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1. Exploring plant cis‐regulatory elements at single‐cell resolution: overcoming biological and computational challenges to advance plant research

   https://doi.org/10.1111/tpj.16351  

   Mendieta, John Pablo ; Sangra, Ankush ; Yan, Haidong ; Minow, Mark A. A. ; Schmitz, Robert J. ( June 2023 , The Plant Journal)

   Cis‐regulatory elements (CREs) are important sequences for gene expression and for plant biological processes such as development, evolution, domestication, and stress response. However, studying CREs in plant genomes has been challenging. The totipotent nature of plant cells, coupled with the inability to maintain plant cell types in culture and the inherent technical challenges posed by the cell wall has limited our understanding of how plant cell types acquire and maintain their identities and respond to the environment via CRE usage. Advances in single‐cell epigenomics have revolutionized the field of identifying cell‐type‐specific CREs. These new technologies have the potential to significantly advance our understanding of plant CRE biology, and shed light on how the regulatory genome gives rise to diverse plant phenomena. However, there are significant biological and computational challenges associated with analyzing single‐cell epigenomic datasets. In this review, we discuss the historical and foundational underpinnings of plant single‐cell research, challenges, and common pitfalls in the analysis of plant single‐cell epigenomic data, and highlight biological challenges unique to plants. Additionally, we discuss how the application of single‐cell epigenomic data in various contexts stands to transform our understanding of the importance of CREs in plant genomes.

    

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2. The changes in plant and soil C pools and their C : N stoichiometry control grassland N retention under elevated N inputs

   https://doi.org/10.1002/eap.2517  

   Yang, Sen ; Liu, Weixing ; Guo, Lulu ; Wang, Chengzhang ; Deng, Meifeng ; Peng, Ziyang ; Liu, Lingli ( March 2022 , Ecological Applications)
3. Community Response to Extreme Drought ( CRED ): a framework for drought‐induced shifts in plant–plant interactions

   https://doi.org/10.1111/nph.15595  

   Ploughe, Laura W. ; Jacobs, Elin M. ; Frank, Graham S. ; Greenler, Skye M. ; Smith, Melinda D. ; Dukes, Jeffrey S. ( January 2019 , New Phytologist)

   Contents
   	Summary	52
   I.	Introduction	52
   II.	The Community Response to Extreme Drought (CRED) framework	55
   III.	Post‐drought rewetting rates: system and community recovery	61
   IV.	Site‐specific characteristics influencing community resistance and resilience	63
   V.	Conclusions	64
   	Acknowledgements	65
   	References	66

   As climate changes, many regions of the world are projected to experience more intense droughts, which can drive changes in plant community composition through a variety of mechanisms. During drought, community composition can respond directly to resource limitation, but biotic interactions modify the availability of these resources. Here, we develop the Community Response to Extreme Drought framework (CRED), which organizes the temporal progression of mechanisms and plant–plant interactions that may lead to community changes during and after a drought. TheCREDframework applies some principles of the stress gradient hypothesis (SGH), which proposes that the balance between competition and facilitation changes with increasing stress. TheCREDframework suggests that net biotic interactions (NBI), the relative frequency and intensity of facilitative (+) and competitive (−) interactions between plants, will change temporally, becoming more positive under increasing drought stress and more negative as drought stress decreases. Furthermore, we suggest that rewetting rates affect the rate of resource amelioration, specifically water and nitrogen, altering productivity responses and the intensity and importance ofNBI, all of which will influence drought‐induced compositional changes. System‐specific variables and the intensity of drought influence the strength of these interactions, and ultimately the system's resistance and resilience to drought.

    

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4. Historical Plant Sales ( HPS ) database: Documenting the spatiotemporal history of plant sales in the conterminous U.S.

   https://doi.org/10.1002/ecy.4106  

   Fertakos, Matthew E. ; Beaury, Evelyn M. ; Ford, Neil R. ; Kinlock, Nicole L. ; Adams, Denise W. ; Bradley, Bethany A. ( May 2023 , Ecology)

   Historical horticultural plant sales influence native and nonnative species assemblages in contemporary ecosystems. Over half of nonnative, invasive plants naturalized in the United States were introduced as ornamentals, and the spatial and temporal patterns of early introduction undoubtedly influence current invasion ecology. While thousands of digitized nursery catalogs documenting these introductions are publicly available, they have not been standardized in a single database. To fill this gap, we obtained the names of all plant taxa (species, subspecies, and varieties) present in the Biodiversity Heritage Library's (BHL) Seed and Nursery Catalog Collection. We then searched the BHL database for these names and downloaded all available records. We combined BHL records with data from an encyclopedia of heirloom ornamental plants to create a single database of historical nursery sales in the US. Each record represents an individual taxon offered for sale at an individual time in a specific nursery's catalog. We standardized records to the current World Flora Online (http://worldfloraonline.org) accepted taxonomy and appended accepted USDA code, growth habit, and introduction status. We also appended whether taxa were reported as invasive in the Global Plant Invaders (GPI) data set or the Global Invasive Species Database (GISD) or regulated in the conterminous US. Lastly, we geocoded all reported publication locations. The data set contains 2,445,875 records from nurseries in at least 2795 unique locations, with the majority of catalogs published between 1890 and 1950. Nurseries were located in all conterminous states but were concentrated in the eastern US and California. We identified 19,140 unique horticultural taxa, of which 8642 matched taxa in the USDA Plants database. The USDA Plants database is limited to native and naturalized taxa in the US. Native or introduced status was listed in USDA Plants for 7018 of included taxa, while 1642 had an unknown status. The remaining 10,498 taxa are not naturalized according to USDA Plants or are of varieties of native and introduced taxa that did not match USDA Plants taxonomy. The majority of taxa in the Historical Plant Sales (HPS) database with an identified status are native (65.5%; 4596 of 7018 taxa), of which 393 taxa are reported as invasive outside of the US. Of the 2381 introduced taxa, 1103 (46.3%) are reported as invasive somewhere globally. Despite a richer pool of native taxa, most cataloged plant records with an identified status were of introduced taxa (54.1%; 1,045,684 of 1,933,925 records). Plants reported as invasive somewhere globally comprised a large portion of records with an identified status (38.7%; 747,953 of 1,933,925 records) underscoring the large role of ornamental introductions in facilitating plant invasions. The HPS database provides a consolidated and standardized perspective on the history of native, introduced, and invasive plant sales in the US. We release these data into the public domain under a Creative Commons Zero license waiver (https://creativecommons.org/share-your-work/publicdomain/cc0/). Individuals who use these data for publication may cite the associated data paper.

    

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5. Calmodulin‐binding transcription activator AtSR1 / CAMTA3 fine‐tunes plant immune response by transcriptional regulation of the salicylate receptor NPR1

   https://doi.org/10.1111/pce.14123  

   Yuan, Peiguo ; Tanaka, Kiwamu ; Poovaiah, B. W. ( June 2021 , Plant, Cell & Environment)

   Calcium (Ca²⁺) signalling regulates salicylic acid (SA)‐mediated immune response through calmodulin‐meditated transcriptional activators, AtSRs/CAMTAs, but its mechanism is not fully understood. Here, we report an AtSR1/CAMTA3‐mediated regulatory mechanism involving the expression of the SA receptor, NPR1. Results indicate that the transcriptional expression ofNPR1was regulated by AtSR1 binding to a CGCG box in theNPR1promotor. Theatsr1mutant exhibited resistance to the virulent strain ofPseudomonas syringaepv.tomato(Pst), however, was susceptible to an avirulentPststrain carryingavrRpt2, due to the failure of the induction of hypersensitive responses. These resistant/susceptible phenotypes in theatsr1mutant were reversed in thenpr1mutant background, suggesting that AtSR1 regulates NPR1 as a downstream target during plant immune response. The virulentPststrain triggered a transient elevation in intracellular Ca²⁺concentration, whereas the avirulentPststrain triggered a prolonged change. The distinct Ca²⁺signatures were decoded into the regulation of NPR1 expression through AtSR1's IQ motif binding with Ca²⁺‐free‐CaM2, while AtSR1's calmodulin‐binding domain with Ca²⁺‐bound‐CaM2. These observations reveal a role for AtSR1 as a Ca²⁺‐mediated transcription regulator in controlling the NPR1‐mediated plant immune response.

    

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