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Analysis of institutional authors

Conde, DanielAuthor

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February 9, 2025
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Review
Hybrid Gold

Investigating biological nitrogen fixation via single-cell transcriptomics

Publicated to: Journal Of Experimental Botany. 76 (4): 931-949 - 2025-01-31 76(4), DOI: 10.1093/jxb/erae454

Authors:

Pereira WJ; Conde D; Perron N; Schmidt HW; Dervinis C; Venado RE; Ané JM; Kirst M
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Affiliations

Univ Florida, Sch Forest Fisheries & Geomat Sci, Gainesville, FL 32611 USA - Author
Univ Politecn Madrid, Ctr Biotecnol & Genom Plantas, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA C, Madrid 28223, Spain - Author
Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA - Author
Univ Wisconsin, Dept Plant & Agroecosyst Sci, Madison, WI 53706 USA - Author
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Abstract

The extensive use of nitrogen fertilizers has detrimental environmental consequences, and it is essential for society to explore sustainable alternatives. One promising avenue is engineering root nodule symbiosis, a naturally occurring process in certain plant species within the nitrogen-fixing clade, into non-leguminous crops. Advancements in single-cell transcriptomics provide unprecedented opportunities to dissect the molecular mechanisms underlying root nodule symbiosis at the cellular level. This review summarizes key findings from single-cell studies in Medicago truncatula, Lotus japonicus, and Glycine max. We highlight how these studies address fundamental questions about the development of root nodule symbiosis, including the following findings: (i) single-cell transcriptomics has revealed a conserved transcriptional program in root hair and cortical cells during rhizobial infection, suggesting a common infection pathway across legume species; (ii) characterization of determinate and indeterminate nodules using single-cell technologies supports the compartmentalization of nitrogen fixation, assimilation, and transport into distinct cell populations; (iii) single-cell transcriptomics data have enabled the identification of novel root nodule symbiosis genes and provided new approaches for prioritizing candidate genes for functional characterization; and (iv) trajectory inference and RNA velocity analyses of single-cell transcriptomics data have allowed the reconstruction of cellular lineages and dynamic transcriptional states during root nodule symbiosis. Single-cell genomics of root nodule symbiosis has revealed its molecular and cellular development program. We review the published literature to identify consistent yet previously hidden features of this symbiosis.
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Keywords

BacteriaDependent protein-kinaseExpressionGene familyLegume noduleLotus japonicusMedicago truncatulaMedicago-truncatulaNitrogen fixationNodulationNodule organogenesisPlantRna-sequencingRootRoot nodule symbiosisSingle-cellSoybeaSoybean

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Journal Of Experimental Botany due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2025, it was in position 24/273, thus managing to position itself as a Q1 (Primer Cuartil), in the category Plant Sciences. Notably, the journal is positioned above the 90th percentile.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2025-12-21:

  • Scopus: 1
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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-12-21:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 11.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 11 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 9.
  • The number of mentions on the social network X (formerly Twitter): 10 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: United States of America.

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Awards linked to the item

This work was supported by the United States Department of Energy (DOE) Office of Science Biological and Environmental Research (grant DE-SC-0018247) to MK and JMA.
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