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Tackling redundancy: genetic mechanisms underlying paralog compensation in plants 处理冗余:植物同源补偿的遗传机制。
IF 9.4 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-09-19 DOI: 10.1111/nph.19267
Sessen Daniel Iohannes, David Jackson

Gene duplication is a powerful source of biological innovation giving rise to paralogous genes that undergo diverse fates. Redundancy between paralogous genes is an intriguing outcome of duplicate gene evolution, and its maintenance over evolutionary time has long been considered a paradox. Redundancy can also be dubbed ‘a geneticist's nightmare’: It hinders the predictability of genome editing outcomes and limits our ability to link genotypes to phenotypes. Genetic studies in yeast and plants have suggested that the ability of ancient redundant duplicates to compensate for dosage perturbations resulting from a loss of function depends on the reprogramming of gene expression, a phenomenon known as active compensation. Starting from considerations on the stoichiometric constraints that drive the evolutionary stability of redundancy, this review aims to provide insights into the mechanisms of active compensation between duplicates that could be targeted for breaking paralog dependencies – the next frontier in plant functional studies.

基因复制是生物创新的强大来源,产生了经历不同命运的同源基因。同源基因之间的冗余是重复基因进化的一个有趣结果,长期以来,它在进化过程中的维持一直被认为是一个悖论。冗余也可以被称为“遗传学家的噩梦”:它阻碍了基因组编辑结果的可预测性,并限制了我们将基因型与表型联系起来的能力。对酵母和植物的遗传学研究表明,古代冗余复制品补偿功能丧失引起的剂量扰动的能力取决于基因表达的重新编程,这种现象被称为主动补偿。从对驱动冗余进化稳定性的化学计量约束的考虑开始,这篇综述旨在深入了解重复之间的主动补偿机制,这些机制可以用来打破并行依赖关系 - 植物功能研究的下一个前沿。
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引用次数: 0
Deductive automated pollen classification in environmental samples via exploratory deep learning and imaging flow cytometry 通过探索性深度学习和成像流式细胞术对环境样本中的花粉进行演绎式自动分类
IF 9.4 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-09-07 DOI: 10.1111/nph.19186
Claire M. Barnes, Ann L. Power, Daniel G. Barber, Richard K. Tennant, Richard T. Jones, G. Rob Lee, Jackie Hatton, Angela Elliott, Joana Zaragoza-Castells, Stephen M. Haley, Huw D. Summers, Minh Doan, Anne E. Carpenter, Paul Rees, John Love

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引用次数: 0
Conservation of beneficial microbes between the rhizosphere and the cyanosphere 根际和蓝层之间有益微生物的保护
IF 9.4 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-09-05 DOI: 10.1111/nph.19225
Qing Zheng, Yuntao Hu, Suzanne M. Kosina, Marc W. Van Goethem, Susannah G. Tringe, Benjamin P. Bowen, Trent R. Northen

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引用次数: 0
Thinking outside the F-box: how UFO controls angiosperm development F盒子之外的思考:不明飞行物如何控制被子植物的发育
IF 9.4 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-09-04 DOI: 10.1111/nph.19234
Philippe Rieu, Mo?ra Arnoux-Courseaux, Gabrielle Tichtinsky, Fran?ois Parcy

The formation of inflorescences and flowers is essential for the successful reproduction of angiosperms. In the past few decades, genetic studies have identified the LEAFY transcription factor and the UNUSUAL FLORAL ORGANS (UFO) F-box protein as two major regulators of flower development in a broad range of angiosperm species. Recent research has revealed that UFO acts as a transcriptional cofactor, redirecting the LEAFY floral regulator to novel cis-elements. In this review, we summarize the various roles of UFO across species, analyze past results in light of new discoveries and highlight the key questions that remain to be solved.

花序和花朵的形成对被子植物的成功繁殖至关重要。在过去的几十年里,遗传学研究已经确定LEAFY转录因子和不明飞行物F-box蛋白是广泛被子植物物种花朵发育的两个主要调节因子。最近的研究表明,不明飞行物是一种转录辅因子,将LEAFY花调节因子重定向到新的顺式元件。在这篇综述中,我们总结了不明飞行物在不同物种中的各种作用,根据新发现分析了过去的结果,并强调了有待解决的关键问题。
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引用次数: 1
MicroRNA 4407 modulates nodulation in soybean by repressing a root-specific ISOPENTENYLTRANSFERASE (GmIPT3) MicroRNA 4407通过抑制根特异性异戊基转移酶(GmIPT3)调节大豆结瘤
IF 9.4 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-08-31 DOI: 10.1111/nph.19222
Kejing Fan, Zhili Wang, Ching-Ching Sze, Yongchao Niu, Fuk-Ling Wong, Man-Wah Li, Hon-Ming Lam

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引用次数: 0
Red macroalgae in the genomic era 基因组时代的红藻
IF 9.4 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-08-30 DOI: 10.1111/nph.19211
Michael Borg, Stacy A. Krueger-Hadfield, Christophe Destombe, Jonas Collén, Agnieszka Lipinska, Susana M. Coelho

Rhodophyta (or red algae) are a diverse and species-rich group that forms one of three major lineages in the Archaeplastida, a eukaryotic supergroup whose plastids arose from a single primary endosymbiosis. Red algae are united by several features, such as relatively small intron-poor genomes and a lack of cytoskeletal structures associated with motility like flagella and centrioles, as well as a highly efficient photosynthetic capacity. Multicellular red algae (or macroalgae) are one of the earliest diverging eukaryotic lineages to have evolved complex multicellularity, yet despite their ecological, evolutionary, and commercial importance, they have remained a largely understudied group of organisms. Considering the increasing availability of red algal genome sequences, we present a broad overview of fundamental aspects of red macroalgal biology and posit on how this is expected to accelerate research in many domains of red algal biology in the coming years.

红藻门(或红藻)是一个多样性和物种丰富的类群,形成了古菌门的三个主要谱系之一,古菌门是一个真核超类群,其质体来源于单一的初级内共生。红藻有几个特征,如相对较小的内含子贫乏的基因组,缺乏与运动相关的细胞骨架结构,如鞭毛和中心粒,以及高效的光合能力。多细胞红藻(或大型藻类)是最早进化出复杂多细胞性的分化真核生物谱系之一,尽管它们在生态、进化和商业上具有重要意义,但它们仍然是一组研究不足的生物。考虑到红藻基因组序列的可用性越来越高,我们对红藻生物学的基本方面进行了广泛的概述,并假设这将如何在未来几年加速红藻生物学许多领域的研究。
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引用次数: 0
A genome-scale metabolic reconstruction of soybean and Bradyrhizobium diazoefficiens reveals the cost–benefit of nitrogen fixation 大豆和重氮慢生根瘤菌的基因组级代谢重建揭示了固氮的成本效益
IF 9.4 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-08-30 DOI: 10.1111/nph.19203
Bethany L. Holland, Megan L. Matthews, Pedro Bota, Lee J. Sweetlove, Stephen P. Long, George C. diCenzo

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引用次数: 0
How deep should we go to understand roots at the top of the world? 我们应该深入到什么程度才能理解世界之巅的根源?
IF 9.4 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-08-26 DOI: 10.1111/nph.19220
S?ren E. Weber, Colleen M. Iversen

Informed by vegetation maps across high-latitude landscapes, terrestrial biosphere models are a tool that can be used to predict changes in the composition and function of vegetation, above- and belowground, across the land surface in response to changing environmental conditions. However, terrestrial biosphere models represent vegetation characteristics at a finer grain than mapped vegetation communities. These models group plant species that colonize high-latitude biomes by their functional trait variation into plant functional types (PFTs) that characterize the impacts of plant species on, and their response to changes in, their surrounding abiotic and biotic environment. Blume-Werry et al. (2023) found that vegetation mapping units that broadly incorporate multiple plant species and functional types are too coarse, or encompass too much biological variation, to fully capture belowground plant trait variation. However, they did find that they could successfully cluster rooting depth observations into ‘Root Profile Types’, suggesting that modeling PFTs may be a useful tool to characterize above- and belowground linkages across high-latitude environments.

In many arctic and boreal ecosystems, plant roots are constrained by permafrost to a shallow ‘active layer’ of soil that thaws progressively over the course of each growing season. Blume-Werry et al. (2023) identified active layer thickness and the closely related minimum temperature of the coldest month as two of three main abiotic drivers constraining rooting depth distribution in their analysis (a third, cation exchange capacity, is more indicative of nutrient availability than a physical impediment). Furthermore, waterlogging can limit root distribution to surface, oxic soils, and can lead to a thick layer of poorly decomposed, organic peat at the soil surface with different characteristics from mineral soils (Fig. 1; Walker et al., 2003). Indeed, Blume-Werry et al. (2023) found that despite similarities in species composition between wetland and graminoid tundra in CAVM mapping units, rooting depth in wetland tundra was shallower than graminoid tundra. This may indicate that waterlogged conditions can constrain rooting depth distribution, even in vegetation communities dominated by species with aerenchymatous roots. Ranging from rootless mosses and plant-like lichens to vascular graminoids and shrubs, and deciduous and evergreen trees, PFTs inhabiting the arctic tundra and boreal forest vary in their rooting depth distributions, their interactions with soil microbiota, and their ratio of belowground to aboveground tissues (e.g. root : shoot ratio; Chapin et al., 1996). However, terrestrial biosphere models have often neglected the unique characteristics of the species that colonize high-latitude biomes, especially belowground (Iversen et al., 2015, 2018

根据高纬度景观的植被图,陆地生物圈模型是一种工具,可用于预测地表上和地下植被组成和功能的变化,以应对不断变化的环境条件。然而,陆地生物圈模型比绘制的植被群落更精细地代表了植被特征。这些模型将通过功能特征变化定居在高纬度生物群落中的植物物种分为植物功能类型(PFTs),PFTs表征了植物物种对周围非生物和生物环境变化的影响及其对变化的反应。Blume Werry等人。(2023)发现,广泛包含多种植物物种和功能类型的植被制图单元过于粗糙,或包含了太多的生物变异,无法完全捕捉地下植物特征变异。然而,他们确实发现,他们可以成功地将生根深度观测结果聚类为“根剖面类型”,这表明PFT建模可能是一个有用的工具,可以用来表征高纬度环境中的地上和地下联系。在许多北极和北方生态系统中,植物根系被永久冻土限制在一层浅的“活动层”土壤中,在每个生长季节逐渐融化。Blume Werry等人。(2023)在他们的分析中确定,活性层厚度和最冷月的密切相关的最低温度是限制生根深度分布的三个主要非生物驱动因素中的两个(第三个,阳离子交换能力,更能表明营养物质的可用性,而不是物理障碍)。此外,内涝会限制根系在表层有毒土壤中的分布,并会在土壤表面形成一层厚厚的分解不良的有机泥炭,其特征与矿物土壤不同(图1;Walker等人,2003年)。(2023)发现,尽管在CAVM绘图单元中,湿地和类禾本科苔原的物种组成相似,但湿地苔原的生根深度比类禾本科冻土带浅。这可能表明,积水条件会限制生根深度的分布,即使在由具有通气性根系的物种主导的植被群落中也是如此。从无根苔藓和植物状地衣到维管类禾本科植物和灌木,以及落叶和常绿树木,栖息在北极苔原和北方森林中的PFT在生根深度分布、与土壤微生物群的相互作用以及地下组织与地上组织的比例(如根 : 芽率;Chapin等人。,1996)。然而,陆地生物圈模型往往忽视了定居在高纬度生物群落,特别是地下的物种的独特特征(Iversen等人,20152018)。而Blume-Werry等人。(2023)没有发现CAVM植被分类可以用于预测和缩放泛北极地区的生根深度分布,他们的方法可以在模型中进一步完善,将苔原植物的生根深度分配与周围土壤特征联系起来(Drewniak,2019)。预测北高纬度广阔地区地下形态和功能的能力是一个复杂的问题,涉及空间和时间尺度,包括生物和环境因素。作者建议通过考虑“根函数类型”来向前推进。在这里,我们提出了一些额外的前进道路,以便我们作为地下研究社区能够找到联系,从而解锁我们对世界快速变化地区地下过程的理解和预测。Blume Werry等人。(2023)承担了从整个泛北极地区观测到的地上植被群落组成预测根系形态和功能的重要而艰巨的挑战。Blume Werry等人的植被图无法捕捉根系深度的大规模变化,以及随之而来的模拟碳排放的差异。源于多种可能的来源,尤其是这些地图是地上植被。作者提出的一个解决方案是根据地下而不是地上的特征对生态系统进行分类。了解地下环境在北极和北方生态系统中的作用可能需要一种以地下环境为重点的方法,并结合遥感(Blume Werry et al.,2023;Yang et al.,2021)、机械建模、机器学习(Langford et al.,2019;施等人,2021;Sulman等人,2021),以及与实证研究人员的跨学科合作(Sulman等人,2021;Blume Werry等人,2023)。
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引用次数: 0
SlTCP24 and SlTCP29 synergistically regulate compound leaf development through interacting with SlAS2 and activating transcription of SlCKX2 in tomato SlTCP24和SlTCP29通过与SlAS2相互作用和激活SlCKX2的转录协同调节番茄复叶发育
IF 9.4 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-08-24 DOI: 10.1111/nph.19221
Guoyu Hu, Danqiu Zhang, Dan Luo, Wenhui Sun, Rijin Zhou, Zonglie Hong, Shoaib Munir, Zhibiao Ye, Changxian Yang, Junhong Zhang, Taotao Wang

  • The complexity of compound leaves results primarily from the leaflet initiation and arrangement during leaf development. However, the molecular mechanism underlying compound leaf development remains a central research question.
  • SlTCP24 and SlTCP29, two plant-specific transcription factors with the conserved TCP motif, are shown here to synergistically regulate compound leaf development in tomato. When both of them were knocked out simultaneously, the number of leaflets significantly increased, and the shape of the leaves became more complex. SlTCP24 and SlTCP29 could form both homodimers and heterodimers, and such dimerization was impeded by the leaf polarity regulator SlAS2, which interacted with SlTCP24 and SlTCP29.
  • SlTCP24 and SlTCP29 could bind to the TCP-binding cis-element of the SlCKX2 promoter and activate its transcription. Transgenic plants with SlTCP24 and SlTCP29 double-gene knockout had a lowered transcript level of SlCKX2 and an elevated level of cytokinin.
  • This work led to the identification of two key regulators of tomato compound leaf development and their targeted genes involved in cytokinin metabolic pathway. A model of regulation of compound leaf development was proposed based on observations of this study.
复叶的复杂性主要源于叶片发育过程中小叶的起始和排列。然而,复叶发育的分子机制仍然是一个核心研究问题。SlTCP24和SlTCP29是两种具有保守TCP基序的植物特异性转录因子,它们协同调节番茄复叶的发育。当它们同时被敲除时,小叶的数量显著增加,叶片的形状变得更加复杂。SlTCP24和SlTCP29可以形成同源二聚体和异二聚体,并且这种二聚作用受到叶极性调节因子SlAS2的阻碍,该调节因子与SlTCP24、SlTCP29相互作用。SlTCP24和SlTCP29可以与SlCKX2启动子的TCP结合顺式元件结合并激活其转录。具有SlTCP24和SlTCP29双基因敲除的转基因植物具有较低的SlCKX2转录水平和较高的细胞分裂素水平。这项工作鉴定了番茄复叶发育的两个关键调控因子及其参与细胞分裂素代谢途径的靶向基因。在此基础上,提出了一个复叶发育调控模型。
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引用次数: 0
Epigenomic divergence correlates with sequence polymorphism in Arabidopsis paralogs 拟南芥旁系表观基因组差异与序列多态性
IF 9.4 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-08-24 DOI: 10.1111/nph.19227
Sunil K. Kenchanmane Raju, Mariele Lensink, Daniel J. Kliebenstein, Chad Niederhuth, Grey Monroe

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引用次数: 1
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New Phytologist
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