New Phytologist最新文献_第5页

Identification of cell-type specificity, trans- and cis-acting functions of plant lincRNAs from single-cell transcriptomes. 从单细胞转录组中鉴定植物长链核糖核酸的细胞类型特异性、反式和顺式作用功能。

IF 9.4 1区生物学

New Phytologist Pub Date : 2024-11-17 DOI: 10.1111/nph.20269

Jiwei Xu, Enhui Shen, Fu Guo, Kaiqiang Wang, Yurong Hu, Leti Shen, Hongyu Chen, Xiaohan Li, Qian-Hao Zhu, Longjiang Fan, Qinjie Chu

{"title":"Identification of cell-type specificity, trans- and cis-acting functions of plant lincRNAs from single-cell transcriptomes.","authors":"Jiwei Xu, Enhui Shen, Fu Guo, Kaiqiang Wang, Yurong Hu, Leti Shen, Hongyu Chen, Xiaohan Li, Qian-Hao Zhu, Longjiang Fan, Qinjie Chu","doi":"10.1111/nph.20269","DOIUrl":"https://doi.org/10.1111/nph.20269","url":null,"abstract":"Long noncoding RNAs, including intergenic lncRNAs (lincRNAs), play a key role in various biological processes throughout the plant life cycle, and the advent of single-cell RNA sequencing (scRNA-seq) technology has opened up a valuable avenue for scrutinizing the intricate roles of lincRNAs in cellular processes. Here, we identified a new batch of lincRNAs using scRNA-seq data from diverse tissues of plants (rice, Arabidopsis, tomato, and maize). Based on well-annotated single-cell transcriptome atlases, plant lincRNAs were found to possess the same level of cell-type specificity as mRNAs and to be involved in the differentiation of certain cell types based on pseudo-time analysis. Many lincRNAs were predicted to play a hub role in the cell-type-specific co-expression networks of lincRNAs and mRNAs, suggesting their trans-acting abilities. Besides, plant lincRNAs were revealed to have potential cis-acting properties based on their genomic distances and expression correlations with the neighboring mRNAs. Furthermore, an online platform, PscLncRNA (http://ibi.zju.edu.cn/psclncrna/), was constructed for searching and visualizing all identified plant lincRNAs with annotated potential functions. Our work provides new insights into plant lincRNAs at single-cell resolution and an important resource for understanding and further investigation of plant lincRNAs.","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":" ","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644655","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}

引用次数: 0

Exploring the metabolic daylength measurement system: implications for photoperiodic growth. 探索新陈代谢昼长测量系统：对光周期生长的影响。

IF 9.4 1区生物学

New Phytologist Pub Date : 2024-11-15 DOI: 10.1111/nph.20275

Man-Wah Li, Joshua M Gendron

引用次数: 0

A systematic review of nurse objects as safe sites for seedling establishment and implications for restoration. 对作为育苗安全场所的哺育对象及其对恢复的影响进行系统审查。

IF 9.4 1区生物学

New Phytologist Pub Date : 2024-11-15 DOI: 10.1111/nph.20247

Hagai Shemesh

{"title":"A systematic review of nurse objects as safe sites for seedling establishment and implications for restoration.","authors":"Hagai Shemesh","doi":"10.1111/nph.20247","DOIUrl":"10.1111/nph.20247","url":null,"abstract":"Direct human activity and global climatic changes are threatening the existence of many vegetated habitats. Seedling establishment, one of the riskiest plant life stages, must be successful for such habitats to persist. The establishment of seedlings is known to be enhanced by nurse effects, but most studies to date have looked at the nursing effects of plants while sidelining inanimate objects. Nevertheless, nurse objects can support seedling establishment via diverse mechanisms such as moderating abiotic stresses like extreme temperatures and drought, reducing negative biological interactions such as herbivory while enhancing positive processes like seed dispersal, and providing protection from physical disturbances such as trampling and fire. The robust nature of nurse objects highlights their potential in habitat restoration. The addition of nurse objects allows a simple, single-effort rehabilitation strategy that can later draw on natural seed dispersal and establishment. By achieving a better understanding of the processes in which nurse objects are involved we should be able to better predict vegetation dynamics and manipulate them to minimize adverse processes and support regeneration in natural habitats.","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":" ","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142630942","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}

引用次数: 0

Phosphorylation-dependent activation of the bHLH transcription factor ICE1/SCRM promotes polarization of the Arabidopsis zygote. 磷酸化依赖性激活 bHLH 转录因子 ICE1/SCRM 可促进拟南芥子实体的极化。

IF 9.4 1区生物学

New Phytologist Pub Date : 2024-11-14 DOI: 10.1111/nph.20265

Houming Chen, Feng Xiong, Alexa-Maria Wangler, Torren Bischoff, Kai Wang, Yingjing Miao, Daniel Slane, Rebecca Schwab, Thomas Laux, Martin Bayer

{"title":"Phosphorylation-dependent activation of the bHLH transcription factor ICE1/SCRM promotes polarization of the Arabidopsis zygote.","authors":"Houming Chen, Feng Xiong, Alexa-Maria Wangler, Torren Bischoff, Kai Wang, Yingjing Miao, Daniel Slane, Rebecca Schwab, Thomas Laux, Martin Bayer","doi":"10.1111/nph.20265","DOIUrl":"10.1111/nph.20265","url":null,"abstract":"In Arabidopsis thaliana, the asymmetric cell division (ACD) of the zygote gives rise to the embryo proper and an extraembryonic suspensor, respectively. This process is controlled by the ERECTA-YODA-MPK3/6 receptor kinase-MAP kinase-signaling pathway, which also orchestrates ACDs in the epidermis. In this context, the bHLH transcription factor ICE1/SCRM is negatively controlled by MPK3/6-directed phosphorylation. However, it is unknown whether this regulatory module is similarly involved in the zygotic ACD. We investigated the function of SCRM in zygote polarization by analyzing the effect of loss-of-function alleles and variants that cannot be phosphorylated by MPK3/6, protein accumulation, and target gene expression. Our results show that SCRM has a critical function in zygote polarization and acts in parallel with the known MPK3/6 target WRKY2 in activating WOX8. Our work further demonstrates that SCRM activity in the early embryo is positively controlled by MPK3/6-mediated phosphorylation. Therefore, the effect of MAP kinase-directed phosphorylation of the same target protein fundamentally differs between the embryo and the epidermis, shedding light on cell type-specific, differential gene regulation by common signaling pathways.","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":" ","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142630944","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}

引用次数: 0

Mapping of drought-induced changes in tissue characteristics across the leaf profile of Populus balsamifera. 绘制杨树叶片轮廓中由干旱引起的组织特征变化图。

IF 9.4 1区生物学

New Phytologist Pub Date : 2024-11-06 DOI: 10.1111/nph.20240

Mina Momayyezi, Cheyenne Chu, Jarvis A Stobbs, Raju Y Soolanayakanahally, Robert D Guy, Andrew J McElrone, Thorsten Knipfer

{"title":"Mapping of drought-induced changes in tissue characteristics across the leaf profile of Populus balsamifera.","authors":"Mina Momayyezi, Cheyenne Chu, Jarvis A Stobbs, Raju Y Soolanayakanahally, Robert D Guy, Andrew J McElrone, Thorsten Knipfer","doi":"10.1111/nph.20240","DOIUrl":"10.1111/nph.20240","url":null,"abstract":"Leaf architecture impacts the ease of gases diffusion, biochemical process, and photosynthetic performance. For balsam poplar, a widespread North American species, the influence of water availability on leaf anatomy and subsequent photosynthetic performance remains unknown. To address this shortcoming, we characterized the anatomical changes across the leaf profile in three-dimensional space for saplings subjected to soil drying and rewatering using X-ray microcomputed tomography. Our hypothesis was that higher abundance of bundle sheet extensions (BSE) minimizes drought-induced changes in intercellular airspace volume relative to mesophyll volume (i.e. mesophyll porosity, θIAS) and aids recovery by supporting leaf structural integrity. Leaves of 'Carnduff-9' with less abundant BSEs exhibited greater θIAS, higher spongy mesophyll surface area, reduced palisade mesophyll surface area, and less veins compared with 'Gillam-5'. Under drought conditions, Carnduff-9 showed significant changes in θIAS across leaf profile while that was little for 'Gillam-5'. Under rewatered conditions, drought-induced changes in θIAS were fully reversible in 'Gillam-5' but not in 'Carnduff-9'. Our data suggest that a 'robust' leaf structure with higher abundance of BSEs, reduced θIAS, and relatively large mesophyll surface area provides for improved photosynthetic capacity under drought and supports recovery in leaf architecture after rewatering in balsam poplar.","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":" ","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142591288","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}

引用次数: 0

StCDF1: A 'jack of all trades' clock output with a central role in regulating potato nitrate reduction activity. StCDF1：万能 "时钟输出，在调节马铃薯硝酸盐还原活性方面发挥核心作用。

IF 9.4 1区生物学

New Phytologist Pub Date : 2024-11-06 DOI: 10.1111/nph.20186

Maroof Ahmed Shaikh, Lorena Ramírez-Gonzales, José M Franco-Zorrilla, Evyatar Steiner, Marian Oortwijn, Christian W B Bachem, Salomé Prat

{"title":"StCDF1: A 'jack of all trades' clock output with a central role in regulating potato nitrate reduction activity.","authors":"Maroof Ahmed Shaikh, Lorena Ramírez-Gonzales, José M Franco-Zorrilla, Evyatar Steiner, Marian Oortwijn, Christian W B Bachem, Salomé Prat","doi":"10.1111/nph.20186","DOIUrl":"https://doi.org/10.1111/nph.20186","url":null,"abstract":"Transcription factors of the CYCLING DOF FACTOR (CDF) family activate in potato the SP6A FT tuberization signal in leaves. In modern cultivars, truncated StCDF1.2 alleles override strict SD control by stabilizing the StCDF1 protein, which leads to StCOL1 suppression and impaired activation of the antagonic SP5G paralog. By using DAP-seq and RNA-seq studies, we here show that StCDF1 not only acts as an upstream regulator of the day length pathway but also directly regulates several N assimilation and transport genes. StCDF1 directly represses expression of NITRATE REDUCTASE (NR/NIA), which catalyses the first reduction step in nitrate assimilation, and is encoded by a single potato locus. StCDF1 knock-down lines performed better in N-limiting conditions, and this phenotype correlated with derepressed StNR expression. Also, deletion of the StNR DAP-seq region abolished repression by StCDF1, while it did not affect NLP7-dependent activation of the StNR promoter. We identified multiple nucleotide polymorphisms in the DAP-seq region in potato cultivars with early StCDF1 alleles, suggesting that this genetic variation was selected as compensatory mechanism to the negative impact of StCDF1 stabilization. Thereby, directed modification of the StCDF1-recognition elements emerges as a promising strategy to enhance limiting StNR activity in potato.","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":" ","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142584658","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}

引用次数: 0

From synthetic communities to synthetic ecosystems: exploring causalities in plant-microbe-environment interactions. 从合成群落到合成生态系统：探索植物-微生物-环境相互作用的因果关系。

IF 9.4 1区生物学

New Phytologist Pub Date : 2024-11-05 DOI: 10.1111/nph.20250

Guillaume Chesneau, Johannes Herpell, Rubén Garrido-Oter, Stéphane Hacquard

引用次数: 0

New insights into a sensitive life stage: hydraulics of tree seedlings in their first growing season. 对敏感生命阶段的新认识：树苗第一个生长季节的水力学。

IF 9.4 1区生物学

New Phytologist Pub Date : 2024-11-05 DOI: 10.1111/nph.20243

Barbara Beikircher, Magdalena Held, Adriano Losso, Stefan Mayr

{"title":"New insights into a sensitive life stage: hydraulics of tree seedlings in their first growing season.","authors":"Barbara Beikircher, Magdalena Held, Adriano Losso, Stefan Mayr","doi":"10.1111/nph.20243","DOIUrl":"https://doi.org/10.1111/nph.20243","url":null,"abstract":"The first year in a tree's life is characterized by distinct morphological changes, requiring constant adjustments of the hydraulic system. Despite their importance for the natural regeneration of forests and future vegetation composition, little has been known about the hydraulics of tree seedlings. At different times across the first growing season, we analysed xylem area-specific (Kshoot_Axyl) and leaf area-specific (Kshoot_L) shoot hydraulic conductance, as well as embolism resistance of three temperate conifer trees, two angiosperm trees and one angiosperm shrub, and related findings to cell osmotic parameters and xylem anatomical traits. Over the first 10 wk after germination, Kshoot_Axyl and Kshoot_L sharply decreased, then remained stable until the end of the growing season. Embolism resistance was remarkably low in the youngest stages but, coupled with an increase in cell wall reinforcement, significantly increased towards autumn. Contemporaneously, water potential at turgor loss and osmotic potential at saturation decreased. Independent of lineage, species and growth form, the transition from primary to secondary xylem resulted in a less efficient but increasingly more embolism-resistant hydraulic system, enabling stable water supply under increasing risk for low water potentials.","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":" ","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142584641","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}

引用次数: 0

The first intron and promoter of Arabidopsis DIACYLGLYCEROL ACYLTRANSFERASE 1 exert synergistic effects on pollen and embryo lipid accumulation. 拟南芥二乙酰甘油 ACYLTRANSFERASE 1 的第一个内含子和启动子对花粉和胚胎脂质积累有协同作用。

IF 9.4 1区生物学

New Phytologist Pub Date : 2024-11-05 DOI: 10.1111/nph.20244

Sean T McGuire, Jay Shockey, Philip D Bates

{"title":"The first intron and promoter of Arabidopsis DIACYLGLYCEROL ACYLTRANSFERASE 1 exert synergistic effects on pollen and embryo lipid accumulation.","authors":"Sean T McGuire, Jay Shockey, Philip D Bates","doi":"10.1111/nph.20244","DOIUrl":"https://doi.org/10.1111/nph.20244","url":null,"abstract":"Accumulation of triacylglycerols (TAGs) is crucial during various stages of plant development. In Arabidopsis, two enzymes share overlapping functions to produce TAGs, namely acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) and phospholipid:diacylglycerol acyltransferase 1 (PDAT1). Loss of function of both genes in a dgat1-1/pdat1-2 double mutant is gametophyte lethal. However, the key regulatory elements controlling tissue-specific expression of either gene has not yet been identified. We transformed a dgat1-1/dgat1-1//PDAT1/pdat1-2 parent with transgenic constructs containing the Arabidopsis DGAT1 promoter fused to the AtDGAT1 open reading frame either with or without the first intron. Triple homozygous plants were obtained, however, in the absence of the DGAT1 first intron anthers fail to fill with pollen, seed yield is c. 10% of wild-type, seed oil content remains reduced (similar to dgat1-1/dgat1-1), and non-Mendelian segregation of the PDAT1/pdat1-2 locus occurs. Whereas plants expressing the AtDGAT1pro:AtDGAT1 transgene containing the first intron mostly recover phenotypes to wild-type. This study establishes that a combination of the promoter and first intron of AtDGAT1 provides the proper context for temporal and tissue-specific expression of AtDGAT1 in pollen. Furthermore, we discuss possible mechanisms of intron mediated regulation and how regulatory elements can be used as genetic tools to functionally replace TAG biosynthetic enzymes in Arabidopsis.","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":" ","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142584665","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}

引用次数: 0

Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids. 不对称基因组合并通过衣藻三倍体中的核-细胞质破坏和转录组冲击导致基因表达的新颖性。

IF 9.4 1区生物学

New Phytologist Pub Date : 2024-11-05 DOI: 10.1111/nph.20249

Lucas Prost-Boxoen, Quinten Bafort, Antoine Van de Vloet, Fabricio Almeida-Silva, Yunn Thet Paing, Griet Casteleyn, Sofie D'hondt, Olivier De Clerck, Yves Van de Peer

{"title":"Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids.","authors":"Lucas Prost-Boxoen, Quinten Bafort, Antoine Van de Vloet, Fabricio Almeida-Silva, Yunn Thet Paing, Griet Casteleyn, Sofie D'hondt, Olivier De Clerck, Yves Van de Peer","doi":"10.1111/nph.20249","DOIUrl":"10.1111/nph.20249","url":null,"abstract":"Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well-understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression-level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression-level dominance and a pattern of 'functional dominance' from the haploid parent was observed. Despite major genomic and nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.","PeriodicalId":48887,"journal":{"name":"New Phytologist","volume":" ","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7616817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142584626","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}

引用次数: 0