The Plant Cell publishes outstanding research in the plant sciences, especially in the areas of cellular biology, molecular biology, biochemistry, genetics, development, and evolution. A major criterion for acceptance is that the work provide substantial insight into molecular mechanisms or describe new pathways governing biological processes.

Breakthrough Reports showcase studies with conceptual novelty, whether in pointing the way to a deeper understanding of natural phenomena, opening new areas of research, bringing together disparate fields of study, identifying new biological processes, discovering new mechanisms and pathways, or overturning established dogma. These papers are not required to be a "full story" but they should be especially novel and exciting and open a new area of investigation in the field. The category includes manuscripts with a primary focus on new and exciting methods and resources. Breakthrough Reports are limited to about 12 printed pages, 5 figures/tables, and little to no supplemental figures or tables (i.e. supplemental data should be limited to supplemental data sets in Excel format, alignments used in phylogenetic analysis, etc.; manuscripts may not be shortened by placing important data, figures or methods in supplemental materials). Include “BREAKTHROUGH REPORT” above the title on the first page of the manuscript.

Large-Scale Biology studies introduce a new resource of significant value to the broader plant science community and/or present significant new methodology or computational, analytical, etc. tools for the creation or analysis of large-scale data sets. The methodology reported and/or data or resources provided should be useful to a significant number of researchers, and in that way help to move the field forward.

The Presubmission Inquiry category is for research articles (whether in the Research Article, Large-Scale Biology, or Breakthrough Report category) or review articles that are not in standard journal format (for example, articles that may be formatted for another journal). The presubmission inquiry should be submitted as a complete manuscript (with all figures and data), which may be in a single pdf file with the main text in any format. Authors should include a cover letter describing the primary results and main claims of the manuscript and why it is a good fit for the journal. As for all articles, these articles will undergo pre-review consultation with members of the editorial board to determine if they will be sent for external review. If the editors determine that an article is not suitable for the journal, it will be declined (typically within 1 week) and authors will not have wasted time formatting to journal specifications. If the editors are willing to have the manuscript externally reviewed, the corresponding author will be invited to make a "full submission" in the appropriate category, and will be instructed to re-format the article if necessary (in this case, when re-submitted in the appropriate category, such an article will be sent out for external review promptly, and not subjected a second time to a pre-review editor consultation).

The Plant Cell aims to publish regular broadly focused in-depth review articles on topics of high interest and currency. Perspective articles are more highly focused than Reviews and often seek to introduce a new concept or point of view. Reviews and Perspectives should aim to present a novel view point that is nonetheless well-balanced and supported by existing literature. Authors should strive to include interpretive ideas, rather than merely a summary or catalogue of recent literature. All Reviews and Perspectives (even if invited) are subjected to peer review and held to the same standards of scholarship as research articles. A Review or Perspective may be submitted without invitation, but may be declined without external peer review if found to be of insufficient interest by journal editors.

Letters to the Editor: these are short articles (limited to ~1500 words) that cover aspects of plant biological research of interest to the wide readership of the journal such as best practices, nomenclature, resources, science policy, and education. All Letters are assessed by members of the editorial board and will be externally reviewed if found to be of potential interest and importance to the general plant science community. Articles will be declined (with or without external review) if considered of insufficient interest to the readership. In general, Letters to the Editor should not include primary data. A limited amount of primary data may be acceptable if directly related and of critical importance to the main message (which must have a strong aspect of public service to the plant science community). Any primary data will be held to the same standards as for regular research articles, and must be accompanied by complete description of methods (in figure legends, a short methods section, or supplemental material as may be deemed appropriate).

Reader Comments: letters that focus on a particular previously published manuscript in The Plant Cell, and raise questions or perceived problems of interpretation or methodology, will be considered for publication as a reader Comment. Such Comments (limited to ~1000 words) are posted as supplemental to the original manuscript of focus with a link in the “Extras” box on the right hand side of the article online. As for Letters to the Editor, all such Comments are assessed by members of the editorial board and will be externally reviewed if found to be of potential interest and importance to the readership. Authors of the original publication that is the focus of a reader Comment will be given the opportunity to publish an author Reply in the same manner. Reader Comment and author Reply submissions will be declined (with or without external review) if considered of insufficient interest, lacking in scholarship or accuracy, or lacking in providing new insight to the debated issue. Authors should submit a potential reader Comment as a Letter to the Editor for assessment and potential review; if accepted for publication, journal editors will take care of formatting and posting as a reader Comment or author Reply, as appropriate.

If necessary, corrections of errors in published articles will be published in a later issue of the journal. A correction will be linked to the original article online and may be published with or without resupplying the original article with changes, depending on the nature of the correction and decision of the editorial board.

A correction should provide a detailed explanation of the nature of any errors in the original figures or tables, how the errors occurred, and how they are being corrected. The original and corrected versions of the figure or table being corrected should be presented side-by-side, with the specific errors highlighted if necessary, such that readers may easily compare the original with the corrected image or table (i.e. do not put original and corrected images on separate pages, but arrange them side-by-side on the same page where possible). For figures with multiple panels, only the affected panels need be shown, especially if doing so makes it easier to compare the original and corrected versions side-by-side. The correction should state whether or not any changes are being made to figure/table legends and whether or not any of the original conclusions are affected. The text of the correction also should state that all authors are in agreement, or name any exceptions along with the reason (could not be located, deceased, etc.). Please also ensure that you have checked the entire manuscript carefully; authors are responsible for providing a complete listing and accurate explanations for all known errors associated with the original publication.

Please prepare your correction document and figures/tables for the correction as described above and send with a cover letter to Senior Features Editor Nan Eckardt (neckardt[at]aspb.org ). Please provide current email addresses for all of the original authors, and ensure that all of the authors are in agreement with the correction. If any of the original authors is unavailable or can no longer be located, please inform the editors. All corrections will be reviewed by members of the editorial board.

Articles may be retracted by their authors, academic or institutional sponsor, editors, or the publisher because of pervasive errors or unsubstantiated or irreproducible data. The text of a retraction will explain why the article is being retracted and include a bibliographic reference to it.

The Plant Cell now requires authors to complete and submit an author revisions checklist upon submission of a revised manuscript. The aim of the checklist is to aid authors in preparing a high quality manuscript, facilitate the review and assessment of revised manuscripts, and help to ensure that journal standards are maintained across the board. Upon acceptance and publication, the completed checklist will be published as supplemental material attached to the manuscript. Please download a copy of the checklist (pdf fillable form) here:

Author revisions checklist

Your cover letter should:

• Explain the importance of your work and how and why your major findings relate to the scope of the journal.
• Identify any closely related work that is in press or submitted elsewhere.
• Confirm that new gene symbols do not already appear in the literature or community databases and indicate whether each new symbol has been registered in the community database.
  
• Provide reasoning for reviewer exclusion (if applicable).
• List supplemental data and state why it should be supplemental and not be included in the article.

Your Word doc should have:

• Numbered pages.
• 1.5 line spacing.
• 8.5 x 11 formatting.
• 12-point type.

Acceptable fonts: Arial, Times New Roman, Symbol font (for Greek characters)

Organize your manuscript in the following order:

Title Page

Abstract

Introduction, Results, and Discussion

Methods

Author Contributions and Acknowledgments

References

Figure legends

Tables

Submit a separate file for each main figure; include the single-spaced legend below the figure and fit the figure plus legend on a single page when possible (the legend may be placed on a second page if necessary).

• Ensure that all elements of a figure (text and images) are readily visible at printed size (print copies of figures at final size to check).
• Use the same type and size of sans serif font for all of your figures (Arial at a minimum 8 pt size is recommended).
• 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, and text is well placed (not cut off or too crowded near a figure margin or axis).
• Provide image files at high resolution (see detailed guidelines).

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.

Detailed figure guidelines

What constitutes supplemental material?

• Large-scale data sets and other data that are impractical to include in the main manuscript.
• Detailed experimental protocols or additional supporting data that would be of interest only to specialists.

Supplemental materials should be restricted to large datasets and tables, presentation of replicates, and validation of reagents, methods, or genotypes. 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.

Quick guidelines for accepted manuscripts

• Supplemental figure legends must indicate what figure in the main manuscript is supported by the supplemental data presented.
• Please use Arial font for all elements of supplemental data files.
• Combine multiple supplemental figures and tables into a single PDF (10 MB max).
• Supplemental tables larger than 1-2 pages should be presented in Excel format and labeled "Supplemental Data Sets" (see detailed supplemental data guidelines below).
• 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

Supplemental Movies

Please upload your video as supplemental data in QuickTime (.mov) 3.0 or higher format (other acceptable video formats include .mpeg and .avi). To avoid excessive delays in downloading, video files should be no larger than 10 MB and should run between 30 and 60 seconds. Use QuickTime's compress option when preparing files to help control file size. Cropping frames and image sizes can also significantly reduce file sizes. Files can be looped to play more than once, provided the file size does not become excessive. All videos should be submitted at the desired reproduction size and length. No editing will be done to videos at the editorial office; all changes are the author's responsibility.

Supplemental materials that cannot be submitted for review via eJournalPress are occasionally hosted by authors, or for authors, on a third-party hosting site. For supplemental data of this nature, it is the responsibility of the authors to both provide instructions for access to this material within the manuscript under the heading "Supplemental Material" and remove or disable access to this material upon completion of the peer-review process. Authors providing this sort of supplemental data are responsible for the security of the data and accept that third-party access to the confidential account may be a risk. We encourage reviewers to use an anonymous web-browsing site, such as (http://anonymouse.org), to further promote confidentiality.

Each cover of The Plant Cell will feature an image representative of an article published in that issue. All authors are encouraged to submit their images for consideration; images are not required to be part of a figure in the manuscript, but should provide an accurate representation of the work. Original artwork and false-color images are ok, but should be clearly described; “cartoon” images generally are discouraged. Authors who wish to have an image considered for the cover may submit candidate images and descriptions when submitting a revised manuscript or after initial acceptance (authors are given the opportunity to upload files during the scientfic editing stage). The following files are needed for consideration of your cover candidate image(s):

• candidate image(s) files uploaded as additional supplemental files (please upload a jpg file; other file types are not accepted for cover submissions).
• upload a separate Word document that includes both a caption (maximum of 60 characters including spaces) and a brief one-paragraph description of the work and the image presented, including image credit(s), if appropriate (see examples associated with recent covers online).
• indicate on the final submission checklist provided at acceptance that a cover candidate has been submitted.

If you indicate in the online submission system that your article is part of a companion group and some or all of the group is accepted for publication, we will make an effort to publish final versions back-to-back in the same issue of the journal. Companion articles accepted before others in the companion group will be published in advance without delay, but publication of the final version may be delayed, with author permission, to appear in the same final issue with the companion articles.

In the Abstract, text, and Methods, organisms should be referred to by their common name at first use (if a standard common name applies), and the Latin name should be given in parentheses. Subsequent references to organisms can be either Latin or common names but should be consistent throughout the manuscript.

Latin names are always italicized (e.g. Arabidopsis thaliana), whereas common names are not italicized. Arabidopsis (no italics, first letter capitalized) may be used as a common name specifically for A. thaliana. Other genus names often used in this manner, as a common name for a particular species, include Chlamydomonas for Chlamydomonas reinhardtii and Drosophila for Drosophila melanogaster. The first letter typically is not capitalized for other widely used common names, e.g. maize, petunia. When italicized, Arabidopsis alone refers to the entire genus (and the same applies to any genus name).

All gene and protein symbols must have priority in the literature. When introducing new symbols, the manuscript cover letter must state that the authors have conducted a search of the literature and relevant community databases and that the new symbol has priority and has been registered in the appropriate community database (if one is available for the species in question). New gene symbols should be compliant with the naming conventions of the relevant research community. Priority may be established for a gene symbol either by publication in the literature or formal registration in a community gene symbol database. Possible conflicts and/or confusion regarding nomenclature should be resolved prior to submission, if possible, and/or addressed in the cover letter. New Arabidopsis gene names should be registered with TAIR. The full name for a gene should be stated where first used in the manuscript. Full gene names, not symbols, should generally be used in the title of the manuscript.

Authors are responsible for determining that all nomenclature conforms to accepted community standards prior to submission. Some helpful resources are as follows:

http://www.arabidopsis.org/portals/nomenclature/guidelines.jsp (Arabidopsis)

http://www.maizegdb.org/maize_nomenclature.php (Maize)

http://link.springer.com/article/10.1007%2Fs12284-008-9004-9(Rice)

http://wheat.pw.usda.gov/ggpages/wgc/98/ (Wheat)

http://tgrc.ucdavis.edu (Tomato)

http://www.brassica.info/info/reference/gene-nomenclature.php (Brassica gene nomenclature)

http://www.chlamy.org/nomenclature.html (Chlamydomonas)

http://www.chem.qmw.ac.uk/iupac/ (protein nomenclature)

http://www.expasy.org/cgi-bin/lists?nomlist.txt (list of nomenclature-related references for proteins)

VandenBosch, A., and Frugoli, J. 2001. Guidelines for genetic nomenclature and community governance for the model legume Medicago trunculata. MPMI 14: 1364-1367.

Nomenclature conventions differ among species and thus, for instance, Arabidopsis nomenclature should not be used for other species or vice versa. Note also the requirements for case: nearly all plant species use uppercase for the first letter and lowercase for subsequent letters, whereas all letters are uppercase in Arabidopsis and Petunia genes and proteins. Maize genes are referred to with only lowercase letters except when referring to dominant alleles. Prefixes indicating species (e.g., At, Zm, Os) are not generally allowed as part of a gene symbol, except to avoid confusion in cross-species comparisons. When used, a two-letter prefix (e.g., At for Arabidopsis thaliana) should be separated from the gene name by a space or hyphen and should not be italicized as it is not part of the gene symbol. Although a lowercase "p" is used to indicate the protein product of a gene in Saccharomyces cerevisiae nomenclature (e.g., SNF2p), this is not used in most plant nomenclature systems; please use the accepted protein nomenclature system for the species in question.

Symbols for putative orthologs often differ between species. If probable orthology has not been established, genes should not be named or renamed for homologs in other species because this may create confusion in the future when more gene sequences are known in the species and true orthologs can be predicted with greater confidence. Authors may propose a revised nomenclature for a given clade of orthologs using a shared symbol (e.g., Xyz1), accompanied by two-letter prefixes (e.g., Zm, At, Hv, etc.; defined in Methods and not italicized) to indicate species: e.g., Zm-Xyz1 and Os-Xyz1. All such proposals must be based on good phylogenetic information demonstrating probable orthology (see definition below).

The Plant Cell follows the recommendations of Theissen (Nature 415:741, 2002) and Fitch (Trends in Genetics 16:227-231, 2000) for usage of terms that describe relationships between genes. Homology is a relationship between features or genes that share a common evolutionary origin. DNA sequences may be homologous or not, but they may not be partially or highly homologous; percent sequence similarity may be used but not percent homology. Paralogy is a relationship between genes that have originated by gene duplication, whereas orthology is a relationship between genes that originated by speciation. If orthology or paralogy have not been established by a proper phylogenetic analysis, homolog(ue) or modified terms such as putative ortholog(ue) or likely paralog(ue) should be used. Homoeolog(ue) is preferred over paralog when gene pairs have arisen via polyploidy as opposed to gene or segmental duplication.

Gene fusions may be indicated by either a single colon or a hyphen but not a double colon. For example, 35S_pro:GFP and CRY2-GFP are acceptable to refer to promoter-coding sequence fusions and fusions of coding sequences. A double colon should be used only for insertions (such as insertions by transposable elements) as in An1::dTph1, Bz1::Ac, or LFY::TAG1. Lowercase "p" should be used to refer to plasmids (e.g., pBR322), and to avoid confusion, it should not be used to refer to promoters. Authors should designate promoters as, e.g., Pro35S, or 35S_pro, and promoter/coding sequence fusions as Pro35S:LFY or 35S_pro:LFY. Transactivations should be written, e.g., P_FIL>> or FIL_pro>>.

To avoid confusion, double or triple mutations should contain names of mutated genes separated by a space, e.g., sad1 sad2 or cad4 cad5 cad6, and should not be given entirely new names.

Authors should note that insertional mutations are not necessarily knockout mutations and should not be referred to as such unless they have been shown experimentally to be null alleles. Also, putative insertional mutations should generally be characterized at both ends of an insertion prior to manuscript submission; otherwise, the possibility cannot be ruled out that the observed sequence fusion represents a translocation rather than an insertion.

Generally, characterization of multiple, independent alleles is necessary to establish that a mutation (such as a T-DNA insertion or chemically induced mutation) is responsible for an observed phenotype, as opposed to an undetected, linked mutation. Complementation tests via transformation can be valuable, although their interpretation may be limited by the possibility of redundancy, and thus statements of proof should be limited to cases in which multiple independent alleles have been characterized.

Authors must ensure that appropriate experimental design and statistical analyses are carried out where necessary to support conclusions, such as large-scale analyses and experiments related to effects of various treatments, environmental conditions, or genotype on plant growth and development or other aspects of plant phenotype. In evaluating experiments, we look for a clear and complete description of each experiment and any statistical analyses performed; the rationale for using a particular statistical test; the use of multiple comparison corrections where necessary to control for Type I family-wise error; a clear description of replicates. Replicates should not be defined as technical, biological, experimental without a specific description of what this means in your experiments. A good understanding of the experimental design and any statistical analyses performed is critical both for proper interpretation of data and independent verification of claims. Authors are encouraged to involve statisticians in both the design and analysis of experiments, to whatever extent is necessary, to properly interpret results. Figures and tables should include clearly defined error bars where appropriate.

Additional resources:

Statistics for Biologists (Nature)

Use of ANOVA versus T-test (The Plant Cell)

How Robust Are Your Data? (Nature)

Error Bars in Experimental Biology (J. Exp. Bot.)

Know When Your Numbers Are Significant (Nature)

Ten Simple Rules for Reproducible Computational Research

Accession numbers must be provided for all genes reported and major genes discussed. All large-scale data (e.g., genome sequences, annotations, genetic maps, transcript profiles, other sequencing data, proteomic data sets, metabolic profiles) that are integral to the manuscript must be submitted to a permanent public repository with open access prior to submission, and must be made publically available immediately upon publication. Accession codes, unique identifiers, or web links for publicly available data sets must be provided in an Accession Numbers section at the end of the Methods.

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, and next-gen sequencing data) 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/) as they will not be stored at The Plant Cell 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. 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 The Plant Cell 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 Microsoft Excel format for publication on The Plant Cell site (not as PDF files); otherwise they should be made available via public databases. Excel files should be organized with column headers and complete legends that describe the data presented. 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) and MINSEQE (Minimum Information About a Next-generation Sequencing Experiment) standards for microarray and sequencing analyses, respectively https://www.ncbi.nlm.nih.gov/geo/info/MIAME.html.

If conclusions are not drawn and such experiments are used simply as a screen, the preceding does not apply, as long as the manuscript explicitly indicates that the experiment should be regarded only as a screen, results were used only to identify candidates that were then validated independently, and no conclusions have been or should be drawn from the data (such as what number or fraction of genes respond in a given manner). Provision of data sets used only as screens as supplemental information is encouraged, but not necessarily required.

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.

Methods for quantification of levels or differences in levels of molecules in biological samples must be described fully and shown to be quantitative and reproducible, using true biological replicates (samples from different starting material; i.e. different plants or organisms exposed to the same experimental conditions). Any conclusion that levels differ between samples must be supported by presentation of methods and data shown to be reliable; supporting information demonstrating reliability of an assay may sometimes be provided as Supplemental Information rather than in the body of the manuscript, subject to the approval of the handling editor.  

RNA and DNA

Methods used for sequence analysis must be reported in full with citations and software and parameter values (even if only default values were used) in a separate section of Methods entitled "Phylogenetic Analysis". Please note that CLUSTAL does not produce an acceptable phylogeny; use a true phylogenetic analysis program (e.g., MEGA, RAxML, IQ-TREE, RevBayes, BEAST). Alignments used to produce phylogenies should be produced with an appropriate alignment program (e.g., MAFFT, T-Coffee). Statistical support for nodes in any phylogenetic tree figures must be reported (i.e., posterior probabilities or bootstrap values with MCMC search sample or replicate numbers reported in text), and tree branch lengths (e.g. time, substitutions per site, coalescence units) properly described in tree figure captions. If phylogenetic trees are depicted or interpreted as rooted, the criterion used for rooting (e.g., midpoint, outgroup) must be provided, and if outgroup rooting is used, the basis for the choice of outgroup should be explained. Sequence alignments (e.g. FASTA, PHYLIP, Nexus format) and machine-readable tree files (e.g. Newick, Nexus, NeXML format) must be deposited in a persistent database (e.g. Dryad, TreeBASE) or provided as Supplemental Files. Authors are encouraged to consult with an expert in molecular phylogenetics if they do not have such expertise themselves. Authors are encouraged to consult with an expert in molecular phylogenetics if they do not have such expertise themselves.

Expressing unfused YFP fragments is not a sufficient control for BiFC experiments (see the Commentary from Bock and Kudla https://doi.org/10.1105/tpc.16.00043). Ideally, negative controls should include a mutated version of one of the interacting proteins carrying a defect in the interaction domain or a related non-interacting protein from the same protein family. If neither a mutated protein version nor a suitable closely related protein are available as negative controls, an unrelated protein (but, ideally, structurally similar and expressed in same subcellular compartment) can be used. It is essential that exactly the same orientations are used for negative controls as for the positive interaction. It is also desirable to show results as quantitative data (for example, from 10 randomly chosen regions of interest of infiltrated leaves) and not merely one or two “representative images” (many papers show only a single image). Any representative image should display a complete cell, with the nucleus and the center of the cell in the focal plane.

EMSA is commonly used to show binding of proteins to nucleic acids. Typically, it is of interest to know if the binding of the protein shows sequence specificity for the nucleic acid. Competition experiments are often used to demonstrate sequence-specific binding.

Competition typically is performed by adding e.g. 50-100 molar excess of unlabeled competitor DNA to the reaction mix with the labeled probe DNA. Depending on what is already known about the binding site, one can use a mutated binding site that is known to be non-functional in vivo or a scrambled binding site. Typically, unlabeled wild-type DNA is used as a positive control in these experiments. It is not necessary nor meaningful to show competition with unlabeled wild-type DNA unless the competition with a mutated or scrambled site is included. Without the competition using mutated or scrambled sites, competition with wild-type only indicates that binding is not specific for the label (e.g. 32P or biotin). Other controls may include: 1) adding an antibody to the purified protein – this increases the size of the DNA–protein complex to create a “supershifted” band, demonstrating that it is indeed the protein of interest causing the shift, and 2) use of a nonspecific protein known not to bind DNA to ensure that the DNA probe is not "sticky" and binding to all manner of proteins.

All relevant structural data must be submitted to an appropriate database (e.g. wwPDB, EMDB) prior to submission and must be made publicly available immediately upon publication. For or all macromolecular structures studied, the structural data must be submitted to wwPDB and validation reports from wwPDB provided before the manuscript can be reviewed. For any electron microscopy results, density maps and coordinate data must deposited in EMDB and ID numbers provided.

You will receive one of the following decisions regarding your manuscript:

• Accept and send to science editor.
• Accept pending minor revisions; no further external review.
• Revision requested; some experimentation and/or revision is required (the revised submission may or may not be sent back to external reviewers at editors' discretion).
• Decline after external review: the manuscript does not meet the criteria for publication in The Plant Cell.
• Decline after editor review: the manuscript is not a good fit for The Plant Cell and will not be sent to external review.

A decline decision letter should clearly indicate whether or not resubmission is encouraged, and if the manuscript was reviewed, whether or not editors will try to use some or all of the same reviewers for a revised submission.

Members of the editorial board will evaluate all manuscripts upon submission to determine whether they are appropriate for evaluation by expert outside reviewers. Reviewers are required to follow ASPB's policy regarding conflicts of interest. Authors may suggest reviewers but should not suggest persons who have a conflict of interest as defined by the ASPB policy. 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 in the cover letter; such requests may be considered at the discretion of the editor. Decisions will be made as rapidly as possible, and the journal strives to return reviewers' comments to authors within 4 weeks whenever possible. If revision is requested, the editorial board will evaluate revised manuscripts and determine whether outside review is required. The board normally will consider only one revised manuscript, and this manuscript must be submitted within 2 months unless an extension is granted. In the case that extensive revision including additional experimentation is required, journal policy is to decline the manuscript. 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. It is the goal of the journal to publish manuscripts within 4 months after submission, but this can only be achieved if the original submission meets all journal requirements.

The Plant Cell publishes Peer Review Reports as additional supplemental material, subject to author approval. Reviewer anonymity is strictly maintained. The reports include decision letters, anonymous reviewer comments, and author responses, showing only the most substantive parts of letters and comments; minor comments for revision, mundane paragraphs from letters, and miscellaneous correspondence, and comments from the editors (including pre- and post-review consultation sessions) are not published. Unpublished data submitted confidentially in response to reviewer comments (e.g. figures, tables; data not intended for the manuscript under review but only to support responses to reviewer comments) may also be omitted at the author's request. The text of reviewer comments and author responses is unedited except to correct typos and minor grammatical errors (where noticed and easily corrected), and to remove minor comments.

After provisional acceptance by the reviewing editor, all manuscripts are assigned to a science editor for final scientific editing. Manuscripts are evaluated with respect to scientific content presentation, appearance of figures, tables, and supplemental data, compliance with journal policies, and presentation for a broad readership. Science editors communicate directly with corresponding authors and provide instructions for further editing and uploading of final files, and issue final acceptance. The scienctific editing process normally takes 2-3 weeks. To facilitate rapid publication, accepted manuscripts will be published in raw pdf format immediately upon final acceptance by the science editor, and then sent to our compositor. At that point, manuscripts are copyedited for grammar and journal style before a proof is generated; the final type-set version is published with the subsequent monthly issue of the journal. The official date of publication is the date that the article first appears online

PDF page proofs will be made available to the corresponding author, who will receive an e-mail with a link to the ArticleExpress online editing system, enabling the review and corrections of proofs within a web browser. Page proofs are considered to be the final version of the manuscript. Changes are restricted to typographical or minor clerical errors. Notes added in proof will be sent to the editor assigned to the manuscript prior to publication and reviewed for appropriate content and wording. Authors will receive proofs approximately 2 to 3 weeks after final acceptance of the manuscript, and should relay all additions and corrections within 48 hours of receipt of proofs. For questions about the proof process please contact the managing editor Jennifer Regala jregala@aspb.org

Each cover of The Plant Cell will feature an image representative of an article published in that issue. All authors are encouraged to submit their images for consideration; images are not required to be part of a figure in the manuscript, but should provide an accurate representation of the work. Original artwork and false-color images are ok, but should be clearly described; “cartoon” images generally are discouraged. Authors who wish to have an image considered for the cover should:

• upload the candidate image(s) as additional supplemental files (please upload a jpg file; other file types are not accepted for cover submissions).
• upload a separate Word doc that includes both a caption (maximum of 60 characters including spaces) and a brief one-paragraph description of the work and the image presented (see examples associated with recent covers online).
• indicate on the checklist provided at acceptance that a cover candidate has been submitted.

The journal uses a graphic icon to represent each paper on the Table of Contents for each issue. The author should submit an icon with the final production version of the manuscript. The icon must be 96 x 96 pixels in size and should illustrate or exemplify the topic of the paper. Summary rules for icons:

• 96 x 96 pixels
• GIF or JPEG format (in RGB color mode)
• If using type, ensure it is legible in the final icon.

Making an icon from a figure

• Remove unessential text and graphic elements
• Reduce the figure to its strongest, most important graphic elements
• Useful tools for creating and editing icons are Adobe Illustrator, Adobe Photoshop, and GraphicConverter. If an original figure is an EPS file, Illustrator can be used to edit graphic elements and adjust the font size and thickness. The result can be saved as a small GIF version using the "File>Save for web" function. Photoshop and GraphicConverter can be used to edit the GIF image.

Corresponding authors who are ASPB members will be assessed a flat rate fee of $2200 per article. Corresponding authors who are not ASPB members will be assessed a flat rate fee of $2500 per article. Publication of an article in The Plant Cell is not contingent upon the author's ability to pay the charges. Under exceptional circumstances that are explained in writing to the Managing Editor, authors may request waiver of the flat rate charges. For all solicited articles, the flat rate fee is waived. Please note that The Plant Cell is unable to review submissions from any corresponding author whose account is in arrears.

ASPB offers an OPEN option that allows authors to have their articles available for free to all users immediately upon publication. The fee for OPEN, which is in addition to the usual author charges, is $1800 (discounted to $950 if the author's institution subscribes to the journal).

For authors whose funders require that the work be published under a Creative Commons or similar license, ASPB offers a CC-BY license for $2000. The CC-BY license allows noncommercial and commercial reuse of all or part of a paper without restriction.

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 stipulate that all those designated as authors should meet all four of the following criteria:

1. Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND

2. Drafting the work or revising it critically for important intellectual content; AND

3. Final approval of the version to be published; AND

4. 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 (after Acknowledgments) to detail how each author contributed to the research 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. A valid, unique e-mail address must be provided for each author. An e-mail acknowledging submission of the manuscript will be sent automatically to every author, and all authors must respond and declare their approval of the submission. After submission, any requested change in authorship will require the written agreement of all coauthors.

Publication in The Plant Cell implies that the authors agree to provide materials that are integral to the results presented in the article, including whatever would be necessary for a skilled investigator to verify or replicate the claims. Authors are generally expected to take advantage of public repositories or commercial vendors to the extent possible. Authors should refer to the Materials Distribution Policy below for an explanation of the journal's expectations of authors and requestors.

The Plant Cell does not allow certain electronic enhancements or manipulations of micrographs, gels, or other digital images using Photoshop or any other means. Images submitted with a manuscript should be minimally processed, and the final images must accurately represent the original, unprocessed data. Authors may be asked to provide the original, unaltered source data or images on which figures were based (for example, the original, complete, uncropped images may be requested for any figures constructed of heavily cropped images or photographs). It is not uncommon for reviewers and editors to request source files, so please be sure that they are organized and available to avoid delays in the review process.

• No specific feature within an image may be enhanced, obscured, moved, removed, or introduced.
• Any grouping of images from different parts of the same gel, or from different gels, fields, or exposures must be made explicit by the arrangement of the figure (e.g., using dividing lines) and clearly described in the figure legend.
• Any adjustments of brightness, contrast, or color balance must be applied to the entire image must not obscure or eliminate any information present in the original. Nonlinear adjustments (e.g., changes to gamma settings) must be disclosed in the figure legend.
• Any reuse or duplication of images or parts of images, including control data, within a figure or across multiple figures (or across multiple manuscripts) must be explicitly stated and justified in the figure legend.

 Corresponding Authors and Senior Authors should inspect all figures carefully and be confident that the data is sound and all images have been prepared appropriately. Authors may wish to make use of freely available software or a professional service to check for potential inappropriate manipulation prior to submission.

Resources:

Manipulation and Misconduct in the Handling of Image Data Plant Cell Editorial September 2013

Avoiding image fraud: 7 rules for editing images

The art of detecting data and image manipulation (Elsevier)

Avoiding ethical violations: a primer for authors (JBC)

Image Integrity service

The Plant Cell will review manuscripts that include data posted on an author’s website or posted on preprint servers such as the bioRxiv. Final published manuscripts will reside on the Journal site. Once the published article has appeared online at the Journal site, a toll-free link providing barrier-free access to the HTML and PDF versions of the article will be e-mailed to all authors. These links may be deposited in open access institutional repositories.

On behalf of authors, The Plant Cell deposits final published articles in PubMed Central for release 12 months after the date of publication. If a paper was funded in whole or in part by the National Institutes of Health, this fulfills the requirements of the NIH Public Access Policy. However, authors of NIH-funded papers, if they choose, may deposit the peer-reviewed, accepted version of their manuscript in PubMed Central, provided the release date is set for 12 months after the date of final publication in the journal.

The journals of the American Society of Plant Biologists (ASPB), Plant Physiology and The Plant Cell, make all articles free 12 months after publication. Authors can purchase immediate free access in one of several ways:

1. Authors whose work is published in The Plant Cell may purchase immediate free access for $950 (if they work at a subscribing institution) or $1800 (if their institution does not have a subscription). ASPB retains copyright.
2. For authors whose funders require that the work be published under a Creative Commons or similar license, ASPB offers a CC-BY license for $2000. The CC-BY license allows noncommercial and commercial reuse of all or part of a paper without restriction.

On behalf of all authors, the ASPB journals deposit final published articles in PubMed Central for release 12 months after the date of publication (unless a free-access option applies).

Permission to reuse part or all of a copyrighted work published in an ASPB journal is granted without fee for personal or educational use, provided that copies are not made or distributed for profit or commercial advantage and that copies bear the full citation, the journal URL (www.plantphysiol.org; www.plantcell.org ), and the following notice: “Copyright American Society of Plant Biologists.” Please request permission in writing from the Copyright Clearance Center (www.copyright.com) if the use is commercial or if you wish to make multiple copies other than for educational purposes. Please note that the ASPB journals allow authors to reuse their content for any purpose (noncommercial or commercial) without written permission from ASPB, so long as the original source and a copyright notice are cited.

Publication in The Plant Cell requires that authors make available all materials integral to the reported results (i.e., necessary to support the major claims and enable their verification or replication) for non-commercial research purposes. Such materials include mutants, genetic stocks, transgenic plants, cell lines, recombinant constructs, vectors, viruses, enzymes, antibodies, and software. In general, authors are expected to deposit novel materials in public repositories to the extent possible and consistent with the policy stated here. All manuscripts submitted to The Plant Cell will be reviewed for compliance with journal policy and should include the following statement as an unnumbered footnote: "The author(s) responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is (are): John D. Author (author@college.edu)." Contact information for the author(s) responsible for distribution of materials must be provided.

Authors should expect to comply with requests for materials within 60 days. Requestors should expect to comply with conditions (including via a signed Materials Transfer Agreement) that do not unreasonably limit use for non-commercial research purposes. Authors are expected to make materials available to all qualified investigators in private or public organizations on similar, if not identical, terms. If authors do not possess rights to distribute materials, upon request, they should supply contact information for the source of the materials and make their best efforts to facilitate the transfer of these materials within the expected timeframe, preferably by arranging for standard, reasonable terms in advance of publication or even prior to the initiation of research with such materials. In the case of an unreasonable delay (and lack of extenuating circumstances, such as travel or illness, or special circumstances, such as significant and reasonable regulatory or safety issues), the requestor may contact the managing editor. Non-compliance with this policy by authors may result in denial of future rights to publish in The Plant Cell and/or notification of authors' funding agencies or employers and/or retraction of the publication describing the materials on the grounds that it is not possible to confirm the results and conclusions. It is reasonable for authors to require that requestors obtain a license for research use of patented materials. Reasonable approaches to protect ownership rights are allowable if they are described in the Methods. For instance, mutants or alleles that exist only in proprietary inbred lines may be provided via hybrids if the inbred line itself is not integral to the findings. In lieu of providing plasmid constructs, complete DNA sequences necessary to replicate them could be provided via a public repository or supplemental data, assuming component elements are readily available and the constructs are not so complex that they could not be replicated in a timely manner. Authors may reasonably limit amounts of materials (such as enzymes, antibodies, and natural products) that will be distributed in the case that substantial effort is required for their isolation. Sufficiently detailed procedures must be provided to permit the production of such materials; detailed protocols should be provided as supplemental material.

To facilitate the sharing of materials, authors may choose to use one of the following services:

Addgene (http://www.addgene.org)

Arabidopsis Biological Resource Center (http://www.biosci.ohio-state.edu/pcmb/Facilities/abrc/abrchrome.htm)

Maize Genetics Cooperation Stock Center (http://maizecoop.cropsci.uiuc.edu/)

NOTE: ASPB provides these links as a service to our author community. The Society does not take responsibility for or endorse the services these companies offer and cannot attest to the quality of their work. If you have questions, or if you use one of these services and would like to send ASPB feedback on your experience, please contact Nancy Winchester, ASPB Director of Publications, at nancyw@aspb.org.

The Plant Cell and The Arabidopsis Information Resource (TAIR) are collaborating to collect functional annotation data about Arabidopsis genes from authors. This includes information about the gene's molecular function (e.g., kinase activity, ATP synthetase activity), the biological process/es it is involved in (e.g., endosperm development, threonine biosynthesis), its subcellular location (e.g., nucleus, ER), anatomical or developmental expression pattern (e.g., leaf, ovule, flower stage 10, seedling stage), or its partner in a protein-protein interaction (e.g., AT1G01010 interacts with AT1G01020). If your paper contains results falling into one or more of these categories for Arabidopsis genes, we request that you now submit these data for inclusion in TAIR by filling in the form provided at the following URL: http://www.arabidopsis.org/doc/submit/functional_annotation/123. If you need further clarification on what types of data can be submitted, please contact curator@arabidopsis.org

Supplemental materials presented at The Plant Cell are subject to the same copyright restrictions as published manuscripts and cannot be presented elsewhere without proper citation.