Nature Plants最新文献

Ferns are essential for understanding plant evolution; however, their large and intricate genomes have kept their genetic landscape largely unexplored, with only a few genomes sequenced and limited transcriptomic data available. To bridge this gap, we generated extensive RNA-sequencing data across various organs from 22 representative fern species, resulting in high-quality transcriptome assemblies. These data enabled us to construct a time-calibrated phylogeny for ferns, encompassing all major clades, which revealed numerous instances of whole-genome duplication. We highlighted the distinctiveness of fern genetics, discovering that half of the identified gene families are unique to ferns. Our exploration of fern cell walls through biochemical and immunological analyses uncovered the presence of the lignin syringyl unit, along with evidence of its independent evolution in ferns. Additionally, the identification of an unusual sugar in fern cell walls suggests a divergent evolutionary trajectory in cell wall biochemistry, probably influenced by gene duplication and sub-functionalization. To facilitate further research, we have developed an online database that includes preloaded genomic and transcriptomic data for ferns and other land plants. We used this database to demonstrate the independent evolution of lignocellulosic gene modules in ferns. Our findings provide a comprehensive framework illustrating the unique evolutionary journey ferns have undertaken since diverging from the last common ancestor of euphyllophytes more than 360 million years ago.

Auxins are a group of phytohormones that control plant growth and development. Their crucial role in plant physiology has inspired development of potent synthetic auxins that can be used as herbicides. Phenoxyacetic acid derivatives are a widely used group of auxin herbicides in agriculture and research. Despite their prevalence, the identity of the transporters required for distribution of these herbicides in plants is both poorly understood and the subject of controversial debate. Here we show that PIN-FORMED auxin transporters transport a range of phenoxyacetic acid herbicides across the membrane. We go on to characterize the molecular determinants of substrate specificity using a variety of different substrates as well as protein mutagenesis to probe the binding site. Finally, we present cryogenic electron microscopy structures of Arabidopsis thaliana PIN8 bound to either 2,4-dichlorophenoxyacetic acid or 4-chlorophenoxyacetic acid. These structures represent five key states from the transport cycle, allowing us to describe conformational changes associated with the transport cycle. Overall, our results reveal that phenoxyacetic acid herbicides use the same export machinery as endogenous auxins and exemplify how transporter binding sites undergo transformations that dictate substrate specificity. These results provide a foundation for future development of novel synthetic auxins and for precision breeding of herbicide-resistant crop plants.

DNA-binding with one-finger (Dof) proteins are a family of plant-specific transcription factors distinguished by the highly conserved Dof DNA-binding domain. Various members play crucial roles in diverse plant biological processes. However, it remains unclear how the Dof domain recognizes a restricted set of promoters for gene regulation by binding to just four nucleotides, AAAG/CTTT. Here we present the crystal structure of the Dof domain of CYCLING DOF FACTOR 1 (CDF1), a well-characterized Dof protein acting as a transcriptional repressor by binding to the CONSTANS promoter to regulate photoperiodic flowering, in complex with DNA containing two cis elements. The data reveal that the Dof domain exhibits a unique zinc ribbon fold that includes a three-stranded antiparallel β-sheet and a carboxy-terminal loop, enabling DNA recognition accompanied by directional expansion of the major groove. These features facilitate binding to contiguous target cis elements in a proper arrangement to effectively regulate gene expression.

Genome editing is transforming plant biology by enabling precise DNA modifications. However, delivery of editing systems into plants remains challenging, often requiring slow, genotype-specific methods such as tissue culture or transformation¹. Plant viruses, which naturally infect and spread to most tissues, present a promising delivery system for editing reagents. However, many viruses have limited cargo capacities, restricting their ability to carry large CRISPR-Cas systems. Here we engineered tobacco rattle virus (TRV) to carry the compact RNA-guided TnpB enzyme ISYmu1 and its guide RNA. This innovation allowed transgene-free editing of Arabidopsis thaliana in a single step, with edits inherited in the subsequent generation. By overcoming traditional reagent delivery barriers, this approach offers a novel platform for genome editing, which can greatly accelerate plant biotechnology and basic research.

Climate-driven forest mortality events have been extensively observed in recent decades, prompting the question of how quickly these affected forests can recover their functionality following such events. Here we assessed forest recovery in vegetation greenness (normalized difference vegetation index) and canopy water content (normalized difference infrared index) for 1,699 well-documented forest mortality events across 1,600 sites worldwide. By analysing 158,427 Landsat surface reflectance images sampled from these sites, we provided a global assessment on the time required for impacted forests to return to their pre-mortality state (recovery time). Our findings reveal a consistent decline in global forest recovery rate over the past decades indicated by both greenness and canopy water content. This decline is particularly noticeable since the 1990s. Further analysis on underlying mechanisms suggests that this reduction in global forest recovery rates is primarily associated with rising temperatures and increased water scarcity, while the escalation in the severity of forest mortality contributes only partially to this reduction. Moreover, our global-scale analysis reveals that the recovery of forest canopy water content lags significantly behind that of vegetation greenness, implying that vegetation indices based solely on greenness can overestimate post-mortality recovery rates globally. Our findings underscore the increasing vulnerability of forest ecosystems to future warming and water insufficiency, accentuating the need to prioritize forest conservation and restoration as an integral component of efforts to mitigate climate change impacts.

Molecular and physiological changes across crop developmental stages shape the plant phenome and render its prediction from genetic markers challenging. Here we present dynamicGP, an efficient computational approach that combines genomic prediction with dynamic mode decomposition to characterize the temporal changes and to predict genotype-specific dynamics for multiple morphometric, geometric and colourimetric traits scored by high-throughput phenotyping. Using genetic markers and data from high-throughput phenotyping of a maize multiparent advanced generation inter-cross population and an Arabidopsis thaliana diversity panel, we show that dynamicGP outperforms a baseline genomic prediction approach for the multiple traits. We demonstrate that the developmental dynamics of traits whose heritability varies less over time can be predicted with higher accuracy. The approach paves the way for interrogating and integrating the dynamical interactions between genotype and environment over plant development to improve the prediction accuracy of agronomically relevant traits.