Instructions for Authors
Last Updated April 15, 2008

TABLE OF CONTENTS
STATEMENT OF SCOPE
     Ethics
FEATURE ARTICLES
MANUSCRIPT SUBMISSION
     Authorship
     Cover Letter
     Companion Articles
     Availability of Materials
     Language-Editing Services
MANUSCRIPT PREPARATION AND ORGANIZATION
     Title Page
     Manuscript Title
     Abstract
     Introduction, Results, and Discussion
     Nomenclature and Terminology
     Methods
          Large-scale experiments
          Quantification of molecules, including DNA, RNA, and proteins
          Molecular phylogenetic analyses
     Tables
     References
     Figures
          Figure legends
          Figure manipulation
          Figure size
          Black and white figures
          Color figures
          Figure format
          Figure resolution
          Figure file size
          Help with digital art
     Supplemental Data
          Supplemental data presentation
          Large-scale data sets
          Movies
     Cover Submissions
PEER REVIEW
MANUSCRIPT ACCEPTANCE
PROOFS
FEES AND CHARGES
POLICIES
     Electronic Posting of Articles
     Materials Distribution Policy
     Corrections and Retractions

STATEMENT OF SCOPE
The Plant Cell publishes novel research of special significance in plant biology, especially in the areas of cellular biology, molecular biology, genetics, development, and evolution. The primary criterion for publication is new insight that is of broad interest to plant biologists, not only specialists. The presentation of results must be appropriate for a wide audience of plant biologists. Research on the biology of plant pathogens falls within our scope if it is directly relevant to the plant's response to the pathogen. (Back to top)

Ethics. Please see http://www.aspb.org/publications/ethics.cfm for expectations for authors and ASPB procedures for handling allegations of scientific misconduct in journals. (Back to top)

FEATURE ARTICLES
The front section of the journal features occasional Editorials, Letters to the Editor, In This Issue articles, Current Perspective Essays, Historical Perspective Essays, Reviews, and Commentaries. Prospective authors may inquire about contributing to an article to one of these feature sections by contacting Dr. Nancy Eckardt, News and Reviews Editor (neckardt{at}aspb.org), or Dr. Richard Jorgensen, Editor in Chief (raj{at}ag.arizona.edu). (Back to top)

MANUSCRIPT SUBMISSION
Before initiating the submission process, these Instructions for Authors should be reviewed in full to ensure that the article is in compliance with Plant Cell standards. Even if authors have previously read them, it is strongly recommended that these pages be reread in their entirety, as they are updated periodically.

If an author does not have access to the Internet, contact Annette Kessler, Manuscript Manager, at 301/251-0560, ext. 120; e-mail: akessler{at}aspb.org

Authors should submit manuscripts online at http://submit.plantcell.org/. The Bench>Press submission system will prompt authors through the process. Help is also available from http://submit.plantcell.org/submission/submissionhelp and from Annette Kessler in the ASPB manuscript tracking office (301/251-0560, ext. 120; akessler{at}aspb.org ). A manuscript file in Microsoft Word (or some other word processing format) is required and will be automatically converted to a PDF. If using Microsoft Word, you must submit a .doc file. Please do not submit .docx files as they cannnot be processed by the Bench>Press submission system. If it is your preference or if conversion is not satisfactory, authors may submit their own PDF, which will not be subjected to any conversion. Although there are no file size limitations, note that large files will take longer to upload and convert to PDF depending on the Internet connection. Please try to keep the maximum combined PDF file size to less than 5 MB. If you are not satisfied with the final conversion results when the submission is proofed, the complete manuscript can be reloaded as a PDF file. (Back to top)

Authorship. Contribution to a manuscript must be substantive in order to justify authorship. An author is responsible for major aspects of the research that is presented. All other contributors should instead be acknowledged appropriately in the Acknowledgments section. 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. For more information on corresponding authors, see "Title Page" below. An e-mail acknowledging submission of the manuscript will be sent automatically to every author (a valid, unique e-mail address must be provided for each author). If any author has not approved this submission or has any concern about the nature of this submission, the author should first contact the corresponding author about their concern and contact The Plant Cell directly only if the concern cannot be resolved to the satisfaction of all coauthors. Some concerns may be resolvable by reviewing ASPB's Ethics in Publishing policy. In the case of an unresolved concern, the corresponding author is obligated to notify The Plant Cell and explain the nature of the disagreement. After submission, any requested change in authorship will require the agreement of all coauthors. (Back to top)

Companion Articles. If you indicate in the online submission system that your article is part of a companion group and some or allof the group is accepted for publication, the articles will be published online on the same date. Note that since there could be a difference in the amount of time that it takes to peer review the separate articles, the publication of some articles may be delayed until all are ready.(Back to top)

Cover Letter. A cover letter must be submitted along with the manuscript, stating that the manuscript has not been submitted for publication elsewhere. Any closely related papers that are in press or that have been submitted elsewhere should be noted in the cover letter, cited in the submitted manuscript as is appropriate, and uploaded as additional supplemental files in the Bench>Press manuscript submission system. If any new gene symbols are introduced, the authors should state that they have conducted a search of the literature and of community databases and whether each new symbol has been registered in the appropriate community database (see Nomenclature and Terminology). If authors wish to request exclusion of any reviewers, specific reasons must be provided (for journal policy, see Peer Review). Authors should list the supplemental data they are submitting with the manuscript and state why it should be supplemental rather than integral to the article (aside from movies, large-scale data tables, unusual imaging software, etc). Also in the cover letter, we recommend that authors also explain the importance of their work and how and why their major findings relate to the scope of the journal. (Back to top)

Availability of Materials. 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 in these instructions for explanation of the journal's expectations of authors and requestors. (Back to top)

Language-Editing Services. Authors who believe their manuscripts would benefit from professional editing are encouraged to use language-editing services, such as the ones described at the following web sites, prior to submission.
http://www.prof-editing.com/
http://www.bostonbioedit.com/
http://www.internationalscienceediting.com/
http://www.asiascienceediting.com/
http://www.biosciencewriters.com/
http://www.biomeditor.com/
http://www.oleng.com.au/
http://davidherron.tripod.com/index-6.html
http://www.scientific-editor.com
http://www.bluepencilscience.com/
http://www.journalexperts.com/
http://www.writescienceright.com/
http://documentclinic.com

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. Use of such services in no way guarantees acceptance of a manuscript for publication. If you have questions, or if you do 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{at}aspb.org. (Back to top)

MANUSCRIPT PREPARATION AND ORGANIZATION
Manuscripts should follow The Plant Cell style, be written in concise and grammatically correct English, and be presented in a manner and at a level that will be accessible to the broad readership of the journal. Papers that do not meet these standards will be returned to the authors without further review. Consult a current issue of The Plant Cell for guidance on format, organization, and preparation of figures, legends, tables, and references. While there are no limits to the length of manuscripts published in The Plant Cell, papers of more than 10 journal pages will be published only if the coeditor judges that the content is sufficiently novel to warrant a long paper. Ten published pages in The Plant Cell correspond to approximately 30 manuscript pages, including tables and figure legends and an average of six one-column figures.

Original manuscripts must be prepared using a standard word processing program (such as Microsoft Word) and should be prepared with 1.5 line spacing and in 12 point type using one of the following fonts: Times Roman, Courier, Helvetica, or Arial for text and Symbol font for Greek characters to avoid inadvertent character substitutions. Please do not use Chinese, Japanese or Korean fonts. Use settings for standard 8.5 x 11-inch paper. Figures should be digitally prepared (see below).

Organize manuscripts in the following order: Title Page, Abstract, Introduction, Results, Discussion, Methods, Acknowledgments, Figure Legends, Tables, and References. Note that when submitting your manuscript the References must be placed at the end of your document file. Tables should be included as part of your manuscript file. Figures and normal supplemental data (supplemental text, figures and small tables) should be included in separate files and not as part of the manuscript. These will be converted, along with the manuscript, into a single PDF on upload. See the sections on Figures and Supplemental Data below for more details. (Back to top)

Title Page. The title page should include the authors' full names and affiliations, a running title of 40 characters or less (in addition to the full paper title), and the e-mail address of the corresponding author. A second corresponding author may be listed but only in cases in which the authors are from different collaborating labs. Both corresponding authors will assume full and equal responsibility for the manuscript, including compliance with journal policies. One of the corresponding authors will be designated in the online submission system to be the primary contact with the journal office. In the manuscript, please provide each author's institutional affiliation at the time the research was done. If an author has since moved to a different institution, the new location can be indicated in a footnote. In the online submission system, the most current contact information for each author should be provided. The title page also must 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 material(s) should be provided. (See Materials Distribution Policy for journal expectations in this regard.) (Back to top)

Manuscript Title. The full manuscript title should be succinct (approximately 120 characters) and informative. The title should include sufficient detail for indexing but be general enough to be clear to the broad readership of the journal. Abbreviations and acronyms, including those for gene and protein names, should be avoided in titles or the general nature of the abbreviated entity should be clear. The journal encourages active titles over merely descriptive ones. The title must mention the subject organism (or general group in the case of comparative works). Common names are allowed for major model systems (maize, rice, yeast); Latin names should be used for all organisms that have no widely accepted common name. (Back to top)

Abstract. The abstract should summarize for a broad audience the question being addressed, the approach taken, and the major findings and their significance. It should also be concise (approximately 200 words) and stand on its own with no reference to the text. General background should be reserved for the introduction. Literature references should not be included. (Back to top)

Introduction, Results, and Discussion. Manuscripts should be written to be understood by a wide audience of plant biologists. The use of abbreviations and jargon should be avoided, and terms that are not widely known should be explained clearly at first use. The Introduction should provide the necessary background information for the average reader; it should be both complete and concise. Previous publications that form a basis for the work presented must be cited. Citation of reviews is not a substitute for citing primary research articles. Citation of recent research articles is not a substitute for citing original discoveries. An author's own work should not be cited preferentially over equally relevant work of others. Authors' previously published data that are presented along with new data must be identified clearly and cited appropriately; duplicate publication of data (including data previously published as supplemental material) is not allowed without citation. The Plant Cell discourages the use of "data not shown" or "unpublished results" for nontrivial results and instead requires the submission of supplemental data to support any conclusions being presented. The Results and Discussion can be subdivided if subheadings give the manuscript more clarity. The Discussion should not repeat the Results; instead, the Discussion should explore the implications of the Results, citing relevant published research, and should also be as concise as possible. A Conclusions section is generally not permitted. Statements of priority or first finding are generally not permitted in The Plant Cell. (Back to top)

Nomenclature and Terminology. The Plant Cell requires that all nomenclature, including gene names and symbols, conform to nomenclature conventions adopted by the scientific community and that all genetic terminology be used in a scientifically accurate manner.

     Organisms. 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.

     Gene and protein symbols. Prior to submission, authors should determine that all gene and protein symbols used in a manuscript 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 of 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. 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 follow.

http://www.arabidopsis.org/portals/nomenclature/guidelines.jsp (Arabidopsis)
http://www.maizegdb.org/maize_nomenclature.php (Maize)
http://www.gramene.org/newsletters/rice_genetics/rgn3/v3C.html (Rice) Nomenclature rules are being revised by the rice community at this time. When a new link is available, it will appear here.
http://wheat.pw.usda.gov/ggpages/wgc/98/ (Wheat)
http://tgrc.ucdavis.edu (Tomato)
http://www.chlamy.org/nomenclature.html (Chlamydomonas)
VandenBosch, A., and Frugoli, J. 2001. Guidelines for genetic nomenclature and community governance for the model legume Medicago trunculata. MPMI 14, 1364-1367.
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)

Nomenclature conventions differ among species and so, 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 Arabiodopsis 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. Where used, a two-letter prefix (e.g., At for Arabidopsis thaliana) should not be italicized as it is not part of the gene symbol and should be separated from the gene name by a space or hyphen. 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. However, 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 the 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).

     Relationships between homologous genes. 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. Homeolog(ue) is preferred over paralog when gene pairs have arisen via polyploidy as opposed to gene or segmental duplication.

     Gene fusions and constructs. Gene fusions may be indicated by either a single colon or a hyphen, but not by a double colon. For example, 35S:GFP, 35S-GFP, CRY2: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., P35S, Pro35S, or 35S_pro and promoter/coding sequence fusions as P35S:LFY, Pro35S:LFY or 35S_pro:LFY. Transactivations should be written, e.g., P_FIL>> or FIL_pro>>.

     Genes and mutations. The standard definition of the term gene in molecular terms is the complete segment of chromosome that is required for expression of a gene product (i.e., including promoters, enhancers, introns, exons, untranslated regions, etc.) Thus, a coding sequence or transcription unit should not be referred to as a gene, but rather as a component of a gene. To avoid confusion, double or triple mutations should contain the names of the 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 so statements of proof should be limited to cases in which multiple independent alleles have been characterized. (Back to top)

Methods. Methods must be described completely enough that other laboratories can replicate results and verify claims. Generally, standard procedures should be referenced, though significant variations should be described. Appropriate experimental design and statistical methods should be applied and described wherever necessary for proper interpretation of data and verification of claims. All novel materials and the procedures to prepare them should be described in sufficient detail to allow their reproduction (e.g., DNA constructs, genetic stocks, enzyme preparations, and analytical software). The penultimate section of Methods should be the section entitled "Accession Number," and the last section should be "Supplemental Data," containing the titles only of all supplemental materials that will be posted online.

     Accession numbers. Accession numbers should be provided as the last paragraph of Methods (just before Acknowledgements) with the heading “Accession Numbers” for any genes or new sequence data discussed in the article. Insert the following statement and provide accession numbers: “Sequence data from this article can be found in the EMBL/GenBank data libraries under accession number(s) XX000000.” In the case of Arabidopsis, the AGI locus identifier (“At number”) must be provided for each gene described (see http://www.arabidopsis.org). If a list of accession numbers is provided in a table or figure, that can be stated in this section, rather than listing all of the numbers. If an accession number has not been assigned at the time of submission, please use Xs as placeholders to be updated later. In general, accession numbers should be provided only in the Methods, not elsewhere in the manuscript, unless needed for clarity. Accession numbers for genes must be specific for each gene; accession numbers for BAC clones or chromosomes are not acceptable substitutes. Accession numbers must also be provided for any supplemental data that is placed in a permanent public repository (e.g., GEO http://www.ncbi.nlm.nih.gov/geo, Array-Expresshttp://www.ebi.ac.uk/arrayexpress, or Protein Data Bank (http://www.rcsb.org/pdb).

     Novel nucleotide and amino acid sequences must be deposited in a public repository such as the GenBank database (http://www.ncbi.nlm.nih.gov). If a new function or mutation is found to be associated with a previously known DNA sequence (i.e., an existing GenBank entry), authors are encouraged to create a new GenBank entry in order to link the sequence and the gene symbol/function in the database. In the case of (partially or completely) sequenced vectors and constructs, accession numbers should be provided. All data necessary to validate protein structure determinations, including x-ray amplitudes and phases and the derived atomic coordinates, should be submitted to the Protein Data Bank (http://www.rcsb.org/pdb).

     Large-scale experiments. In evaluating large-scale experiments such as transcript profiling, we will consider whether there is a clear and complete description of each experiment; whether biological and/or technical replicates should have been used; what statistical analysis has been performed; whether a multiple comparison correction has been used to control for Type I family-wise error, where necessary; and/or whether the need for statistical analysis to support the claims has been obviated through validation of claims by independent experiments. Authors are encouraged to involve statisticians in both the design and analysis of experiments, to whatever extent is necessary, to properly interpret results. Large-scale data sets must be made available for review at the time of submission and must be deposited in an accepted format to a permanent public repository with open access (e.g., GEO http://www.ncbi.nlm.nih.gov/geo or Array-Express http://www.ebi.ac.uk/arrayexpress). The purpose of this policy is to ensure that conclusions are scientifically sound, i.e., based on an appropriate experimental design and statistical analysis of the data. If conclusions are not drawn and such experiments are used simply as a screen, then the preceding does not apply, as long as the manuscript explicitly indicates that the experiment should be regarded only as a screen, that results were used only to identify candidates which were then validated independently, and that 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 datasets used only as screens as supplemental information is encouraged, but not necessarily required.

     Quantification of molecules, including DNA, RNA, and proteins. 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. 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. Use of the term ‘semi-quantitative’ is not acceptable in The Plant Cell; instead, assays must be shown to be sufficiently quantitative to support a conclusion of changes in levels.