Manuscript submission

Formats and organization

In order for manuscripts to be suitable for publishing as Online Accepted papers, authors are required to adhere strictly to the following formatting guidelines.  Even though we do not have a page limit, we highly recommend that manuscripts are written concisely. Around 6000 words (40000 characters with space)  with 3 to 7 data displays should be aimed for.

Layout

The layout of the manuscript should be as follows:

• Title
• Full name(s) of author(s) (the corresponding author should be indicated)
• Address(es) of author(s) (including e-mail address for the corresponding author)
• Funding
• Abstract
• Introduction
• Materials and methods
• Results and Discussion (combined or separated)
• Author contributions
• Acknowledgements
• Data availability statement
• AI generative statement
• References
• Supporting information
• Figure legends (included in the main text document)
• Figures and tables are submitted as separate documents

Title

The title should be concise and appealing. Long and descriptive titles should be avoided.

Abstract

The abstract should not exceed 250 words, not be divided into paragraphs, sum up the most pertinent areas of the article and be self-contained for information retrieval purposes. There should be no unexplained abbreviations and preferably no references but the scientific name(s) and, where applicable, cultivar or variety of the plant(s) used should be spelt out in full. EC numbers should be given for the enzymes mentioned. A good abstract should therefore contain:

• a brief statement of the problem
• a brief statement of the authors’ objectives
• the major method(s)
• the main result(s)
• a concluding statement indicating how the results have increased our knowledge of the problem.

Introduction

The introduction should be concise, giving the reader an outline of the subject, presenting the “state-of-the-art”, leading into the reasons for the present study and its aims.

Materials and methods

The materials and method section should be detailed. It should provide information on the number of independent experiments and replicates as well as statistical methods. All growth conditions should be properly described, including the trade name and manufacturer of all lamps used, as well as irradiance (W m⁻²) or photosynthetic photon flux density (μmol m⁻² s⁻¹); lux or μE are not acceptable. The trade name(s) and suppliers of apparatus and chemicals used should also be given.

EC numbers should be given for enzymes used.

If the data includes microarray/Affimetrix analysis, authors should refer to the MIAME recommendations for guidance in preparing their manuscripts.

Statistical analysis and the detailed number of repetitions (what do you consider as repetition: a pool of X plants, X individuals coming from time-independent replications…) should be clearly stated. This information should be repeated in the legend of the corresponding Figures/Tables.

Results

The result section should be as objective and descriptive as possible and written in the past tense. Tables and figures should be comprehensible as far as possible without reference to the main text (including brief but descriptive legends).

Discussion

The discussion should not merely be a catalogue of results. The authors need to show how their findings advance our knowledge and understanding of the topic investigated. The discussion must be concisely written with the main points of the work logically presented and with reference to the relevant tables, figures and literature.

Author contributions

The contributions made by all authors should briefly be described. Physiologia Plantarum asks all authors to follow the guidelines outlined in the Committee on Publication Ethics (COPE) report from 2003. Detailed guidelines for the preparation of manuscripts and recommendations for ethical authorship can be found online.

Data availability statement

All accepted manuscripts are required to publish a Data availability Statement. Mostly to confirm the presence or absence of publicly shared data (“omics” results, gene sequence…) but also to confirm availability of all raw data and materials.

 1- Depositable data/publicly shared in a repository
All omics data should be made available online in public repositories.  The availability statement will describe how the data can be accessed and include a persistent identifier (e.g, a DOI for the data or an accession number) from the repository where you shared the data.

“omics” raw data, gene, protein, mutant accession number
“The data that support the findings of this study are openly available in [repository name e.g “figshare”] at http://doi.org/[doi], reference number [reference number].”

2- Non-depositable data/not publicly available in a repository
3.1 Physical data not deposited in a bank
Such as seeds, plasmids, antibodies….
“The data that support the findings of this study are available from the corresponding author upon reasonable request.”

3.2 Data self-contained within the manuscript or in the Supporting information
“Data sharing is not applicable to this article as all new created data is already contained within this article”
or
“The data that supports the findings of this study are available in the supplementary material of this article”

3.3 Data generated from already publicly available data (meta-analysis) 
“The data that support the findings were derived from the following resources available in the public domain: [list resources and URLs]”

4- Non-generation of data (review, opinions…)
“Data sharing is not applicable to this article as no new data were created or analyzed in this study.”

 

Generative AI statement

Although AI could be used for text and figures (see below for details), authors must ensure that AI-generated content:
– Complies with the specific usage policies of the AI tools
– Includes proper attribution where applicable.
– Does not violate copyright laws.
– Has not introduced biases, inaccuracies, or misleading information.

All accepted manuscripts are required to publish a generative AI Statement. If you have used AI tools to generate ideas for improving the content of your text, asked for feedback regarding the structure
of the text, or asked an AI tool to rewrite it, this needs to be declared. The declaration does not apply to the use of basic tools used to check grammar, spelling and references. Figures partially or completely generated via AI should be declared in figure legend and in the AI statement.

Generative AI tools and related technologies
These guidelines apply to the use of generative AI technologies, such as Large Language Models (ChatGTP, Claude, Jasper etc) and text-to-image generators (DALL·E, Midjourney etc) in the writing, composing and editing of manuscripts submitted to Physiologia Plantarum.

AI-generated text
Generative AI tools do not meet the criteria for authorship, as they cannot be held accountable for the integrity of the scientific work and, therefore, must not be listed as authors or co-authors.

If the authors have used generative AI to generate text or data visualizations, the use must be disclosed in an AI generative statement. Additionally, the use should be clearly described in the Material and Methods section, including the tool’s names, its version, model and source. We encourage the authors to provide examples of input prompts and AI-generated outputs as supplementary materials to ensure transparency. The authors are responsible to check and curate for inaccuracies generated by the use of AI.

AI-generated/modified figures
AI generated data visualization need to be disclosed (see AI generative statement), thoroughly described and scientifically validated by you and your coauthors.

However, it is prohibited to generate a full scientific model using specific AI prompts.

It is also not allowed to replace photographs of species with idealized & enhanced AI visuals.

Adjustments such as brightness, contrast and colour are allowed only if the changes do not obscure or eliminate any information present in the original. Otherwise, we encourage our authors to take the safe route and use either paid programs like the Creative Cloud Suit for brightness, contrast, and color adjustments, or freely available programs like Krita or Inkscape.

When it comes to resolution problems for figures, we discourage using AI tools as well, as they degrade and modify the written text in the figures. Please make sure you save your files at high resolutions from the beginning.

 

Citations and References

Citations and references follow the Harvard style. While small styling mistakes are not a problem (adjusted by our typesetter team), citations and references should be properly formatted:

Citations (in-text reference) should have the form:

• One author: Gabriel (2000) and (Gabriel, 2000).
• Two authors: (Mathes & Severa, 2004) and Mathes and Severa (2004).
• Three or more authors Waterman et al. (1993) and (Waterman et al., 1993).

References should be listed alphabetically (no numbering) according to the first-named author.

Authors (date) Title. Journal, volume: pages

ex: Holding, M.Y., Saulino, M.F., Overton, E.A., Kornbluth, I.D. & Freedman, M.K. (2008) Interventions in chronic pain management. 1. Update on important definitions in pain management. Archives of Physical Medicine and Rehabilitation, 89 (3), 38–40
Note: Replace volume number and pages by the doi number when the article is published ahead of print.

Not peer-reviewed articles/ pre-print (ArXiv, bioRxiv, psyArXiv, SocArXiv, engrXiv)
Silas, P., Yates, J.R. & Haynes, P.D. (2008) Density-functional investigation of the rhombohedral to simple cubic phase transition of arsenic. Arxiv. [Preprint] Available from: http://arxiv.org/abs/0810.1692. [Accessed: 23rd July 2010].

Supporting information

Authors are welcome to submit additional supporting information, such as data sets or additional figures or tables.
It will be published online in the format supplied by the author and are not copyedited by the Editorial office or the Publisher.

If possible, supporting information should be provided as a single pdf including figures, tables and corresponding legends as well as the manuscript’s title and authors’ names. Figure legend and number need to be included with the figure itself (stand-alone figure) and not in the main text as it is for the main figures. Excel files or movies can be sent separately.

Authors should include a ’supporting information’ section immediately after their references section, which should be in the following form:

Tables and figures

Tables

Each table should be on a separate page furnished with explanatory headings. Tables must be planned to fit a printed width of either 80 or 166 mm. Footnotes are usually not allowed. Tables should be submitted as editable text files, such as DOCX, or ODT.

Figures

Figure format and aesthetics

Each figure should be placed in a separate file and named according to its figure number (ex. Figure 1). Save photographic images in TIFF format at a resolution of no less than 300 dpi. Line art and combination figures should be saved in PDF or TIFF format at a resolution of no less than 600 dpi. Save TIFF files using LZW compression. The colour mode for black and white figures should be greyscale. Colour images should be saved in RGB colour mode.

 

Figures should have a maximum final width of 85,5 mm (single-column), 120-155 mm (1.5-column) or 178 mm (double-column). The font used should be either Helvetica regular or Arial regular. Letters, numbers and symbols must appear clearly but not oversized. The suitable final size for lettering is 2–3 mm (8-12 pt) at printed size.

Avoid complicated symbols or patterns. Use open and closed circles, squares and triangles; open, striped and closed bars in histograms. Graphs and histograms should be boxed in and scale marks (turning inwards) provided. Lines should be clear, but not thick and heavy, line weights of between 0.35 and 1.5 pt are suitable.

Adjustments for colour vision-impaired readers

When preparing your figures please take into account that some readers have deficient colour vision. Images of fluorescent double-staining micrographs and DNA chips should preferably not contain a combination of red and green. Please use magenta and green instead. Also, avoid using red characters on a dark background. In colour graphs and line art, use both colour and shape (different symbols and line types) to convey information. More detailed information can be found at: http://jfly.iam.u-tokyo.ac.jp/color/.

A simple tool to convert your red into magenta is ImageJ, a freely available program. Open the figure in Image J (it opens all formats). In the tab ‘Image’, choose ‘lookup table’ and then ‘magenta’.

 

Image processing

Photographic images submitted to the journal should be minimally processed. No parts, regions or specific features of an image may be changed, moved, removed, obscured or enhanced. Changes of brightness, contrast and colour balance are allowed if they are applied to the whole image and equally to controls, provided that no information in the original image is misrepresented by the adjustments.

Images from different parts of a gel, or from different gels, that are grouped into a single figure must be clearly separated, e.g. with dividing lines.

All images in manuscripts accepted for publication will be scrutinized by the Editorial Office. Any indication of improper image manipulation will be reported to the Editor-in-Chief, who may request original image files and/or data from the authors. Failure to comply will lead to the revocation of the manuscript.

Photographs for social media

Authors are welcome to submit photographs suitable for social media use. They can either be sent to the Editorial Office or uploaded when submitting a manuscript with the label “social media”.

Style points

Units and numerals

The SI system should be used throughout. Use negative indices rather than solidus (e.g. mg L⁻¹, not mg/L). Use space between numeral and unit (e.g. 14 h, not 14h) and between units (e.g. μmol m⁻² s⁻¹) but no space between numeral and % or °C (34%, 5°C)

Use g (italic) and not rpm for centrifugation speed as rpm gives an indication of speed only when linked to a rotor size.

Scientific names

Give the full scientific name(s) of plant(s) used, as well as the cultivar (cv.) or variety (var.), where applicable. Spell out genus name at first mention abbreviated thereafter: e.g. Eucalyptus globulus in article title, at first mention in the abstract, main text, tables, figures or at the beginning of a sentence, but E. globulus thereafter.

As much as the field allows, use the Arabidopsis nomenclature for GENE, PROTEIN and mutant to facilitate the reading experience.

 

Data deposition and sharing

Physiologia Plantarum expects authors to share the data supporting their results by archiving it in an appropriate public repository. Authors should include a data availability statement, including a link to the repository they have used, that will be published alongside their paper. The chosen repository should offer guaranteed preservation (see the registry of research data repositories at https://www.re3data.org/) and allow for findable, accessible, interoperable, and re-useable data, according to FAIR Data Principles. Physiologia Plantarum notes that FAIR data sharing allows for access to shared data under restrictions (e.g, to protect confidential or proprietary information). We note that the FAIR principles encourage you to share data in ways that are as open as possible (but can be as closed as necessary).

Any novel nucleic acid and sequence data should be deposited by the authors and referred to in their paper with the EMBL Data Library, GenBank or DDBJ. Deposition of such data should, at the latest, be made immediately after the paper has been accepted for publication, so that the authors can add the relevant accession number in the text at the proof stage. Please note that Arabidopsis names must be registered to TAIR before use to check for availability and avoid redundancy. A similar procedure should be made for other plant species, where relevant.