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October 28, 2024
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Article

A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology

Publicated to: Nature Plants. 9 (9): 1558-1571 - 2023-08-10 9(9), DOI: 10.1038/s41477-023-01489-8

Authors:

Ranawaka; B; An; J; Lorenc; MT; Jung; H; Sulli; M; Aprea; G; Roden; S; Llaca; V; Hayashi; S; Asadyar; L; LeBlanc; Z; Ahmed; Z; Naim; F; de Campos; SB; Cooper; T; de Felippes; FF; Dong; P; Zhong; S; García-Carpintero; V; Orzaez; D; Dudley; KJ; Bombarely; A; Bally; J; Winefield; C; Giuliano; G; Waterhouse; P
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Affiliations

ARC Ctr Excellence Plant Success Nat & Agr, Brisbane - Author
Casaccia Res Ctr, Italian Natl Agcy New Technol, Energy & Sustainable Econ Dev ENEA - Author
Chinese Univ Hong Kong, Sch Life Sci, State Key Lab Agrobiotechnol - Author
Corteva Agrisci, Genom Technol - Author
Curtin Univ, Ctr Crop & Dis Management, Sch Mol & Life Sci, Bentley - Author
Lincoln Univ, Dept Wine Food & Mol Biosci - Author
Queensland Univ Technol QUT, Ctr Agr & Bioecon, Brisbane - Author
Queensland Univ Technol QUT, QUT Cent Analyt Res Facil, Brisbane - Author
Univ Milan - Author
Univ Politecn Valencia, CSIC, Inst Biol Mol & Celular Plantas IBMCP - Author
Univ Queensland, Ctr Anim Sci, Queensland Alliance Agr & Food Innovat QAAFI, Brisbane - Author
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Abstract

Nicotiana benthamiana is an invaluable model plant and biotechnology platform with a similar to 3 Gb allotetraploid genome. To further improve its usefulness and versatility, we have produced high-quality chromosome-level genome assemblies, coupled with transcriptome, epigenome, microRNA and transposable element datasets, for the ubiquitously used LAB strain and a related wild accession, QLD. In addition, single nucleotide polymorphism maps have been produced for a further two laboratory strains and four wild accessions. Despite the loss of five chromosomes from the ancestral tetraploid, expansion of intergenic regions, widespread segmental allopolyploidy, advanced diploidization and evidence of recent bursts of Copia pseudovirus (Copia) mobility not seen in other Nicotiana genomes, the two subgenomes of N. benthamiana show large regions of synteny across the Solanaceae. LAB and QLD have many genetic, metabolic and phenotypic differences, including disparate RNA interference responses, but are highly interfertile and amenable to genome editing and both transient and stable transformation. The LAB/QLD combination has the potential to be as useful as the Columbia-0/Landsberg errecta partnership, utilized from the early pioneering days of Arabidopsis genomics to today.
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Keywords

AccurateArabidopsisBiotechnologyEvolutionGeneticsGenome sequenceGenome, plantGenomicsIdentificationMultiomicsPlant genomePlant genomesProvides insightsRead alignmentRecombinationSyntenyTobaccoTransposable elementsWeb server

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Nature Plants 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, 2023, it was in position 4/265, thus managing to position itself as a Q1 (Primer Cuartil), in the category Plant Sciences. Notably, the journal is positioned above the 90th percentile.

This publication has been distinguished as a “Highly Cited Paper” by the agencies WoS (ESI, Clarivate) and ESI (Clarivate), meaning that it ranks within the top 1% of the most cited articles in its thematic field during the year of its publication. In terms of the observed impact of the contribution, this work is considered one of the most influential worldwide, as it is recognized as highly cited. (source consulted: ESI Nov 13, 2025)

And this is evidenced by the extremely high normalized impacts through some of the main indicators of this type, which, although dynamic over time and dependent on the set of average global citations at the time of calculation, already indicate that they are well above the average in different agencies:

  • Normalization of citations relative to the expected citation rate (ESI) by the Clarivate agency: 13.28 (source consulted: ESI Nov 13, 2025)
  • Weighted Average of Normalized Impact by the Scopus agency: 12.5 (source consulted: FECYT Mar 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2026-04-02, the following number of citations:

  • WoS: 64
  • Scopus: 65
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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 2026-04-02:

  • 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: 113.
  • 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: 113 (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: 102.
  • The number of mentions on the social network X (formerly Twitter): 125 (Altmetric).
  • The number of mentions in news outlets: 4 (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: Australia; China; Hong Kong; Italy; New Zealand; United States of America.

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