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Author Instructions
Plant Direct is a sound science journal for the plant sciences that give prompt and equal consideration to papers reporting work dealing with a variety of subjects. Topics include but are not limited to genetics, biochemistry, development, cell biology, biotic stress, abiotic stress, genomics, phenomics, bioinformatics, physiology, molecular biology, and evolution.
Manuscript Types
Editorial: These manuscripts serve as opinion pieces and are invitation only. Bespoke editorials that are not requested the Editor-in-Chief will not be permitted for peer review.
Original Research Articles: Includes primary research articles, negative reports with justifications, replication studies, and other studies that contribute to the advancement of the field.
Corrigendum: All requests for corrections should first be submitted to the editorial office at plantdirect@wiley.com .There is no publication fee charged for Corrigenda.
All submitted manuscripts will be screened by our CrossCheck similarity software. The journal reserves the right to return any manuscript that is deemed to have too much textual similarity to other published works even if the similar texts are cited properly. In these matters, the journal follows COPE guidelines.
To find out more about CrossCheck visit http://www.crossref.org/crosscheck.html.
Submission requirements
To represent our support of a global identifier and standardization in academic publishing, we require that all authors include a valid ORCID ID and email address during the submission process. Peer review of manuscripts will not commence until this information has been provided for all authors.
There are two ways to add your ORCID ID:1. On the Plant Direct Submission Homepage , click the “Use an Existing ID” to log into your ORCID ID and register it with Plant Direct.2. If you are already logged into the Plant Direct Submission Site, go to the “Modify Profile/Password” link at the bottom of the page underneath General Tasks. On the next page, go to the ORCID field to add the ID.Please Note: The email provided during submission must match the email associated with your ORCID account. If these emails are different, you will not be able to link the two accounts. At this time, each author must add their ORCID information individually. The system does not currently allow author information to be updated on behalf of an author.
Preprint policy
Plant Direct enthusiastically endorses the use of preprint servers. To show our enthusiasm, all manuscripts published using a preprint service before submission to the journal will be eligible for a discount. Please note that proof of prior upload to a preprint server (such as a valid link to the preprint server paper) must be provided during submission in order to qualify for the discount. At this time, we are not able to extend the discount to papers uploaded to a preprint server after the manuscript has already been submitted to Plant Direct.
We encourage authors to upload papers to the BioRxiv (http://biorxiv.org/) preprint server and use the direct submission option to submit their manuscripts to Plant Direct.
At this time, we also extend the APC discount to papers previously uploaded to the preprint servers Arxiv (https://arxiv.org/) and Peerjpreprints (https://peerj.com/about/author-instructions/)
If you have used a different preprint server that is not listed above, please contact the editorial office for guidance.
General Instructions
Manuscripts must be submitted in grammatically correct English. Manuscripts that do not meet this standard cannot be reviewed. Authors for whom English is a second language may wish to consult an English-speaking colleague or consider having their manuscript professionally edited before submission to improve the English. A list of independent suppliers of editing services can be found at http://authorservices.wiley.com/bauthor/english_language.asp. All services are paid for and arranged by the author, and use of one of these services does not guarantee acceptance or preference for publication.
A manuscript is considered for review and possible publication on the condition that it is submitted solely to Plant Direct, and that neither the manuscript nor a substantial portion of it is under consideration elsewhere.
Manuscript Preparation
In order to make the submission process as easy as humanly possible, we place very few restrictions on the way in which you prepare your article and it is not necessary to try to replicate the layout of the journal in your submission. We ask only that you consider your reviewers by ensuring that your manuscript is presented in a clear, generic and readable layout, and that all relevant sections are included. Line numbers are often helpful to reviewers. Fonts and spacing are not mandatory but do remember that the more readable your manuscript, the easier it will be for editors and reviewers to properly evaluate it. Post-acceptance, our production team will ensure that the paper is formatted and designed according to our journal style.
Please use the list below as a checklist to ensure the manuscript has all the information necessary for a successful review:
- Title page, including title, authors list along with authors’ names, authors’ affiliations, and contact information
- Abstract and 4–6 keywords
- Text (introduction, materials and methods, results, discussion)
- Literature cited (see below for tips on references)
- Tables (may be sent as a separate file if necessary)
- Figure legends
- Acknowledgements, including details of funding bodies with grant numbers
Please keep the following guidelines in mind while preparing your article for Plant Direct:
- Write for a wide audience of plant biologists.
- Avoid abbreviations and define those that are necessary on first use.
- Provide background info in the Introduction.
- Cite previous publications supporting your work.
- Cite primary research (not reviews) when possible; note that citation of recent research articles is not a substitute for citing original discoveries.
- Avoid “data not shown” or “unpublished results” – critical data must be available, or should not be cited.
- Citation to work “submitted” or “in preparation” is not permitted; all cited work must be on a preprint server, published or accepted and in press.
- Discussion should not repeat the Results, but explore the implications of the Results.
- Be concise.
Abstract (Maximum of 500 words)
Briefly describe the manuscript’s purpose, your hypothesis, methods, results and conclusions.
Methods
- Should be complete enough that other laboratories can replicate results.
- Standard procedures should be referenced with variations specifically described.
- Include complete description of experimental design and any statistical methods used.
- Describe novel DNA constructs, genetic stocks, enzyme preparations, antibodies and other reagents, and analytical software sufficiently to allow their reproduction. Provide any genes or new sequence data discussed in the article. Novel nucleotide and amino acid sequences must be deposited in a public repository such as the GenBank database (http://www.rcsb.org/pdb).
- The penultimate section should be Accession Numbers. Insert the following and list accession numbers: Sequence data from this article can be found in the EMBL/GenBank data libraries under accession number(s) XX000000 (list the locus identifier or gene model number where applicable, e.g., Arabidopsis AGI locus identifier, maize ZEAMMB73 number, rice OsXXg number, etc.).
- If a list of accession numbers is in a table or figure, identify which one.
- Accession numbers for genes must be specific for each gene; accession numbers for BAC clones or chromosomes are not acceptable substitutes.
- List numbers for any supplemental data placed in a permanent public repository (e.g., GEO http://www.ncbi.nlm.nih.gov/geohttp://www.ebi.ac.uk/arrayexpress, or Protein Data Bank http://www.rcsb.org/pdb).
- The last section should list all Supplemental Data files (titles only).
Author Contributions and Acknowledgments
Contribution to a manuscript must be substantive to justify authorship. An author is responsible for major aspects of the research presented. The corresponding author is responsible for ensuring that all authors have made bona fide, substantive contributions to the research and have seen and approved the manuscript in final form prior to submission. We recommend the guidelines of the International Committee of Medical Journal Editors (ICMJE) for authorship and contributorship, which stipulates that all those designated as authors should meet all four of the following criteria (http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html):
- Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND
- Drafting the work or revising it critically for important intellectual content; AND
- Final approval of the version to be published; AND
- Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.
Each article must include an Author Contributions section (to appear after Acknowledgments) that explains how each author contributed to the research and/or writing of the manuscript. Note which of the following tasks each author performed: designed the research; performed research; contributed new analytic/computational/etc. tools; analyzed data; or wrote the paper. All other contributors should instead be acknowledged appropriately in the Acknowledgments section, and authors should seek written permission to include any individuals mentioned in acknowledgments.
References
Upon first submission, references may be submitted in any standard format (e.g. AMA style).
Figure legends
- Provide a short title.
- Describe each panel.
- Define symbols and abbreviations.
- Define error bars.
- Move accession numbers to end of Methods.
- Separate from the Figures.
Figure preparation
- Ensure that label text is highly visible and explanatory text only appears in the figure caption/legend.
- Ensure that all axes and figure elements are well-defined and explained, but avoid unnecessary text.
- Include (and define) error bars where appropriate.
- Avoid complex hatched patterns – use simple patterns and color schemes. Make consistent use of color throughout a manuscript (e.g. use the same color or pattern for wild type and different genotypes/treatments in each figure where possible).
- Ensure that multiple panels in a figure are evenly spaced.
If necessary, we will request higher-quality figures prior to production of proofs. Figures should be conceptual and unambiguous. Guiding principles of good figure preparation are listed below. Click on or follow the “detailed figure guidelines” link below for additional information and examples. See links below on inappropriate figure manipulation and preparing figures for color vision-deficient readers.
Detailed figure guidelines (http://media.wiley.com/assets/7323/92/electronic_artwork_guidelines.pdf)
Figure manipulation
Plant Direct does not allow certain electronic enhancements or manipulations of micrographs, gels, or other digital images using Photoshop or any other software. If multiple images are collected into a single figure, be sure to separate them clearly with lines. If a digital tool is used to adjust contrast, brightness, or color, it must be applied uniformly to an entire image; targeted alteration of only part of an image is prohibited. Plant Direct reserves the right to ask authors to provide supporting data on which figures were based. Please refer to J Cell Biol 158: 1151 (http://www.jcb.org/cgi/content/full/158/7/1151) for guidance on acceptable and unacceptable digital image manipulation.
Preparing figures for color vision-deficient readers
Many readers of the Journal (1 in 12, on average) have some form of color-deficient vision; therefore, when preparing your figures, please observe the following guidelines to ensure that all readers will be able to comprehend your data.
- In fluorescent double-staining micrographs and DNA chips, do not use the combination of red and green; use magenta and green instead.
- For micrographs with triple or more channels, additionally show either grayscale image of each channel or the combination of the two most important channels in magenta and green.
- For graphs and line drawings, label elements on the graph itself rather than making a separate color-coded key. Do not try to convey information in color only, but use BOTH color and shape (solid and dotted lines, different symbols, various hatchings, etc.).
- For more information, see the following web site: http://jfly.iam.u-tokyo.ac.jp/color/
Supplemental materials
Data and methods that are integral to the main conclusions of the article must be presented in the main manuscript; for example, it is not acceptable to put critical results or methods into supplemental materials in an attempt to shorten the main text. Supplemental figures and tables should be prepared to the same standards of quality and visual appeal as regular manuscript figures and tables, with all data and elements of the figures clearly defined and fully explained. Manuscripts that have been accepted or for which revision has been requested should follow the guidelines below for preparation of Supplemental Figures, Tables, and Data Sets.
- Combine multiple supplemental figures and tables into a single PDF (10 MB max).
- Include a title and complete legend for each item.
- Briefly refer to each item in Results or Methods (e.g., Supplemental Figure 1).
- List the titles of each piece of material at the end of your Methods.
Detailed Supplemental Data Guidelines
What constitutes supplemental material?
- Large-scale data sets and other data that is impractical to include in the main manuscript.
- Detailed experimental protocols or additional supporting data that would be of interest only to specialists.
Large-scale data sets
Large-scale data sets (e.g., complete or draft genome sequences, genome annotations, genetic maps, EST data sets, transcript profiles, proteomic data sets, metabolic profiles, next-gen sequencing data and plant phenotyping image datasets) that are integral to the manuscript must be provided at time of manuscript submission. These include data from small RNA, mRNA, specialized RNA libraries, ChIP-seq, whole-genome re-sequencing or genotyping, whole-genome bisulfite sequencing, etc.
At the time of publication, these large-scale data sets must be available to readers in a permanent public repository with open access (e.g., GEO http://www.ncbi.nlm.nih.gov/geo, Array-Express http://www.ebi.ac.uk/arrayexpress, NCBI’s Short Read Archive sequence database; the microRNA database http://www.mirbase.org/ or a general purpose data repository such as Zenodo) as they will not be stored at Plant Direct permanently, only during the review process if necessary. Full data sets must be released, even if only a subset of the data was selected for use in the analysis. Image datasets should be provided with the corresponding extracted data (e.g. as a .csv file). Non-permanent URLs may be provided additionally at the option of authors as a means to enable readers to access or query information more conveniently. Non-permanent URLs may also be provided for software and unusual file types requiring special software downloads or those that are not compatible with Plant Direct website. The Methods section should also contain the following information: algorithms and parameters used in assembly of genomic data; description of procedures for normalization for measurements of transcript abundances; mismatch parameters for genome-matched reads for all libraries; library adapter sequences.
In general, large-scale data sets must be complete (e.g., must include the complete set of genome sequences analyzed, ESTs identified, genes queried in transcript profiling, peptides identified, molecules identified, etc.). When appropriate and suitably sized, these should be provided in comma separated value (csv) format for publication on Plant Direct site (not as PDF files); otherwise they should be made available via public databases. Data supporting transcript profiling experiments must include complete sequence information (e.g., accession numbers, any relevant annotation data, and in the case of Arabidopsis, TAIR locus identifiers [http://www.arabidopsis.org/]). Authors are encouraged to follow the MIAME (Minimal Information for a Microarray Experiment) standards for microarray analyses http://www.clinchem.org/content/55/4/611. For plant phenotyping datasets, authors are encouraged to follow the MIAPPE (Minimum Information about Plant Phenotyping Experiment) standards (http://cropnet.pl/phenotypes/?page_id=15).
Genome sequencing
The entire raw sequence data on which the genome is based, the final assembled version, and the complete annotation (insofar as possible) of the assembled genome must be available at a public repository at the time of publication. Typical files available for download would include, for example, the genome sequences (contigs or pseudomolecules as FASTA files), a GFF or GTF file describing the gene models, together with cDNA, CDS, and protein sequences as FASTA files. Depending on the focus of the work, information about contig scaffolding and additional annotated features such as transposable elements, miRNAs and ncRNAs may be required.
Peer review
Members of the editorial board will evaluate all manuscripts upon submission to determine whether they are appropriate for evaluation by external expert reviewers.
At submission, authors are required to suggest a minimum of two reviewers. All reviewers will be vetted for legitimacy but authors should take care not to suggest people who have a conflict of interest as defined by the ASPB policy (http://aspb.org/publications/aspb-journals/policies-procedures/).
While authors’ suggested reviewers may be considered, Plant Direct editors are permitted to use any reviewer reasonably believed to be an appropriate scientific expert, except reviewers who would be excluded by ASPB’s conflict of interest policy.
If authors wish to request the exclusion of certain reviewers for other reasons, specific justification must be provided; such requests may be considered at the discretion of the editor.
Publication process
After the review, authors will receive one of the following decisions regarding their paper:
Accept: Paper is deemed suitable for publication. Publication is dependent on receipt of any final changes/proofs and payments.
Revision Requested: Some experimentation and/or revision is required
Reject: In light of the reviewers’ and editors’ comments and evaluations, the manuscript does not meet the standards for publication in Plant Direct. Decline to further consider: Our editors find this paper too far outside of their area of expertise to properly evaluate and manage. We are withdrawing this paper from consideration and returning it to the authors in a timely manner so as not to affect or delay the chances of publishing it elsewhere.
Turnaround Times
Decisions will be made as rapidly as possible. If our editors feel the paper is too far outside of their area for them to properly evaluate, the manuscript will be returned to the authors with a “Decline to Further Consider” decision within three weeks.
If revision is requested, the editorial board will evaluate revised manuscripts and determine whether outside review is required. Plant Direct strongly encourages authors to first deposit manuscripts to preprint servers so that any peer-review delays have no effect on the scientific community’s ability to access the science.
The board will strive to render a decision after only one revision. Requested revisions must be submitted within 2 months unless an extension is granted.
If the authors choose to resubmit a declined manuscript after completing additional experiments, the resubmitted version will be treated as a new manuscript and subject to the full review process.
Accepted articles are published online within five working days, provided payment and the return of final proof files.
Article Publication Charges
All articles published by Plant Direct are fully open access: immediately freely available to read, download and share, and enjoy the benefits of a CC-By license (https://creativecommons.org/licenses/by/3.0/). To cover the cost of publishing, Plant Direct requires the payment of an Article Publication Charge or APC. Current members of the ASPB and/or the SEB are afforded a discount.
Direct submissions to the Journal from non-society members who do not upload to an approved preprint service prior to submission – $2,200
Direct submissions to the Journal from non-society members who do upload an approved preprint service prior to submission – $1,980
Direct submissions to the Journal from current society members who do not upload to an approved preprint service prior to submission – $1,760
Direct submissions to the Journal from current society members who do upload to an approved preprint service prior to submission – $1,650
Submissions transferred to the Journal from the Supporting Journals that do not upload to an approved preprint service prior to submission – $1,760
Submissions transferred to the Journal from the Supporting Journals that do upload to an approved preprint service prior to submission – $1,650
Appeal Policy
All decision appeals should be formally submitted to the editorial office at PlantDirect@wiley.com. Please be sure to include the manuscript ID number, original decision letter, and basis for appeal.
Contact Any other questions or concerns may be sent to the editorial office at PlantDirect@wiley.com.
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