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The Plant Genome Author Instructions

Scope

The Plant Genome (TPG) publishes original research investigating all aspects of plant genomics including genome biology, functional genomics, genomic analyses of important traits, genomic resources, genomics-assisted breeding, and genome engineering. Technical breakthroughs reporting improvements in the efficiency and speed of acquiring and interpreting plant genomics data are welcome. The editorial board gives preference to frontier genomic advances and novel reports that use innovative genomic applications that advance our understanding of plant biology that may have applications to the genetic improvement of all economically important plants. The journal also publishes invited review articles and perspectives that offer insight and commentary on recent advances in genomics and their potential for plant improvement.

Manuscript Types

Full papers must be reports of original research, critical reviews, or interpretive articles. The journal also publishes technical advances, data notes, and letters to the editor.

Original Article. Papers that present novel findings that advance current knowledge on a specific research topic. Gene expression, GWAS, and gene family analysis papers must present functional insights including biological hypothesis and/or validation and characterization of gene function, not just simply descriptive results.
Review. Longer, more comprehensive papers that present interpretation of data that has largely been previously published.
Resources. Papers that describe genomic resources such as nuclear genome assemblies and specialized datasets that are accessible to other researchers for developing new studies. Organelle assemblies per se are not considered.
Perspective. Papers presenting a broader, more personal perspective on a single specific topic, usually providing interpretation of data that has largely been previously published.
Technical Advance. Papers that are typically concerned with experimental techniques, method improvements, new analytical equipment, computational tools or other breakthroughs that significantly improve genomic data acquisition and analysis. They may also describe novel findings that do not require extensive background or discussion.
Invited Review. By invitation only, longer, more comprehensive papers presenting interpretation of data that has largely been previously published.
Letters to the Editor. Papers that are published subject to review and approval of the Editor, and provide a forum to discuss specific topics. Letters should be 300 words or less in length.
Book Review. Short description of a book related to the plant genomics field.

TPG also publishes special sections, which are designed to bring to the forefront and promote new areas of research of broad interest to the TPG readership; highlight and provide a platform for scientific exchange resulting from symposia, collaborative projects, and topical conferences through rigorous and professional peer review process; and provide a periodic overview of the state of the art in various research areas by soliciting contributions from active leaders in the field of plant genetics. A typical special section size varies from 6 to 25 manuscripts. A proposal for a special section solicits and calls for papers along a theme (approved by the TPG Editor) to be submitted, reviewed, and published within the time frame of approximately one year. Submit your proposal using our online form.

Manuscript Submission

Templates

Download the TPG Manuscript Submission Template and Pre-Submission Manuscript Formatting Checklist.

Submission

Submit manuscripts at the TPG Manuscript Submission Site. Submissions to TPG may not be previously published in their entirety or simultaneously submitted to any other scientific or technical journal. American Society of Agronomy (ASA), Crop Science Society of America (CSSA), and Soil Science Society of America (SSSA) journals follow the Publication Manual of the American Psychological Association (APA style) for references. Consult our Publications Handbook and Style Manual for specific questions about style.

Creating the Manuscript File

Microsoft Word or LaTeX files may be submitted for review. For your convenience, we encourage you to use our Word template. The manuscript should be double-spaced, using page and continuous line numbers. See our LaTex File Submission Guidelines for instructions on submitting LaTeX files.

Peer Review and Revisions

All manuscripts submitted undergo single blind peer review. Papers are assigned to an associate editor who is responsible for soliciting at least two reviews. Authors will be prompted to provide a list of potential reviewers. These reviewers must not have a conflict of interest involving the authors or paper, and the editorial board has the right to not use any reviewers suggested by authors. See the ASA, CSSA, SSSA Editorial Policies information page for additional information on review policy. All revisions to the manuscript during the review process will be made by the author only, and revisions will be given the same manuscript number, with an R number on the end (e.g., TPG-2006-04-0017-ORA.R1). Each revision has the opportunity for another round of review—the manuscript status “awaiting reviewer selection” is automatic and does not indicate a resubmission. Authors have four weeks to review and return their manuscript following reviewer and associate editor comments. Manuscripts may be released if revisions are not received, and the paper will have to be submitted as a new manuscript. Within days of submission, we'll decide whether or not to send your paper through review. For papers that are reviewed, the average time from submission to first decision is about eight weeks. Accepted papers go through an average of one revision.

ORCID iD

Corresponding authors are required to use an ORCID iD when submitting a manuscript. More information on ORCID can be found on their website. We encourage all authors to list their ORCID iD in the manuscript.

Plagiarism Screening

Papers submitted to ASA, CSSA, SSSA journals are screened for plagiarism before being sent for review. If there appears to be major repetition from other sources, the editor will evaluate the duplication and take appropriate action as warranted.

Article Requirements

Authors should follow the Publications Handbook and Style Manual when formatting manuscripts for submission.

Please submit the manuscript file in Word format containing the title, abstract, text, references, figures, and tables. The submission should contain the following elements:

Title
Authors
Affiliations
Core Ideas
Abstract
Plain language summary
Abbreviations
Text
Supplemental Material statement
Data Availability statement
Conflict of Interest statement
Author Contributions
Acknowledgments
References list
Tables*
Figures* and figure captions

*Tables and figures (review quality) with captions should be placed into the text document at first mention. If your manuscript is accepted for publication, figures must also be submitted separately as high-resolution image files in the following acceptable formats: PDF, EPS, TIF, or JPEG.

Paper Structure

On the first page, give the title, a byline with the names of all authors, an author–paper documentation, a list of all nonstandard abbreviations used in the paper (standard abbreviations available in the Publications Handbook and Style Manual), and any other necessary footnotes. An abstract is required and is normally the second manuscript page. After the title page and abstract, the usual order of sections is Introduction, Materials and Methods, Results, Discussion, Conclusions (optional), Acknowledgments (optional), and References, followed by any figure captions and the tables. Results and Discussion may be combined and conclusions can be given at the close of the Discussion section. Start each section (including figure captions and tables) on a new page and number all pages.

Title and Byline. A title gives the reader a clear idea of what the article is about; it should be brief and informative. The usual limit for titles is 10 to 12 words (not counting “and,” “of,” and similar conjunctions and prepositions). Titles in a numbered series of articles may be longer. Below the title, list the names of all authors. Place an asterisk after the name of the corresponding author (i.e., the person from whom reprints are to be requested).

Affiliations. The author–paper documentation is a single paragraph. The first sentence lists the authors (without professional titles) and their complete, current addresses. If a paper has only one author, or if all authors are from the same department and institution, omit the names (i.e., give the address only). The second sentence lists institutional sponsors, with the institutional article number of similar contribution acknowledgment. Add such an acknowledgment if an author has moved and using the current address leaves no other mention of the involvement of the former institution. Other information such as author contributions, granting, funding, or dissertation status may follow here or in a separate acknowledgment section at the end of the paper. End the author–paper documentation paragraph with these two statements: “Received ___________. *Corresponding author (e-mail).” The date received will be filled in by an editor.

Core Ideas. Include 3 to 5 summary statements that convey the core findings of the article. The purpose of these short, bullet-pointed statements is to identify the most relevant outcomes of the paper and to provide a synopsis encapsulating the significance of the research and its implications for readers. Each statement must be 115 characters or less (spaces included). If the article is accepted, the core ideas may also be used for promoting and publicizing the research.

Abstract. Abstracts are a single self-contained paragraph of no more than 1500 characters – including word spaces ‑ for papers or 750 characters for Notes. Abstracts should contain the rationale, objectives, methods, results, and their meaning or scope of application. Be specific. Identify the crops or organisms involved, the soil type, chemicals, and other details that are pertinent to the results. Do not cite references.

Plain Language Summary. Include a plain language summary (limit 150 words). The summary should be clear, concise, and free from jargon. See guidelines for writing plain language summaries here.

Abbreviations. Prepare a list in alphabetical order of abbreviations used in your article. Do not include SI units, chemical abbreviations, or abbreviations listed in the style manual as not needing definition.

Supplemental Material. Supplemental material may be included in the online version of articles at the discretion of the editors. The material must be submitted along with the original manuscript and will undergo peer review. Authors are encouraged to submit materials that contribute to the content and quality of the article or to use supplemental material as a means to shorten the text of manuscripts. Ancillary information such as some experimental data, including schematics of apparatus and maps of study sites, or material of interest mainly to specialists, are examples of potential supplemental material. When using supplemental material to shorten the text of a manuscript, keep in mind that the Materials and Methods section should provide enough detail to allow the reader to determine whether the interpretations are supported by the data.

Supplemental tables and figures should be cited in order in the main manuscript, as Supplemental Table S1, etc. Supplemental material should be formatted with a cover sheet listing authors and manuscript title, and the number of pages, figures, and tables. Tables and figures should be numbered Supplemental Table or Supplemental Figure S1, S2, etc. The journal program manager may limit the quantity of supplemental material posted. Ideally, the supplement should consist of a single PDF or MS Word file (rather than a series of files with individual images or structures). Other file types, such as Quick Time or Excel, may be allowed. Contact the program manager with questions about file types. If submitting videos please use the format .FLV (Flash Video) with 640 x 480 or 720 x 480 (widescreen) as the resolution. If you do not have this format available to you please contact the program manager. The following are not allowed: executables (.exe) of any kind, java script, TeX, or PowerPoint.

Include a short (one- or two-sentence) paragraph, titled “Supplemental Material,” describing the supplemental material in the main manuscript directly after the main text.

In place of supplemental material, our journals encourage the use of data repositories that assign DOIs or other persistent unique identifier (PID) to the data.

Data Availability Statement. All authors are required to provide a data availability statement directing readers to research data. If there are no data associated with a manuscript (ex. review, perspective articles), authors should make a statement indicating such. TPG authors are required to make available upon submission any underlying data needed to understand, evaluate, and build upon the reported research. Data must be provided as supplementary material or deposited in a public repository (see Data Policy section for more details and example statements). Authors of GWAS studies must provide the raw phenotypic and genotypic data as a supplemental table or as a link to a data repository to allow subsequent meta-analysis by other researchers. Metadata should be provided to fully describe experimental conditions. In addition, for GWAS studies, a supplemental table (or link) should be provided with (i) the SNP allele scored, (ii) a position in the context of a reference sequence (or with adjacent context sequence provided), and (iii) the p-value for each trait and each SNP.

Conflict of Interest Statement. Authors should include a statement just before the References section that explains any conflicts of interest. If there are none, authors should explicitly state there are no conflicts of interest.

Author Contributions. The contributions of each author must now be indicated at submission. The submitting author is required to assign specific author contribution roles for each coauthor, using the CRediT taxonomy to indicate their respective roles. The 14 roles are Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, and Writing – review & editing. Author Contributions will be published with the accepted article and cannot be edited after article acceptance. Therefore, you must ensure the Author Contribution information you provide is accurate prior to final acceptance.

A final acknowledgments paragraph may be included.

References. ASA, CSSA, SSSA journals follow the APA style for citations and references. The author-year system for citations is required; do not use numbered references. Refer to chapter 1 of the Publications Handbook and Style Manual for examples of our reference and citation style, in addition to following these guidelines:

Arrange the list alphabetically by the surnames of the first authors and then by the second and third authors.
Single-authored articles should precede multiple-authored articles for which the individual is first author.
Two or more articles by the same author are listed chronologically; two or more in the same year are indicated by a, b, c, etc.
Only literature that is available through libraries or other readily accessible public media can be cited. Material that does not meet this standard should be cited as personal communication or unpublished data.

Tables. Each entry should appear in a new table cell. Do not use tabs, spaces, or graphics. Cite each table in the text in numerical order; do not use table parts (1a, 1b). Each table must be cited in the text. Table heads should be brief but complete and self-contained. Define all variables and spell out all abbreviations. Table notes can include “Notes” for general notes that apply to the entire table, superscript lowercase letters for specific notes, and asterisks and other symbols as needed for significance notes.

Figures. At submission, review-quality figures with captions should be placed into the main text document at first mention. Authors may also submit figures as separate files. If the manuscript is accepted for publication, color figures must adhere to our color-figure policy. Figures must also be submitted separately as high-resolution image files (300 dpi preferred) in the following acceptable formats: PDF, EPS, TIFF, or JPEG. PPT files are acceptable if the figure was created in PowerPoint. Width of figures should approximate desired print size, i.e., 80 mm for a one-column figure, 180 mm for a two-column figure. All figure parts should be labeled. Multi-panel figures should be submitted as one image. Biplots should have equally scaled axes with tick marks.

Spell out abbreviations on first mention in figure captions, even if they have already been defined in the main text. Define symbols used either in the caption or in a legend within the figure. For more information on figures, see Chapter 5 of the style manual.

Math. Use keyboard formatting where possible (i.e., bold, super-/subscripts, simple variables, Greek font, etc.); if needed, use MathType (preferred) or Word Equation Editor (only if MathType is not available).

Units of Measure. The International System of Units (SI) must be used. Other units may be indicated in parentheses after the SI unit if this helps understanding or is needed for replication of the work.

Data Availability Policy

An inherent principle of publication is that others should be able to replicate and build upon the authors' published claims. TPG requires that the underlying data needed to understand, evaluate, and build upon the reported research be available at the time of peer review and publication. Source code for any specialized, in-house scripts or programs, that are necessary for the reproduction of results, must be deposited in a public repository such as GitHub, or uploaded as supplementary data.

Compliance with the TPG Data Availability Policy entails:

Depositing the data and software in a community accepted, trusted repository (ex. Figshare, Dryad, NCBI SRA), as appropriate, and preferably with a DOI
Including a Data Availability Statement (see below) as a separate paragraph explaining to the reader where and how to access the data and software
And including citation(s) to the deposited data and software in the Reference Section.

Primary and processed data used for your research should be preserved and made available. Generally, the underlying data are considered to be the types of data usually preserved in domain repositories for each discipline. These may include raw data, but are usually the processed or refined data that support and lead to the described results and allow other readers to assess your conclusions and build off your work.

Any restrictions on the availability of materials or information must be disclosed to the editors at the time of submission. In some cases, up to a six-month embargo may be granted. Note that underlying data must be available upon submission.

Example Data Availability Statements

The datasets generated during and/or analyzed during the current study are available in the [NAME] repository: [PERSISTENT WEB LINK TO DATASETS].
All data generated or analyzed during this study are included in this published article (and its supplementary information files).
There are no original data associated with this article. Referenced data are available in the literature.

Genome Sequencing Paper Guidelines

TPG supports the policy of open access and FAIR data. For manuscripts describing genomic sequencing data (genome assembly, pan-genome, whole genome resequencing, genotyping), the respective data (raw data, assembly data, variation information) must be deposited into appropriate public repositories (e.g., NCBI SRA, EMBL ENA) and is mandatory to be publicly accessible upon publication. Data must be accessible to the reviewers during the reviewing process. All bioinformatic procedures need to be described in sufficient detail within the manuscript and custom scripts must be deposited in appropriate repositories (e.g., Github). For sequenced material, biosample IDs are encouraged. Genome assemblies are expected to be provided with at least a basic level of annotation. Any exceptions to these requirements must be approved by the Editor.

Citing Genetic Material

Authors of CSSA publications must cite plant introductions, as well as registered cultivars, germplasm, parental lines, and genetic stocks when they are mentioned in the text of the Introduction, Discussion, or Characteristics section of research papers. Such genetic materials must also be cited when they are used to develop unreleased genetic populations that are the focus of the research paper, unless the development of the population can be cited more directly. Authors are encouraged to cite the Journal of Plant Registrations if possible. Other sources for citation information include the Genetic Resource Information Network (GRIN) maintained by the USDA. Registrations published in Crop Science and the Journal of Plant Registrations are indexed on the GRIN website. A general search in GRIN is available here.

Nomenclature

Both the accepted common name and the chemical name of pesticides must be given upon first mention in the manuscript. Use chemical symbols for elements, ions, and simple compounds except at the beginning of a sentence or in a title or heading. The Latin binomial or trinomial (and authority for plants) must be included with the common name for all plants, insects, pathogens, and animals at first mention. When referring to soils, give at least the subgroup in accord with the US system of soil taxonomy. Ideally, both the series and complete family name should be given.

Changes to Author Byline

From time to time, authors' names are either added or removed from a given manuscript between the time of submission and publication. In situations such as this, the ethical and responsible manner of handling this type of change is for the lead author to advise the author being added or removed of the change and to notify, in writing, the journal editor and program manager for approval. In addition, all coauthors should notify the program manager that they are aware of and approve of the change.

Consent and Permissions

Before submitting the paper, the corresponding author should send each living coauthor a draft copy of the manuscript and obtain the coauthors’ assent to coauthorship. Authors are responsible for obtaining all permissions for use of figures or other material from other publishers and should supply these permissions when the manuscript is accepted. Authors are also responsible for obtaining permission from individuals whose images are included in photographs. Note that ASA, CSSA, and SSSA reserve the right to publish and republish any images you submit with a manuscript.

Errata

Errata may be used by the authors of a paper to correct errors and omissions that affect the integrity of the version of record that are identified after publication. All additions and corrections are subject to editorial approval and must be approved by all coauthors before submission; corrections of minor errors or omissions will not be published. Send all errata requests to the journal's program manager.

Publication Fees

Mandatory Open Access Fees

Authors are assessed a mandatory open access licensing fee of $2,800 to apply an open access license at the time of publication to make the article freely available without a subscription.

Journal articles in are published open access under the CC BY-NC-ND (attribution, noncommercial, no derivatives) license. Learn more

Authors may request that their article be published under the CC BY (attribution) license. Learn more

No licensing fees are charged for invited reviews, comments, book reviews, or letters to the editor.

For authors publishing in this open access journal, fee waivers and discounts may be available to qualifying corresponding authors based in low- and lower middle-income countries. Visit the waivers and discounts web page to learn more.

Institutional Funding and Transformational Agreements

Your institution or funder may be able to help with open access licensing fees through a transformational agreement. For qualified authors, fees may be covered in full or part when publishing in the journal. Visit the institutional funder payments web page to learn if you qualify and for more information.

Authors Funded by cOAlition S

If you or one of your co-authors received funding from a member of cOAlition S, there may be restrictions on where you can publish. Please check your agreement with your funder for specific details. The information and author compliance tool on this web page can help you make an informed decision about where to publish in alignment with funder and journal requirements.

Official Sources

Spelling: Merriam-Webster’s New Collegiate Dictionary
Plant scientific names: USDA–ARS GRIN database
Chemical names: PubChem
Soil series descriptions: USDA–NRCS Official Soil Series Descriptions
Fungal nomenclature: Fungi on Plants and Plant Products in the United States (APS Press)
ASA, CSSA, SSSA journal style: Publications Handbook and Style Manual

For questions about the format of submissions, the process of submitting a manuscript, or about the status of manuscripts that have been submitted and assigned a manuscript number, please contact the TPG program manager.

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