</i> haplotype analysis revealed elite alleles associated with increased Zn level in polished rice, mostly because of the decreased <i>OsMTP1</i> transcripts.</li>\u0000 \u0000 \u0000 <li><i>OsMTP1</i> expression in yeast enhanced Zn tolerance but did not affect that of Cd. While <i>OsMTP1</i> knockout resulted in decreased uptake, translocation and accumulation of Cd in plant and rice grain, which could be attributed to the indirect effects of altered Zn accumulation.</li>\u0000 \u0000 \u0000 <li>Our results suggest that rice OsMTP1 primarily functions as a tonoplast-localized transporter for sequestrating Zn into vacuole. <i>OsMTP1</i> knockout elevated Zn concentration but prevented Cd deposition in polished rice without yield penalty. Thus, <i>OsMTP1</i> is a candidate gene for enhancing Zn level and reducing Cd level in rice grains.</li>\u0000 </ul>\u0000 \u0000 </div>","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":"239 5","pages":"1919-1934"},"PeriodicalIF":9.4,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5824645","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":"Harnessing herbaria to advance plant phenology research under global change","authors":"Kai Zhu,&nbsp;Yiluan Song","doi":"10.1111/nph.19088","DOIUrl":"https://doi.org/10.1111/nph.19088","url":null,"abstract":"<p>Phenology, which refers to the timing of recurring biological events, is rapidly shifting under global change and has thus been a central topic in ecology. In an article published in this issue of <i>New Phytologist</i>, Park <i>et al</i>. (<span>2023</span>; 2153–2165) compiled a large phenological dataset comprising over 70 000 digitized herbarium specimens to investigate the impact of urbanization on the timing of plant reproductive events and the susceptibility of flowers to frost damage. This dataset, which comprehensively represented flowering and fruiting phenology over 120 yr in the eastern US, provided valuable insights into the complex interaction between urbanization and climate in shaping plant reproductive phenology. Their findings revealed that urbanization had diverse effects on plant phenology depending on the regional climatic conditions. Specifically, it advanced flowering in colder and wetter regions while delaying fruiting in wetter regions. Furthermore, the study identified that urbanization led to changes in the timing of spring frost and flowering, thereby increasing the risk of frost damage in areas with colder and wetter springs. These findings help anticipate potential changes in plant phenology in human-dominated landscapes under climate change.</p><p>Herbarium data offer unique strengths for studying shifting phenology under global changes (Willis <i>et al</i>., <span>2017</span>; Fig. 1a), as Park <i>et al</i>. (<span>2023</span>) have demonstrated. Long-term records from herbarium specimens provide a direct way to establish a pre-climate change baseline for the relationship between phenology and environmental factors. These historical data cannot be replaced by ongoing efforts on phenological observation from remote sensing or crowd-sourcing. Furthermore, herbarium specimens are collected on a global scale, which enables phenological studies that transcend local and regional scales. Such temporal and spatial scales allow for investigations of the heterogeneity in phenological responses across the globe, including under-studied areas such as the global south and the tropics. With herbarium data, researchers can obtain a reliable and comprehensive understanding of how phenological shifts are occurring and their implications for ecological systems.</p><p>Herbarium data have emerged as some of the most compelling evidence for the impacts of climate change on phenology (Willis <i>et al</i>., <span>2017</span>), providing researchers with crucial insights into the mechanisms and magnitude of shifts in the timing of biological events. For example, studies conducted on herbarium specimens from the Boston area have shown that flowering times have shifted earlier in response to warming between 1885 and 2002 (Primack <i>et al</i>., <span>2004</span>). Larger datasets spanning wider geographic regions have also shown that flowering phenology advances under warming conditions, while revealing nuanced differences in response be","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":"239 6","pages":"2057-2059"},"PeriodicalIF":9.4,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.19088","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5741254","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":"Is chloroplast size optimal for photosynthetic efficiency?","authors":"Katarzyna G?owacka,&nbsp;Johannes Kromdijk,&nbsp;Coralie E. Salesse-Smith,&nbsp;Cailin Smith,&nbsp;Steven M. Driever,&nbsp;Stephen P. Long","doi":"10.1111/nph.19091","DOIUrl":"https://doi.org/10.1111/nph.19091","url":null,"abstract":"<p>\u0000 </p>","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":"239 6","pages":"2197-2211"},"PeriodicalIF":9.4,"publicationDate":"2023-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.19091","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5714033","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":"Bloodstained flowers and bloodthirsty flies","authors":"Robert A. Raguso","doi":"10.1111/nph.19089","DOIUrl":"https://doi.org/10.1111/nph.19089","url":null,"abstract":"<p>Flowers of <i>C. gerrardii</i> are unusual even by the kaleidoscopic standards of South Africa's flora, as they resemble velvet-green, whiskered starfish with a coat of morning dew (see fig. 1a in Heiduk <i>et al</i>., <span>2023</span>). Who could pollinate such a flower, and how would they find it? The authors answer these questions with a diversified tool kit, including chemical analyses of the floral scent and dew-like secretions, spectrometric and electron-microscopic explorations of flower color and surface texture, field observations of pollinators, and electrophysiological and behavioral assays measuring their responses to the floral bouquet. Their findings are unexpected and provocative.</p><p>Flowers of <i>C. gerrardii</i> are pollinated by minute ‘jackal flies’ (<i>Desmometopa</i> spp., Milichiidae), called ‘kleptoparasites’ because they steal the prey of spiders or mantids by drinking their blood (hemolymph). Previously, Heiduk <i>et al</i>. (<span>2015</span>, <span>2016</span>) identified similar flies as pollinators for other species of <i>Ceropegia</i>, using the term ‘kleptomyiophily’ (literally, ‘lover of thieving flies’), a term coined by Oelschlägel <i>et al</i>. (<span>2015</span>) in a similar study, to describe pollination by kleptoparasitic flies. In these cases, the flowers formed tubular chambers that entrapped the flies, compensating for inefficient pollen transfer by extending the flies' residence time. By contrast, the open flowers of <i>C. gerrardii</i> detain flies by secreting liquid globules containing sugar and protein, a substance closer in composition to insect hemolymph than to floral nectar. This finding recalls earlier research on seed dispersal mutualisms mediated by elaiosomes, the food bodies attached to ant-dispersed seeds in temperate forest herbs. The nutritional content of elaiosomes, including free fatty acids, amino acids, and the disaccharide trehalose, is more similar to that of prey fed to ant larvae (again, insect hemolymph) than the seeds to which they are attached (Fischer <i>et al</i>., <span>2008</span>). Similarly, <i>C. gerrardii</i> plants enlist jackal flies as pollinators by providing a floral reward that mimics their primary source of nutrition: the spilled blood of bees.</p><p>How are such pollinators attracted? Jackal flies arrive rapidly at a kill, hunting wounded insects by responding to cues of their distress (Heiduk <i>et al</i>., <span>2015</span>). Indeed, two of the <i>Desmometopa</i> fly species that pollinate <i>C. gerrardii</i> arrived within 15 s when wounded honey bees were presented in a natural setting. Hence, the floral scent of <i>C. gerrardii</i> should: (1) mimic the chemical signature of injured honey bees; and (2) serve as a key attractant for jackal flies. Chemical analysis confirmed that the volatile cocktail includes components of honey bee alarm pheromone (isoamyl acetate), Nasonov gland (geraniol), and mandibular gland secretions (2-heptanone; Heiduk <i>et","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":"239 4","pages":"1164-1165"},"PeriodicalIF":9.4,"publicationDate":"2023-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.19089","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5669960","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":"Forging a symbiosis: transition metal delivery in symbiotic nitrogen fixation","authors":"Manuel González-Guerrero,&nbsp;Cristina Navarro-Gómez,&nbsp;Elena Rosa-Nú?ez,&nbsp;Carlos Echávarri-Erasun,&nbsp;Juan Imperial,&nbsp;Viviana Escudero","doi":"10.1111/nph.19098","DOIUrl":"https://doi.org/10.1111/nph.19098","url":null,"abstract":"<p>Symbiotic nitrogen fixation carried out by the interaction between legumes and rhizobia is the main source of nitrogen in natural ecosystems and in sustainable agriculture. For the symbiosis to be viable, nutrient exchange between the partners is essential. Transition metals are among the nutrients delivered to the nitrogen-fixing bacteria within the legume root nodule cells. These elements are used as cofactors for many of the enzymes controlling nodule development and function, including nitrogenase, the only known enzyme able to convert N₂ into NH₃. In this review, we discuss the current knowledge on how iron, zinc, copper, and molybdenum reach the nodules, how they are delivered to nodule cells, and how they are transferred to nitrogen-fixing bacteria within.</p>","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":"239 6","pages":"2113-2125"},"PeriodicalIF":9.4,"publicationDate":"2023-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.19098","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5654085","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":"Stable isotope natural abundances of fungal hyphae extracted from the roots of arbuscular mycorrhizal mycoheterotrophs and rhizoctonia-associated orchids","authors":"Sofia I. F. Gomes,&nbsp;Philipp Giesemann,&nbsp;Saskia Klink,&nbsp;Colin Hunt,&nbsp;Kenji Suetsugu,&nbsp;Gerhard Gebauer","doi":"10.1111/nph.18990","DOIUrl":"https://doi.org/10.1111/nph.18990","url":null,"abstract":"<p>Since the first discovery of unique carbon (C) and nitrogen (N) isotope signatures in fungal fruiting bodies (Gebauer &amp; Dietrich, <span>1993</span>; Gleixner <i>et al</i>., <span>1993</span>), natural abundances of stable isotopes have been extensively used to identify the nutritional dynamics of fungi (Mayor <i>et al</i>., <span>2009</span>). Assigning ecological roles of fungi is essential to determine the role of individual taxa in nutrient cycling and forest ecology. The use of isotope natural abundances in forest ecosystems has been crucial in distinguishing fungi with two main modes of life: ectomycorrhizal and saprotrophic fungi (Henn &amp; Chapela, <span>2001</span>). Within saprotrophic fungi, isotope natural abundances further allow the identification of the substrates used (Kohzu <i>et al</i>., <span>1999</span>). Dual isotope analyses of the δ¹³C and δ¹⁵N values consistently indicate a differentiation in isotopic signatures between ectomycorrhizal and saprotrophic fungi within and among ecosystems (Henn &amp; Chapela, <span>2001</span>; Taylor <i>et al</i>., <span>2003</span>; Trudell <i>et al</i>., <span>2004</span>; Mayor <i>et al</i>., <span>2009</span>). These signatures have been shown to reflect the ecophysiology of fungi and demonstrate that fungi that can utilize organic nitrogen exhibit higher δ¹⁵N than those fungi restricted to mineral nitrogen sources (Gebauer &amp; Taylor, <span>1999</span>; Lilleskov <i>et al</i>., <span>2002</span>). Still, the ability to distinguish fungal nutritional modes has been long restricted to fungi that produce macroscopic sporocarps, such as mushrooms, due to their large mass which allows for physical measurements. Thus, for many fungi, particularly those associated with plant roots that do not form evident fruiting bodies, isotope natural abundances of fungal hyphae are scarce.</p><p>Besides ectomycorrhizal fungi, isotope natural abundances are known for sporocarp-forming ericoid (e.g. Hobbie &amp; Hogberg, <span>2012</span>) and orchid-associated nonrhizoctonia saprotrophic fungi (e.g. Ogura-Tsujita <i>et al</i>., <span>2009</span>). Yet, values of δ¹³C and δ¹⁵N are poorly known for arbuscular mycorrhizal fungi (but see e.g. Courty <i>et al</i>., <span>2011</span>; Suetsugu <i>et al</i>., <span>2020</span>, for isotope values of fungal spores), and the orchid-associated fungi known as ‘rhizoctonia’ in natural conditions. Recently, Klink <i>et al</i>. (<span>2020</span>) obtained the δ¹³C and δ¹⁵N of arbuscular mycorrhizal hyphae isolated from roots of a grass and a legume, inoculated in experimental conditions, thereby providing an efficient method to extract hyphae from roots. Using this method with a few modifications, here, we measured the isotope natural abundances δ¹³C and δ¹⁵N of naturally occurring arbuscular mycorrhizal (Fig. 1a–c) and orchid-associated hyphae (Fig. 1d–f) directl","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":"239 4","pages":"1166-1172"},"PeriodicalIF":9.4,"publicationDate":"2023-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.18990","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5762231","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 soybean immune receptor GmBIR1 regulates host transcriptome, spliceome, and immunity during cyst nematode infection","authors":"Tracy E. Hawk,&nbsp;Sarbottam Piya,&nbsp;Sobhan Bahrami Zadegan,&nbsp;Peitong Li,&nbsp;John H. Rice,&nbsp;Tarek Hewezi","doi":"10.1111/nph.19087","DOIUrl":"https://doi.org/10.1111/nph.19087","url":null,"abstract":"<div>\u0000 \u0000 <p>\u0000 </p><ul>\u0000 \u0000 <li>BAK1-INTERACTING RECEPTOR LIKE KINASE1 (BIR1) is a negative regulator of various aspects of disease resistance and immune responses.</li>\u0000 \u0000 <li>Here, we investigated the functional role of soybean (<i>Glycine max</i>) BIR1 (GmBIR1) during soybean interaction with soybean cyst nematode (SCN, <i>Heterodera glycines</i>) and the molecular mechanism through which GmBIR1 regulates plant immunity.</li>\u0000 \u0000 <li>Overexpression of wild-type variant of <i>GmBIR1</i> (<i>WT-GmBIR1</i>) using transgenic soybean hairy roots significantly increased soybean susceptibility to SCN, whereas overexpression of kinase-dead variant (<i>KD-GmBIR1</i>) significantly increased plant resistance. Transcriptome analysis revealed that genes oppositely regulated in <i>WT-GmBIR1</i> and <i>KD-GmBIR1</i> upon SCN infection were enriched primarily in defense and immunity-related functions. Quantitative phosphoproteomic analysis identified 208 proteins as putative substrates of the GmBIR1 signaling pathway, 114 of which were differentially phosphorylated upon SCN infection. In addition, the phosphoproteomic data pointed to a role of the GmBIR1 signaling pathway in regulating alternative pre-mRNA splicing. Genome-wide analysis of splicing events provided compelling evidence supporting a role of the GmBIR1 signaling pathway in establishing alternative splicing during SCN infection.</li>\u0000 \u0000 <li>Our results provide novel mechanistic insights into the function of the GmBIR1 signaling pathway in regulating soybean transcriptome and spliceome via differential phosphorylation of splicing factors and regulation of splicing events of pre-mRNA decay- and spliceosome-related genes.</li>\u0000 </ul>\u0000 </div>","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":"239 6","pages":"2335-2352"},"PeriodicalIF":9.4,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5721485","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":"Increased aridity drives post-fire recovery of Mediterranean forests towards open shrublands","authors":"Mara Baudena,&nbsp;Victor M. Santana,&nbsp;M. Jaime Baeza,&nbsp;Susana Bautista,&nbsp;Maarten B. Eppinga,&nbsp;Lia Hemerik,&nbsp;Angeles Garcia Mayor,&nbsp;Francisco Rodriguez,&nbsp;Alejandro Valdecantos,&nbsp;V. Ramon Vallejo,&nbsp;Ana Vasques,&nbsp;Max Rietkerk","doi":"10.1111/nph.19012","DOIUrl":"https://doi.org/10.1111/nph.19012","url":null,"abstract":"<p>Corrigendum to <i>New Phytologist</i> <b>225</b> (2020), 1500–1515, doi: 10.1111/nph.16252.</p><p>Since its publication, the authors of Baudena <i>et al</i>. (<span>2020</span>) have identified an error for the set of parameter values representing flammability in Table 2. In this correction, the authors would also like to report that, when using the flammability values as originally published in Baudena <i>et al</i>. (<span>2020</span>; i.e. a factor 2 larger than those actually used in the simulations), the main results do not change qualitatively (see Supporting Information Figs S1, S2 to this correction).</p><p>Namely, when increased aridity was simulated as negatively affecting oak post-fire recovery and colonization rate, while positively affecting the community flammability, the authors observed that the forest state was resilient to the separate impact of fires and increased aridity. Yet, water stress could convert forests into open shrublands by hampering post-fire recovery and at the same time either increasing flammability or decreasing the oak forest colonization rate (or both). A tipping point (emerging from bistability of the open shrubland and forest state) was detected at intermediate levels of aridity (Fig. S1). In the ‘short-term’ run, that is a century, the authors observed again that the probability of a mixed successional community becoming an oak forest after 100 yr decreased drastically with increasing aridity (moving from bottom left to top right in Fig. S2, e.g. with flammability equal to 1.5 times the baseline value as published in table 2 in Baudena <i>et al</i>., <span>2020</span>). The main differences between the two parameter sets were that the effects of aridity were more dramatic in Figs S1 and S2, as their baseline flammability (given in table 2 in Baudena <i>et al</i>., <span>2020</span>) was twice as high as the baseline flammability that we actually used in figs 3 and 4 in Baudena <i>et al</i>. (<span>2020</span>) (as reported here in Table 2).</p><p>We apologize to our readers for this mistake.</p><p>The authors would like to kindly acknowledge Matilde Torrassa for finding the error in the original version of the paper.</p>","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":"239 6","pages":"2416-2417"},"PeriodicalIF":9.4,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.19012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5733529","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":"PloiDB: the plant ploidy database","authors":"Keren Halabi,&nbsp;Anat Shafir,&nbsp;Itay Mayrose","doi":"10.1111/nph.19057","DOIUrl":"https://doi.org/10.1111/nph.19057","url":null,"abstract":"<p>Polyploidy, namely the acquisition of additional, complete sets of chromosomes to the genome, is widely recognized as a key feature of extant organismal diversity, particularly in plants. It is generally accepted that all angiosperm species have experienced at least one polyploidization event in their evolutionary past (Jiao <i>et al</i>., <span>2011</span>). Therefore, most (if not all) plant species should be considered as paleo-polyploids that have since diploidized to some extent. As such, the distinction between diploids and polyploids should be made with respect to a reference timepoint. In recent decades, polyploid research has experienced a resurgence among plant evolutionary biologists. This is largely due to the use of genomic analyses that have revealed a rich history of genome duplications across multiple plant lineages. Indeed, numerous studies have investigated the impact of polyploidy on morphological and life-history traits, ecology, diversification patterns, and genome evolution (reviewed in Soltis &amp; Soltis, <span>2000</span>; Otto &amp; Whitton, <span>2003</span>; Ramsey &amp; Schemske, <span>2003</span>; Otto, <span>2007</span>; Ramsey &amp; Ramsey, <span>2014</span>; Wendel, <span>2015</span>; Soltis <i>et al</i>., <span>2016</span>; Van de Peer <i>et al</i>., <span>2017</span>; Fox <i>et al</i>., <span>2020</span>). Notably, many of these studies focus on the effect of polyploidy in the context of a specific taxonomic group, which limits our ability to draw conclusions regarding the universal consequences of polyploidy, and to distinguish broad convergent trends from species-specific idiosyncrasies. There is thus a growing need to expand the examination of ploidy estimates across the seed plants clade, to obtain robust and broad information about the effect of polyploidy.</p><p>In the last few years, multiple methods for ploidy inferences based on sequenced genomic data have been developed (e.g. Jiao <i>et al</i>., <span>2011</span>; Rabier <i>et al</i>., <span>2014</span>; Vanneste <i>et al</i>., <span>2014</span>; Tiley <i>et al</i>., <span>2018</span>; Zwaenepoel &amp; Van de Peer, <span>2020</span>). However, due to the computational complexities and substantial amount of genomic data involved, the applications of such methods are still somewhat limited and are usually applied at phylogenetic scales above the species level, for example, by sampling representatives from several clades of interest. As such, the most comprehensive sequence-based analysis to date, which was conducted by the 1KP initiative and encompassed the transcriptomes of roughly 1100 plant species, has identified 244 whole-genome duplication (WGD) events occurring within Viridiplantae (One Thousand Plant Transcriptomes Initiative, <span>2019</span>; Li &amp; Barker, <span>2020</span>).</p><p>Ploidy estimation at the species level is still largely based on information derived from chromosome numbers. A simple utility of chromosome number informatio","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":"240 3","pages":"918-927"},"PeriodicalIF":9.4,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/nph.19057","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41087842","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}