APPS Instructions for Authors

Scope and Aims of the Journal

Editorial Procedure and Policy || Submission and Review Process || Publication Date || Article Processing Charges || Indexing || Copyright and Licensing Information || Conflict of Interest || Copyrighted Material and Plagiarism || Data Origin || Data Accessibility || Nomenclature || Vouchers ||

Article Types || Protocol Notes || Genomic Resources Articles || Software Notes || Application Articles || Review Articles || Primer Notes ||

Manuscript Preparation

Manuscript Contents || Title and Footnotes || Abstract || Text || Literature Cited || Data Accessibility Statement ||
|| Tables || Appendices || Figure/Illustration || Figure Legend || Multimedia Content || Supplemental Materials

Manuscript Submission || Cover/Response Letter || Additional Documentation || Author Agreement Form ||

|| Contact the Editorial Office ||

Scope and Aims of the Journal
Applications in Plant Sciences (APPS) is a monthly, online-only, open access, peer-reviewed journal promoting the rapid dissemination of newly developed, innovative tools and protocols in all areas of the plant sciences, including genetics, structure, function, development, evolution, systematics, and ecology. Given the unprecedented rapid progress today in technology and its application in the plant sciences, the goal of APPS is to foster communication within the plant science community to advance scientific research. APPS is a publication of the Botanical Society of America (BSA), and is available as part of BioOne’s Open Access Collection ( The journal publishes the following types of articles:

  • Protocol Notes describe new methods and technological advancements for the visualization or quantification of biological information. 
  • Software Notes detail new software applications with examples of how they are used and how results are interpreted.
  • Genomic Resources Articles characterize the development and demonstrate the usefulness of newly developed genomic resources, including transcriptomes and whole plant genomes.
  • Application Articles illustrate the application of a new protocol, method, or software application within the context of a larger study.
  • Review Articles evaluate available techniques, methods, or protocols within any area of the plant sciences, providing a summary of advantages and disadvantages of the techniques that are reviewed.
  • Primer Notes report novel genetic markers within a taxon or taxa with evidence of wide applicability.

The journal originated as the American Journal of Botany's online-only section, AJB Primer Notes & Protocols in the Plant Sciences (AJB PNP), which was begun in 2009 to serve as a publication outlet for researchers in genetic and molecular areas. The first issue of APPS published in January 2013; the journal now addresses all areas of the plant sciences and has been expanded to cover novel protocols, reviews, and applications of new technology in any area.

Articles published in the AJB Primer Notes & Protocols in the Plant Sciences section of the American Journal of Botany can be accessed online on the AJB website (

Editorial Procedure and Policy
Submission and Review Process—To facilitate automated publication, submissions should conform to the word count and the publication template (see below) for each type of article. Authors are not charged for manuscript submission. Papers submitted to APPS will first be reviewed by an editor for content, suitability to the journal, and conformity to the guidelines. Depending upon the type of manuscript and the subject matter, manuscripts will be sent out for peer review by scientists with relevant experience, a panel of reviewing editors, and/or the Associate Editors. Review will generally be completed within one month for Primer Notes and two months for other types of articles. Authors will be expected to return revised manuscripts within two weeks (for Primer, Software, and Protocol Notes) or four weeks (for Genomic Resources, Review, and Application Articles) of an editorial decision. Revisions will be evaluated for satisfactory response to editorial comments and checked for conformity to format guidelines; accepted manuscripts will undergo a light copyedit. Authors will be solely responsible for any errors that appear in the published version.

APPS requires that at least one colleague whose first language is English critically read and edit the manuscript before submission. Clear grammar, sentence structure, and spelling are essential for reader comprehension and are required of all manuscripts. Manuscripts may be returned without review if the English needs significant improvement.

Publication date—Each article will receive a unique digital object identifier (DOI), and the date of publication will be the date on which the article is posted to BioOne.

Article Processing Charges—All APPS papers are Open Access and freely available immediately upon online publication. As APPS does not receive any income from library subscriptions or online pay-per-view charges, article processing charges (APCs) are necessary to cover the editorial and publishing services provided by the journal. These include our manuscript submission and peer review system, plagiarism detection services, professional copyediting, page typesetting, XML generation and metadata tagging, online hosting, article deposit to outside aggregators (PubMed, Web of Science, EBSCO, etc.), article publicity, and editorial staff services. Click here for an exhaustive list of services that journal publishers provide.

APPS is proud to serve as a peer-reviewed, mission-driven Society journal, and we will continue to lead and serve the needs of the botanical community into the future. We strive to keep our APCs as low as possible, and offer discounted levels for BSA members.

APCs are as follows:

Non-BSA members: $1400 per article
BSA members: $800 per article
BSA members with an active membership for longer than two years: $450 per article

This policy applies to all accepted articles, except for invited articles for which the Editorial Board has agreed to waive fees at the time of article submission. Payment must be received before articles are published online.

Indexing Information—ISI impact factor: 1.492 (2016 Journal Citation Report). APPS is indexed in AGRICOLA, Biological Abstracts, BIOSIS Previews, CAB Abstracts, CrossRef, Current Contents/Agriculture, Biology, and Environmental Sciences, the Directory of Open Access Journals (DOAJ), EBSCOhost, Google Scholar, Journal Citation Reports/Science Edition, Mendeley, NCBI, OIAster, PubMed, PubMed Central, Science Citation Index Expanded (SciSearch), Scopus, Web of Science, and WorldCat. APPS is archived in LOCKSS and Portico.

APPS Copyright and Licensing InformationAPPS operates under a Creative Commons Attribution 3.0 license The default license is CC-BY-NC-SA. Under the terms of this license, authors retain ownership of the copyright of their articles. Users are allowed to download, print out, extract, reuse, archive, and distribute the article for noncommercial use; this use is contingent upon appropriate credit being given to the authors and the source of the work and upon the new creation being licensed under the same terms. Authors may also select the CC-BY license, which permits use, distribution, and reproduction in any medium, provided the original work is properly cited. Papers authored by one or more US government employees are licensed under a Creative Commons public domain license (CC0), which allows unlimited distribution and reuse of the article for any lawful purpose.

Each of these licenses ensure wide availability of the article and that the article can be included in any scientific archive. No permission is required from the author or the Botanical Society of America. If a CC-BY-NC-SA license is used, those wishing to use material for commercial purposes should contact the author. The Creative Commons license applies to all submissions on or after 31 October 2012.

Conflict of Interest—The Journal editors expect authors to follow the ethics guidelines of the Botanical Society of America (BSA) ( Authors are responsible for recognizing and disclosing any duality of interest that could be perceived to bias their work, acknowledging all financial support and any other personal connections. All funding sources, including the research funder and grant number, must be given in the acknowledgments section.

Copyrighted Material and Plagiarism—If copyrighted material is reproduced in the manuscript, full attribution must be provided in the text; proof of permission must be sent to the Editorial Office. It is the responsibility of the authors, not the BSA or the editors or reviewers, to ensure that proper attribution is given to data and/or text previously published elsewhere. If suspicion is raised about the originality of the material (unattributed to source), the Editorial Office may check the manuscript for plagiarism. Note that all Primer Note manuscripts are checked for plagiarism at submission using the iThenticate service. In cases where plagiarism is verified, the manuscript will be returned without further review without the possibility of resubmission. Self-plagiarism (i.e., the use of identical sentences from previously published papers by the same author) is also not acceptable. See the editorial in the July 2014 issue of APPS for more information on APPS's stance on self-plagiarism.

If authors wish to reproduce copyrighted material published in APPS before the institution of the Creative Commons license (i.e., manuscripts submitted before 31 October 2012), the permission request form available online at BSAPermission.doc must be completed and returned to the Editorial Office. Those wishing to use material published under the Creative Commons license for commercial purposes should contact the author.

Data Origin—When using unpublished data owned or created by a researcher who is not the author or a co-author, a formal statement from the owner of the data must be sent to the Editorial Office acknowledging the use of the data and granting formal permission.

Data AccessibilityAPPS requires that supporting data be deposited in an appropriate repository to facilitate reader access prior to submission of the manuscript. Genetic information, such as DNA, RNA, or protein sequences, should be submitted to an appropriate data bank, such as GenBank or EMBL. Alignments used to produce phylogenies must be submitted to TreeBase or to APPS to be published with the paper as supplementary material. The data matrices must be in an editable format (i.e., text files) for reanalysis by any interested readers following publication. Authors are encouraged to archive all sequences generated from next-generation sequencing techniques in a suitable public depository, such as the Sequence Read Archive of NCBI, the Sequence Read Archive of ENA, or Dryad ( Any sequence library data used to develop microsatellite markers should be deposited to the Sequence Read Archive, with the Bioproject number reported in the manuscript. Ecological data or software information may also be deposited into Dryad or a similar publicly available site. Media files may also be housed on Figshare ( If necessary, raw data files (e.g., DNA sequences, gel images, chromatograms, data matrices) and/or electropherograms may be requested by the editors during the review process.

To enable readers to locate the supporting data, authors are encouraged to include a "Data Accessibility" section after the Literature Cited (see Manuscript Preparation section below for details). This section should be present at initial submission, and data archiving should be completed before final acceptance.

NomenclatureAPPS requires that nomenclature for all extant and extinct species conform to the current International Code of Nomenclature of Algae, Fungi and Plants. Taxonomic authorities are given at first mention in the text (not in the manuscript title). Authors should refer to the International Plant Names Index ( or Tropicos ( for accepted authority names.

Conventions adopted by the scientific community must be used for genetic symbols and nomenclature.

Vouchers—At the time of submission, supporting genetic and voucher specimen information must be provided, preferably for each population sampled, as appropriate (see Appendices below). Plant vouchers are defined here as mounted herbarium specimens that are permanently housed in an accessible herbarium or museum and that are identified by unique accession numbers; vouchers may be requested for review by future investigators to verify the identity of the material used in the study (especially if taxonomic rearrangements occur in the future). See the editorial in the November 2013 issue of APPS for more information on APPS's voucher requirement. In discussions of morphological character states, access to the data must be provided.

Manuscripts that report data from individual populations must include the GPS coordinates for each of the populations sampled. A waiver of this requirement may be granted for rare, threatened, or endangered species, as explained in the cover letter. Accuracy must be provided to the nearest second, or the fifth decimal place if using decimal degrees. If vouchers or GPS coordinates are unavailable, an explanation must be provided in the cover letter, as well as within the article itself. Exceptions to the voucher requirement will be assessed by the editors.

Article Types

Protocol Notes—Protocols represent novel approaches that improve the accuracy, reproducibility, and/or efficiency of data collection or provide access to novel classes of information. In each manuscript (3000 words or less for the main text without the Abstract or Literature Cited; the word limit may be increased with approval from the editorial office), authors must concisely explain the rationale for the new protocol, provide a detailed description of the procedure(s) and demonstrate the efficacy of the method (e.g., by validation against a control). Authors must also describe both the advantages and any disadvantages of the new technique. Advantages and disadvantages might reflect differences in cost, in the speed and ease with which results are obtained, or the breadth of material for which the new techniques are applicable. The format and space requirements for accurate descriptions of novel protocols will vary, so authors should make an effort to provide succinct and adequate details of their methods and results. A protocol sheet consisting of a step-by-step description of the process must be provided in enough detail to enable another scientist to easily reproduce the method; this may be placed as an appendix along with a supply list. Submissions of protocols that improve investigations in any area of the plant sciences are welcome, including, but not limited to, methods on genetic, morphological, physiological, biochemical, anatomical, and ecological data collection.

View the Protocol Notes template.

Genomic Resources Articles—These articles (6000 words or less for the main text without the Abstract or Literature Cited) characterize the development and demonstrate the usefulness of newly developed genomic resources, including transcriptomes and whole plant genomes. Plastid genomes will generally not be considered. Descriptions of whole plant genomes must consist of more than a simple report; this can include comparisons to other genomes, analysis of genome organization, investigation of structural rearrangements, rates of sequence evolution, etc. Manuscripts that report the development of specific primers (such as microsatellites) that are based on large genomic databases should instead be submitted as a Primer Note.

To clearly indicate the quality and utility of the reported data, authors must include the following information: (1) sequencing description; (2) method of contig and scaffold assembly; (3) metrics on the number, sizes, and distribution of contigs/scaffolds, and estimated genome coverage of the combined scaffolds; and (4) results of gene prediction annotation. Ideally, comparisons should be made to other genomes, which can be shown graphically in terms of divergence.

For transcriptome studies, authors are encouraged to parse genes into functional gene groups (for mRNA) or length classes (for long and short non-coding RNAs). Results from gene ontology term enrichment should be presented if multiple tissues, times, or environments were sampled. Transcriptome assemblies must be deposited to a publicly accessible database archive (such as the NCBI Transcriptome Shotgun Assembly [TSA] sequence database) and include the corresponding accession number(s) in the manuscript.

For whole plant genomes, there must be appropriate coverage, a complete description of the assembly (e.g., N50, L50, maximum scaffold/contig size, total number of bases in scaffolds), and gene prediction and functional annotation, based on either transcriptome resources (reported in the manuscript or published elsewhere) or ab initio gene prediction models. Assembly accuracy should be addressed by at least one method (e.g., BAC end sequence analysis; long single molecule sequencing; linkage mapping). Other elements of a whole plant genome could include potential sections with re-sequencing for genetic diversity, non-coding RNAs, plastid sequence assembly, and analysis of genome duplication (in the case of polyploids). For next-generation-sequencing–based studies, authors must submit raw data to the NCBI Sequence Read Archive (or equivalent databases for EMBL or DDBJ) and include the corresponding accession numbers in the manuscript. Genome assemblies and related resources (scaffolds, protein predictions) must be made publicly available by web server.

Manuscripts that lack the above information will be returned to the authors prior to review.

View the Genomic Resources Article template.

Software Notes—Description of new software applications or substantial revisions of existing applications (3500 words or less for the main text without the Abstract and Literature Cited) must clearly define the goals, provide interpretations of output parameters or data, and list any assumptions or limitations of the method. Compatibility information for operating systems associated with stationary and portable computing devices must also be provided, as appropriate. In addition, submissions on applications for the analysis, filtering, or modification of data, or mining of large data sources are also welcome; these should provide clear descriptions and examples of appropriate types of input data and output formats. We encourage the authors of software packages to make source code available under the terms of a free software license, e.g., GNU General Public License, BSD License, or Apache License.

View the Software Notes template.

Application Articles—These articles (5000 words or less for the main text without the Abstract or Literature Cited) illustrate the extensive application of a new protocol, method, or software application in any area of the plant sciences within a large study. These articles differ from Protocol Notes and Software Notes in that the emphasis is on the use of the protocol or software program, not on the description of the new protocol or program (including its advantages and disadvantages).

View the Application Article template.

Review Articles—Reviews (6500 words or less for the main text without the Abstract or Literature Cited) will address current and proposed techniques and/or protocols within any area of the plant sciences, emphasizing the relative advantages and disadvantages of each method. Authors must describe and compare currently available techniques or protocols, as well as identify any potential new areas for the development of technological advancements. These articles will be primarily by invitation, although authors are also welcome to propose ideas for a review article to a member of the editorial board.

View the Review Article template.

Primer Notes—The intent of these articles (1200 words or less for the main text without the Abstract or Literature Cited) is to demonstrate the usefulness of newly developed primers for subsequent, more detailed studies. These include, but are not restricted to, microsatellite markers or other types of genetic markers. (SNPs reported for a single taxon will generally not be considered for Primer Notes as their nature complicates broad applicability across multiple taxa. SNPs will only be considered if they comprise a large-scale resource.) Markers developed using novel techniques are especially welcome. Please note the specific criteria below.

  • Authors should report an adequate number of markers to assure successful completion of subsequent studies (e.g., at least 15 novel markers for microsatellites, at least 10 of which must be polymorphic) with evidence of wide applicability (such as cross-amplification with related taxa) for species of scientific, economic, or horticultural importance. Although most primers are expected to exhibit polymorphism, monomorphic primers are also acceptable because they may be useful in other populations or related taxa.
  • The use of data from at least three populations in the focal species is required to capture a wider range of potential variation. Sampling distribution and numbers will depend on the life history characteristics of the organism under study, but sample sizes should be adequate to support the genetic parameters presented. For example, sample sizes are expected to be greater for abundant and widely distributed species than for rare species. Sample sizes of less than 15 per population will require justification of why larger population sampling was not possible. Ideally, sampled populations should include 20-30 individuals.
  • Tests of linkage disequilibrium and Hardy-Weinberg equilibrium are encouraged when population sampling is appropriate for such tests (i.e., reflecting limited sampling and biological characteristics such as small population sizes, recent colonization, admixture, clonality, etc.).
  • For microsatellite markers, cross-amplification must be tested in at least one other taxon (represented by at least five individuals) but preferably in three or more related taxa; exceptions can be made, such as in the case of rare taxa.

Exceptions to any of the above criteria will be considered on a case-by-case basis, with adequate justification provided in the cover letter.

Additional requirements:

  • Authors are required to develop and test primers for all suitable sequences that are developed as markers, and submit those sequences to an appropriate repository (such as GenBank) prior to submitting a manuscript to APPS. Studies that do not have GenBank numbers associated with each marker (e.g., those using Illumina sequencing) should include with their submission a supplementary file reporting the sequences of the reads (or scaffolds in the case of using assembled data) that the primers came from (using the file type "Supplemental Materials"). The sequences must also be deposited to NCBI's Sequence Read Archive and the Bioproject number should be reported in the manuscript; exceptions will be considered on a case-by-case basis.
  • All submissions will be scrutinized closely to ensure that primers have not been previously published elsewhere. If other primers have previously been published for a species, authors must convincingly justify the development and usefulness of additional primers. Authors are required to cite papers reporting markers in the same species.
  • In cases where large numbers of markers are identified (as in EST studies or next-generation sequence sets), authors should indicate how they chose which primer pairs to test and briefly what is planned for any additional sequences not analyzed. It is extremely unlikely that multiple primer papers based on the same original data set will be published by APPS.
  • Authors submitting Primer Notes are required to provide references to studies involving primers of any kind (regardless of organism) published in the past three years by any coauthors of the current submission in the cover letter accompanying their submission. PDFs of these previous primer publications should be included with the submission in a single PDF file, using the Item Type "Additional Information."

View the Primer Notes template.

Manuscript Preparation

A cover letter, an author agreement form, a manuscript file, and separate files for figures should be uploaded at Authors of Primer Notes submissions should also include a PDF of any primer studies (regardless of organism) published in the past 3 years by any coauthors of the current submission. This should be uploaded as a single PDF file using the Item Type "Additional Information."

The manuscript file includes in the following order:

  • Short Title [running head: surname of the FIRST author (followed, as appropriate, with the surname of a sole co-author, or with et al. if there are three or more authors)+ 2 or 3 descriptive words]
  • Title [up to 125 characters]
  • Footnotes [authors’ addresses, contact info for corresponding author, Manuscript received ___; revision accepted ___.
  • Abstract [in structured format, no more than 150 words for Protocol, Software, or Primer Notes; 200 words for Genomic Resources, Review, or Application Articles, see below for format]
  • Key words [3-6]
  • Text [See below for format]
  • Literature Cited [limited to 15 references for Primer Notes, 25 references for Protocol Notes, 30 references for Software Notes, 60 references for Genomic Resources and Application Articles, and 85 references for Review Articles]
  • Tables, Appendices, and Figure legends

Double-space with 11-12 pt. font and left justify the margin of the entire manuscript, including Literature Cited, Tables, Appendices, and Figure Legend, using continuous pagination. Leave at least a 2.5-cm margin on all sides. Place a header with last name(s) of author(s) and page number in upper right corner. Manuscripts not following these basic requirements will be returned without review.

The figure and tables should be numbered in the order discussed in the text.

For manuscript files MS Word (.doc or .docx) or Rich Text Format (.rtf) format are preferred.

Manuscript Contents
Follow the appropriate Publication Template for preparing your manuscript (see below). Additional general information is provided below for all types of articles.

1. Title and Footnotes
Place a running head 2.5 cm below the top of page with the surname of the FIRST author (followed, as appropriate, with the surname of a sole co-author, or with et al. if there are three or more authors) + 2 or 3 descriptive words, e.g., “Ziziphus microsatellites”.

Center boldfaced title of no more than 125 characters written with sentence-style capitalization; after a species name include the family name in parentheses.  The title should be followed by superscript 1 (for footnote 1). Include the following footnote:
1Manuscript received _______; revision accepted _______.

Below the title, list authors: each author’s first name, middle initial, surname. On the next line, give affiliation and unabbreviated address. If authors have different affiliations and addresses, add a superscript number after each author’s name to indicate the footnoted address. Include another footnote superscript number to indicate the author for correspondence.

Include the total word count for the main text of the manuscript (Introduction, Methods and Results, Conclusions), e.g., “Number of words: 1000.…”

In the submission process, please include an email for all authors in case we need to contact a co-author during the publication process; this is important due to the quick turnaround, especially at the e-Galley stage.

Place brief acknowledgments, if desired, as a separate paragraph of no more than 75 words, using the following style: “The author(s) thank(s)…”. For brevity, use initials rather than first names (e.g., J. A. Smith). Include funding acknowledgments here.

Other footnotes (e.g., e-mail for correspondence) are permitted: match footnote numbers with those on the title page.

2. Abstract
The abstract must consist of a maximum of 150 words for Protocol, Software, and Primer Notes, and up to 200 words for Genomic Resources, Application, and Review Articles. For all article types except Review Articles, which should be unstructured, the abstract should be written in structured format. For Protocol, Software, and Primer Notes, the format should be:

  • Premise of the study (why the work was done)
  • Methods and Results (how the work was done and what were the results; for Protocol Notes, this must also include a comparison with other existing methods)
  • Conclusions (what major points the reader should take from the article; in the case of Primer Notes, briefly mention other related species in which the markers also amplify)

For Genomic Resources and Application Articles, the format should be:

  • Premise of the study
  • Methods
  • Results
  • Discussion

For all article types, avoid references in the Abstract; if absolutely essential, cite parenthetically with journal name, volume number, pages, and year.

After all abstracts, provide a list of 3 to 6 “Key words” that will be used for indexing purposes. Capitalize proper nouns, place in alphabetical order, and separate by semicolons.

3. Text
Authors must follow the word limit established for the main text (which consists of all headings but excludes the Abstract or Literature Cited), as previously described above under “Types of Articles.” To facilitate the publication process and a rapid turnaround, authors must closely follow the templates provided for each type of article, with emphasis on the formatting and maximum length of each section. The length limits may be adjusted at the discretion of the editors if novel or non-standard methods are being described. The templates also contain additional information regarding content and required sectional headings.

For Protocol, Software, and Primer Notes articles, the required headings consist of ABSTRACT, INTRODUCTION, METHODS AND RESULTS, CONCLUSIONS, and LITERATURE CITED. Further description of the information to be included in each section is provided in the appropriate template—see Protocol Notes TemplateSoftware Notes Template, or Primer Notes Template.

For Genomic Resources and Application Articles, headings should consist of ABSTRACT, INTRODUCTION, METHODS, RESULTS, DISCUSSION, and LITERATURE CITED. For Review Articles, the formatting is less restrictive than above but should include ABSTRACT, INTRODUCTION, and DISCUSSION sections with other customized headings as appropriate. If applicable, informative second-level headings are encouraged, especially for Review Articles. See Genomic Resources Article Template, Application Article Template or Review Article Template for further information.

All headings should be centered above each section and capitalized (e.g., INTRODUCTION, METHODS). Second-level headings should be in boldfaced italics, followed by an em dash (e.g., Current protocols—), and third-level headings should be presented in italics followed by an em dash (e.g., Next-generation methods—).

For any manufacturers and suppliers of reagents or software, authors must provide the name, city, spelled-out state (if in USA) or province, and country of origin.

Common Latin words (e.g., in vivo, sensu lato) are not italicized.

Footnotes are not used in the text.

4. Literature Cited
The number of literature citations is limited to 15 references for Primer Notes, 25 references for Protocol Notes, 30 references for Software Notes, 60 references for Genomic Resources and Application Articles, and 85 references for Review Articles. Verify all entries against original sources. Double check that all references in the manuscript text are in the Literature Cited and vice-versa and that they agree in spelling and year. For online references, provide URL and most recent access date for the website.

For formatting examples (note spacing, italics, etc.), go to APPS_LitCited_Samples.pdf.

Literature citations in text—Cite references in chronological order (oldest first); within a given year, order them alphabetically (e.g., Smith and Flinstone, 1988, 2011; Asher et al., 2007; Brown, 2007; Jackson, 2008, 2012).

Single author: Smith (2009) or (Smith, 2009). Two authors: Smith and Brown (2005) or (Smith and Brown, 2009). More than two authors: Smith et al. (2011) or (Smith et al., 2011).

Manuscripts accepted for publication but not yet published: Smith (in press) or (Smith, in press). Include “In press” citations in LITERATURE CITED (see below).

Unpublished data and manuscripts (e.g., submitted, in prep.) and personal communication: (A. Xu, Institution, unpublished data [or unpublished manuscript or personal observation]). These are not included in LITERATURE CITED.

References listed in LITERATURE CITED—List citations in alphabetical order by author. Single-author titles precede multi-authored titles by the same senior author, regardless of date.

List works by the same author(s) chronologically, beginning with earliest date of publication. Spell out all author(s)’ names. Use “a”, “b” (determined alphabetically) for works with the same author(s) and year citation.

For multi-authored works, list the first seven authors and then “et al.”—unless there are only eight authors and then list all eight.

Type author names in citations in upper and lower case or in large and small caps, not in all caps.


Journal Article:

Doyle, J. J., and J. L. Doyle. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11–15.

Mungall, C. J., C. Torniai, G. V. Gkoutos, S. E. Lewis, and M. A. Haendel. 2012. Uberon, an integrative multi-species anatomy ontology. Genome Biology 13: R5.

Pierre, P. M. O., S. M. Sousa, L. C. Davide, M. A. Machado, and L. F. Viccini. 2011. Karyotype analysis, DNA content and molecular screening in Lippia alba (Verbenaceae). Anais da Academia Brasileira de Ciencias 83: 993–1006.

Timme, R. E., B. B. Simpson, and C. R. Linder. 2007. High-resolution phylogeny for Helianthus (Asteraceae) using the 18S-26S ribosomal DNA external transcribed spacer. American Journal of Botany 94: 1837–1852.


Lynch, M., and B. Walsh. 1998. Genetics and analysis of quantitative traits. Sinauer, Sunderland, Massachusetts, USA.

Richards, A. J. 1986. Plant breeding systems. George Allen and Unwin, London, United Kingdom.

Book Chapter:

Galán, J. M. G., and C. Prada. 2011. Pteridophyte spores viability. In H. Fernández, A. Kumar, and M. A. Revilla [eds.], Working with ferns—Issues and applications, 193–206. Springer, New York, New York, USA.

Hill, R. S. 1994. The history of selected Australian taxa. In R. S. Hill [ed.], History of the Australian vegetation: Cretaceous to recent, 390–420. Cambridge University Press, Cambridge, United Kingdom.

Computer Program:

Peakall, R., and P. E. Smouse. 2006. GenAlEx 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288–295.

R Foundation for Statistical Computing. 2011. Version 2.13.0 (2011-04-13). The R Foundation for Statistical Computing, Vienna Austria. Website [accessed 13 July 2012].

Websites (no print version):

Joint Genome Institute. 2012. JGI Plant Genomics Program—Home [online]. Website [accessed 30 April 2012].

O’Leary, M. A., and S. G. Kaufmann. 2012. MorphoBank 3.0: Web application for morphological phylogenetics and taxonomy. Available at website

Technical Report:

Hocking, D. 1971. Preparation and use of a nutrient solution for culturing seedlings of lodgepole pine and white spruce with selected bibliography. Northern Forestry Research Centre Information Report Nor-XI. Canadian Forest Service, Edmonton, Alberta, Canada.

5. Data Accessibility Statement

To enable readers to locate archived data, we encourage authors to include a "Data Accessibility" section after the Literature Cited section. This should list the database, digital object identifiers (DOIs), stable URLs, and the respective accession numbers for all data from the manuscript, as appropriate. (Note that accession numbers provided in a supplementary table accompanying the article do not need to be duplicated here.) If you have any questions about the formatting or content of this section please contact the editorial office.

6. Tables—include in manuscript file
Tables may be included, as appropriate, in Protocol Notes, Genomic Resources Articles, Software Notes, Review Articles, and Application Articles.

For Primer Notes papers, at least three tables should be presented. One should contain the names of the forward and reverse primers, their DNA sequences, fragment size range, annealing temperatures, and GenBank ID. Based on the marker type, additional information may be required, such as repeat motifs for microsatellite markers. Any fluorescent dye used to tag any primer should also be indicated here. The second table should report the number of alleles and observed heterozygosity in each population surveyed (for microsatellite markers) or nucleotide diversity estimates (for sequence-based markers). In species expected to be primarily outcrossing and if sampling has been extensive enough in one or more natural populations, results of tests for departures from single-locus Hardy-Weinberg expectations and for departures from gametic equilibrium may be included. A third table should provide the cross-amplification results in related taxa, as in the case of microsatellite markers. Voucher accession numbers for each population may be provided with the table, in the text, or in an appendix. Include the name of the herbarium in the table caption. If the paper reports SSRs developed from ESTs, Table 1 should include (a) information on the protein and function most closely matching the EST from a database search, (b) the organism from which the match was obtained, and (c) the E-value associated with the match. An additional table may be included to present cross-amplification results, as appropriate.

Formatting Instructions: Tables should be numbered with Arabic numerals followed by a period. The table title must be concise and fully informative independent of the main text of the manuscript, with all abbreviations explained as footnotes. Capitalize the first word of the title; all others, except proper nouns, are lowercase; spell out names of genera and abbreviations on first mention; place a period at end. Include the study organism (species or group) and geographic location in each caption when appropriate. Place explanatory notes and define all abbreviations below the table after the heading “Note:”. Place footnotes after the Notes.

Tables need to be formatted using the Table feature in Word (preferred) or in a spreadsheet such as Excel. Every column must have an appropriately placed heading (especially the first at left—the stub head), with appropriate subheadings. In the body of the table, capitalize the first word of each entry (and proper nouns); indicate footnotes by lowercase superscript letters.

7. Appendices—include in manuscript file
Herbarium vouchers (preferably one per population sampled) and, if appropriate, gene accession information supporting the study should be listed in an appendix, if it cannot be easily added within the main narrative. (If vouchers are unavailable, an explanation must be provided in the cover letter, as well as within the article itself.) Provide an appendix title and a sentence-style row of headings for the data. For each taxon sampled, include specimen voucher information and/or gene accession numbers, separated by commas. To save space, the taxa can be listed consecutively in a paragraph. Alternately, the data can be set in table format. See for an example.

For Protocol Notes, a protocol sheet consisting of a step-by-step description of the process should also be placed as an Appendix along with a supply list.

Please see "Supplemental Materials" (below) for a description of appendices that should be submitted as Supplemental Materials.

8. Figure/Illustration—upload as separate files (do not include in the manuscript file)
Authors are encouraged to submit figures in color, if doing so enhances the presentation of the scientific information. There is no charge for online publication of color figures. Figures may be especially appropriate for Protocol Notes and Genomic Resources Articles. For details, see APPS_Digital_Art_Guidelines.pdf. A figure checklist is also available at APPS_Figure_Checklist.pdf. TIFF or EPS formats are preferred for color and black-and-white photographs, drawings, and graphs. Prepare figure at the final size desired: 1 column (8.9 cm [3.5 in]), 1.5 column (12.7–15.24 cm [5–6 in]), or 2 columns (18.4 cm [7.5 in]) wide and less than the length of the page (23 cm [9 in]).

Use consistent style, font, and font size (between 6 and 10 pt.) for all figures. Use of standard fonts (Times New Roman, Helvetica) gives better results.

For figures with multiple elements (photos, drawings, or graphs), group elements in a rectangle or square and label the top left corner of each element with a capital letter (e.g., A, B). Keep elements close together for best use of space. Photographs in a composite plate should each be numbered and separated by a thin line or blank space.

Label axes; include Standard International (SI) Units of measure in parentheses; capitalize only the first letter of the first word (e.g., “Observed heterozygosity (Ho)”). Axis label should be c. 0.2 cm from units on axis, but no more than 0.5 cm; x- and y-axis labels should be equidistant from axes.

Use abbreviations consistently in the text and figures.

Figure Manipulations—Certain types of electronic manipulations of micrographs and other digital images may not be ethically acceptable. Images that will be compared with each other must be acquired and processed under the same conditions. Manipulations such as background subtraction or white-balancing should be explained in the Methods section. Note that a selected area within an image may not be altered or enhanced; the entire image must be treated the same. Linear adjustments to contrast, brightness, or color must be applied to an entire image or plate equally (or explained). Detail nonlinear adjustments in the legend. Original raw data files may be requested for documentation.

9. Figure Legend—include in manuscript file and place immediately after the Appendices (or after the tables if there are no appendices)
Each figure legend must be complete and informative so that reference to the text is not necessary to understand the content of the figure. Abbreviations should be defined unless they are standard convention. Place legends as separate paragraphs following the appendices. For figures with multiple lettered panels, a general title for the figure should be followed by a description of each panel (e.g., “Fig. 5. Relationship between… (A) All fruits. (B) Fruits <0.5 mm.”). When applicable, include study organism (species or group) or geographic location, and define scale bar (e.g., Bar = 0.1 µm). For micrographs, include pertinent information such as magnification and type of section, stain, optics, or special techniques. Any nonlinear adjustment to photographs must be detailed.

Define all symbols and abbreviations either in a key within the figure or in the legend; if defined in an earlier legend, the appropriate figure or table may be cited.

10. Multimedia Contentupload as a separate file (do not include in the manuscript file)
Authors may elect to include certain types of multimedia files as appropriate in the manuscript. For example, Protocol Notes may include short videos or animations detailing a complex idea or critical but difficult step. Submissions must include a reference (e.g., Video 1) to the multimedia within the text of the manuscript and file(s) must be uploaded separately. The preferred file format is .mpg files, but .swf, .avi, and .mov files are also accepted. Multimedia files may also be uploaded to BSA’s YouTube channel by the APPS editorial office for greater accessibility with multiple platforms, especially on handheld electronic devices. Authors should contact the Editorial Office if they have additional questions regarding formats or the submission process for multimedia.

11. Supplemental Materialsupload as a separate file (do not include in the manuscript file)
Supplemental materials are differentiated from Tables, Appendices, and Figures as described here:

Tables/Figures should contain information/data that is directly relevant to the questions/aims of the study and directly supports the main conclusions of the study.

Appendices contain information that may be too lengthy for a normal figure or table (i.e., a protocol) or is slightly extraneous (long list of voucher specimens) but is still considered essential and needs to be easily accessible to the reader to understand the methods or results of the study.

Supplemental Materials may be of interest to a subset of readers who would like access to more details regarding sampling, methods, etc. This information may include large data sets and information that is provided in file types that cannot be incorporated into the Word file; it will likely be more extensive than data provided as Tables or Figures within the manuscript. These materials should be submitted as separate files (using the File Type “Supplemental Materials”) and will be published with the full-text article with the Editor’s approval.

Large data sets should be uploaded to a publicly available data repository (see above under Editorial Procedure and Policy, Data Access); alternately, they may be uploaded as Supplemental Materials with the initial manuscript submission.

Include a header on each file using this format: Smith et al.—Applications in Plant Sciences 2016 4(#): ###-###.—Data Supplement S1—Page 1”. Supplementary materials should be referred to as Appendix S1, S2, etc., regardless of whether they are tables, figures, text, other media, or a combination thereof. They should be numbered in the order in which they are cited in the text, separately from the non-supplemental appendices.

Manuscript Submission
Authors should submit their manuscript via the online submission and review system, Editorial Manager, at First-time users need to register for an account at this URL using their active e-mail addresses. The same Username and Password are used to log in as an author or as a reviewer. Authors who have been a reviewer or author for the American Journal of Botany can use their AJB Editorial Manager Username and Password on the APPS Editorial Manager site. All reviews, revisions, and proofs are handled electronically.

Cover/Response Letter
A cover letter should accompany the manuscript and should include a statement that this is the authors’ own work and that all co-authors have contributed to the work.  Any potential conflicts of interest or declarations of competing interests must be mentioned. List any papers on related topics by any of the authors that have been published within the past year or that are in review or in press. Authors submitting Primer Notes are required to provide references to studies involving primers of any kind (regardless of organism) published in the past 3 years by any coauthors of the current submission. For a revision, include a letter detailing your response to all the review comments. The cover letter is an essential part of the submission process and must contain a succinct and convincing argument for why the work reported in the manuscript should be published in APPS.

Additional Documentation
Authors of Primer Notes submissions are required to include a PDF of any primer studies (regardless of organism) published in the past 3 years by any coauthors of the current submission. This should be uploaded as a single PDF using the Item Type "Additional Information"; its inclusion with the submission materials should be noted in the cover letter.

Author Agreement Form
Upon initial submission of a manuscript, the corresponding author must fill out an author agreement form and either upload an electronic version at the online submission site or mail or fax a hard copy to the Editorial Office in St. Louis, Missouri (see contact information below). The author agreement form is available online at APPS_Author_Agreement_Form.docx; on the Editorial Manager website at the “Attach Files” screen; and from the Editorial Office.

Questions? Contact the Editorial Office
Applications in Plant Sciences
Beth Parada, Managing Editor
Editorial Office
P.O. Box 299
St. Louis, MO 63166-0299
phone: 314-577-9486; fax: 314-577-9515
[Last updated 17 July 2017]