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Abstract Background In the past few years, there has been an explosion in single-cell transcriptomics datasets, yet in vivo confirmation of these datasets is hampered in plants due to lack of robust validation methods. Likewise, modeling of plant development is hampered by paucity of spatial gene expression data. RNA fluorescence in situ hybridization (FISH) enables investigation of gene expression in the context of tissue type. Despite development of FISH methods for plants, easy and reliable whole mount FISH protocols have not yet been reported. Results We adapt a 3-day whole mount RNA-FISH method for plant species based on a combination of prior protocols that employs hybridization chain reaction (HCR), which amplifies the probe signal in an antibody-free manner. Our whole mount HCR RNA-FISH method shows expected spatial signals with low background for gene transcripts with known spatial expression patterns in Arabidopsis inflorescences and monocot roots. It allows simultaneous detection of three transcripts in 3D. We also show that HCR RNA-FISH can be combined with endogenous fluorescent protein detection and with our improved immunohistochemistry (IHC) protocol. Conclusions The whole mount HCR RNA-FISH and IHC methods allow easy investigation of 3D spatial gene expression patterns in entire plant tissues.

Feeding an increasing world population in the context of climate change is one of the grand challenges faced by our generation. Here, the authors show that external application of synthetic complementary peptides can increase the abundance of target proteins to modulate plant growth or stress resistance.

Lipochitooligosaccharide (LCO) perception by legumes is required to establish symbiotic relationships with nitrogen fixing bacteria. Here the authors show that nutrient starvation can activate LCO perception in cereals to promote symbiotic association with arbuscular mycorrhizal fungi.

Summary: MicroRNAs (miRNAs) are transcribed as long primary transcripts (pri-miRNAs) by RNA polymerase II. Plant pri-miRNAs encode regulatory peptides called miPEPs, which specifically enhance the transcription of the pri-miRNA from which they originate. However, paradoxically, whereas miPEPs have been identified in different plant species, they are poorly conserved, raising the question of the mechanisms underlying their specificity. To address this point, we identify and re-annotate multiple Arabidopsis thaliana pri-miRNAs in order to identify ORF encoding miPEPs. The study of several identified miPEPs in different species show that non-conserved miPEPs are only active in their plant of origin, whereas conserved ones are active in different species. Finally, we find that miPEP activity relies on the presence of its own miORF, explaining both the lack of selection pressure on miPEP sequence and the ability for non-conserved peptides to play a similar role, i.e., to activate the expression of their corresponding miRNA.

Arbuscular mycorrhizal (AM) symbiosis is an intimate and ancient symbiosis found between most of terrestrial plants and fungi from the Glomeromycota family. Later during evolution, the establishment of the nodulation between legume plants and soil bacteria known as rhizobia, involved several genes of the signalling pathway previously implicated for AM symbiosis. For the past years, the identification of the genes belonging to this Common Symbiotic Signalling Pathway have been mostly done on nodulation. Among the different genes already well identified as required for nodulation, we focused our attention on the involvement of Nodule Inception (NIN) in AM symbiosis. We show here that NIN expression is induced during AM symbiosis, and that the Medicago truncatula nin mutant is less colonized than the wild type M. truncatula strain. Moreover, nin mutant displays a defect in the ability to be infected by the fungus Rhizophagus irregularis. This work brings a new evidence of the common genes involved in overlapping signalling pathways of both nodulation and in AM symbiosis.

Background: In the past few years, there has been an explosion in single-cell transcriptomics datasets, yet in vivo confirmation of these datasets is hampered in plants due to lack of robust validation methods. Likewise, modeling of plant development is hampered by paucity of spatial gene expression data. RNA fluorescence in situ hybridization (FISH) enables investigation of gene expression in the context of tissue type. Despite development of FISH methods for plants, easy and reliable whole mount FISH protocols have not yet been reported. Results: We adapt a 3-day whole mount RNA-FISH method for plant species based on a combination of prior protocols that employs hybridization chain reaction (HCR), which amplifies the probe signal in an antibody-free manner. Our whole mount HCR RNA-FISH method shows expected spatial signals with low background for gene transcripts with known spatial expression patterns in Arabidopsis inflorescences and monocot roots. It allows simultaneous detection of three transcripts in 3D. We also show that HCR RNA-FISH can be combined with endogenous fluorescent protein detection and with our improved immunohistochemistry (IHC) protocol. Conclusions: The whole mount HCR RNA-FISH and IHC methods allow easy investigation of 3D spatial gene expression patterns in entire plant tissues. [ABSTRACT FROM AUTHOR]

Grasslands represent an essential part of terrestrial ecosystems. In particular, coastal grasslands are dominated by the influence of environmental factors resulting from sea–land interaction. Therefore, coastal grasslands are extremely heterogeneous both spatially and temporally. In this review, recent knowledge in the field of biotic interactions in coastal grassland soil is summarized. A detailed analysis of arbuscular mycorrhiza symbiosis, rhizobial symbiosis, plant–parasitic plant interactions, and plant–plant interactions is performed. The role of particular biotic interactions in the functioning of a coastal grassland ecosystem is characterized. Special emphasis is placed on future directions and development of practical applications for sustainable agriculture and environmental restoration. It is concluded that plant biotic interactions in soil are omnipresent and important constituents in different ecosystem services provided by coastal grasslands. [ABSTRACT FROM AUTHOR]

A study published in the Plant Biotechnology Journal explores the use of immune-enhancing microRNA-encoded peptides (miPEPs) to combat plant diseases and improve crop yields. The researchers identified 17 miPEPs that decreased the expression of a gene associated with plant defense responses, and three miPEPs that increased its expression. These miPEPs were found to decrease fungal colonization in Arabidopsis thaliana plants without directly harming the fungi. The study also demonstrated that the miPEPs were effective in reducing the incidence of Botrytis cinerea infection in strawberry, bean, and tomato plants. Field trials with tomato plants treated with a specific miPEP showed a 35% improvement in crop yields. The research highlights the potential of miPEPs as an alternative to chemical fungicides in agriculture. [Extracted from the article]

Their results involve the CLV3 peptide as well as CLV1 and CLV2/CRN receptors that promote auxin-dependent primordium initiation, likely by inducing I YUCCA i auxin biosynthesis genes. Keywords: auxin; morphogenesis; plant development; regeneration; single-cell transcriptomics EN auxin morphogenesis plant development regeneration single-cell transcriptomics 1729 1731 3 11/06/23 20231201 NES 231201 After having spent over 2 years mostly online due to the COVID-19 outbreak, the Mechanism of Plant Development Conference 2022 renewed our ability to meet and engage in-person with fantastic scientists from across the field of plant development. Auxin, morphogenesis, plant development, regeneration, single-cell transcriptomics. [Extracted from the article]

The current agriculture main challenge is to maintain food production while facing multiple threats such as increasing world population, temperature increase, lack of agrochemicals due to health issues and uprising of weeds resistant to herbicides. Developing novel, alternative, and safe methods is hence of paramount importance. Here, we show that complementary peptides (cPEPs) from any gene can be designed to target specifically plant coding genes. External application of synthetic peptides increases the abundance of the targeted protein, leading to related phenotypes. Moreover, we provide evidence that cPEPs can be powerful tools in agronomy to improve plant traits, such as growth, resistance to pathogen or heat stress, without the needs of genetic approaches. Finally, by combining their activity they can also be used to reduce weed growth. Feeding an increasing world population in the context of climate change is one of the grand challenges faced by our generation. Here, the authors show that external application of synthetic complementary peptides can increase the abundance of target proteins to modulate plant growth or stress resistance. [ABSTRACT FROM AUTHOR]

Many plants associate with arbuscular mycorrhizal fungi for nutrient acquisition, while legumes also associate with nitrogen-fixing rhizobial bacteria. Both associations rely on symbiosis signaling and here we show that cereals can perceive lipochitooligosaccharides (LCOs) for activation of symbiosis signaling, surprisingly including Nod factors produced by nitrogen-fixing bacteria. However, legumes show stringent perception of specifically decorated LCOs, that is absent in cereals. LCO perception in plants is activated by nutrient starvation, through transcriptional regulation of Nodulation Signaling Pathway (NSP)1 and NSP2. These transcription factors induce expression of an LCO receptor and act through the control of strigolactone biosynthesis and the karrikin-like receptor DWARF14-LIKE. We conclude that LCO production and perception is coordinately regulated by nutrient starvation to promote engagement with mycorrhizal fungi. Our work has implications for the use of both mycorrhizal and rhizobial associations for sustainable productivity in cereals. Lipochitooligosaccharide (LCO) perception by legumes is required to establish symbiotic relationships with nitrogen fixing bacteria. Here the authors show that nutrient starvation can activate LCO perception in cereals to promote symbiotic association with arbuscular mycorrhizal fungi. [ABSTRACT FROM AUTHOR]

The Plant Cell Atlas (PCA) community hosted a virtual symposium on December 9 and 10, 2021 on single cell and spatial omics technologies. The conference gathered almost 500 academic, industry, and government leaders to identify the needs and directions of the PCA community and to explore how establishing a data synthesis center would address these needs and accelerate progress. This report details the presentations and discussions focused on the possibility of a data synthesis center for a PCA and the expected impacts of such a center on advancing science and technology globally. Community discussions focused on topics such as data analysis tools and annotation standards; computational expertise and cyber‐infrastructure; modes of community organization and engagement; methods for ensuring a broad reach in the PCA community; recruitment, training, and nurturing of new talent; and the overall impact of the PCA initiative. These targeted discussions facilitated dialogue among the participants to gauge whether PCA might be a vehicle for formulating a data synthesis center. The conversations also explored how online tools can be leveraged to help broaden the reach of the PCA (i.e., online contests, virtual networking, and social media stakeholder engagement) and decrease costs of conducting research (e.g., virtual REU opportunities). Major recommendations for the future of the PCA included establishing standards, creating dashboards for easy and intuitive access to data, and engaging with a broad community of stakeholders. The discussions also identified the following as being essential to the PCA's success: identifying homologous cell‐type markers and their biocuration, publishing datasets and computational pipelines, utilizing online tools for communication (such as Slack), and user‐friendly data visualization and data sharing. In conclusion, the development of a data synthesis center will help the PCA community achieve these goals by providing a centralized repository for existing and new data, a platform for sharing tools, and new analytical approaches through collaborative, multidisciplinary efforts. A data synthesis center will help the PCA reach milestones, such as community‐supported data evaluation metrics, accelerating plant research necessary for human and environmental health. [ABSTRACT FROM AUTHOR]

Recent findings revealed that plant pri-miRNAs encode regulatory peptides called miRNA-encoded peptides (miPEPs) (Lauressergues I et al i ., 2015; Sharma I et al i ., 2020). miPEPs specifically enhance the transcription of their pri-miRNA, leading to phenotypes consistent with the functions of their cognate miRNA. Keywords: microRNA; peptide; miPEPs EN microRNA peptide miPEPs 1687 1689 3 09/13/21 20210901 NES 210901 MicroRNAs (miRNAs) are small regulatory RNA molecules (21-24 nt) regulating the expression of target genes at the post-transcriptional level, by cleaving their mRNA. We were able to identify only one miRNA homolog of each in the corresponding genome, and we next searched the corresponding miPEPs in these pre-miRNAs and defined miPEPs in I B. oleracea i and I B. vulgaris i by the identification of the first ORF (Fig. [Extracted from the article]

• Root colonization by arbuscular mycorrhizal (AM) fungi is a complex and finely tuned process. Previous studies have shown that, among other plant hormones, auxin plays a role in this process but the specific involvement of Aux/IAAs, the key regulators of auxin responses, is still unknown. • In this study, we addressed the role of the tomato Sl-IAA27 during AM symbiosis by using Sl-IAA27-RNAi and pSL-IAA27::GUS stable tomato lines. • The data show that Sl-IAA27 expression is up-regulated by the AM fungus and that silencing of Sl-IAA27 has a negative impact on AM colonization. Sl-IAA27-silencing resulted in down-regulation of three genes involved in strigolactone synthesis, NSP1, D27 and MAX1, and treatment of Sl-IAA27-silenced plants with the strigolactone analog GR24 complemented their mycorrhizal defect phenotype. • Overall, the study identified an Aux/IAA gene as a new component of the signaling pathway controlling AM fungal colonization in tomato. This gene is proposed to control strigolactone biosynthesis via the regulation of NSP1. [ABSTRACT FROM AUTHOR]

Arbuscular mycorrhizal (AM) symbiosis is an intimate and ancient symbiosis found between most of terrestrial plants and fungi from the Glomeromycota family. Later during evolution, the establishment of the nodulation between legume plants and soil bacteria known as rhizobia, involved several genes of the signaling pathway previously implicated for AM symbiosis. For the past years, the identification of the genes belonging to this Common Symbiotic Signaling Pathway have been mostly done on nodulation. Among the different genes already well identified as required for nodulation, we focused our attention on the involvement of Nodule Inception (NIN) in AM symbiosis. We show here that NIN expression is induced during AM symbiosis, and that the Medicago truncatula nin mutant is less colonized than the wild-type M. truncatula strain. Moreover, nin mutant displays a defect in the ability to be infected by the fungus Rhizophagus irregularis. This work brings a new evidence of the common genes involved in overlapping signaling pathways of both nodulation and in AM symbiosis. [ABSTRACT FROM AUTHOR]

The article discusses the study on usage of exogenous application of synthetic microRNA-encoded peptide (miPEP)172c to stimulate nodulation in soybean. It shows that the exogenous treatment and synthetic peptides (miPEPs) has an impact on the cultured plant development and microbial interactions, and inhibiting the growth of adventives or exotic plants.

Thanks to the contribution of our reviewers, in 2021, the median time to first decision was 19 days and the median time to publication was 38 days. Thanks to the great efforts of our reviewers, I Agronomy i was able to maintain its standards for the high quality of its published papers. Rigorous peer-reviews are the basis of high-quality academic publishing. [Extracted from the article]