APPS Instructions for Authors
Editorial Procedure and Policy || Submission and Review Process || Publication Date || Open Access Fees || Indexing || Copyright and Licensing Information || Conflict of Interest || Copyrighted Material and Plagiarism || Data Origin || Data Access || Nomenclature || Vouchers ||
Scope and Aims of the Journal
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 (http://www.amjbot.org/).
Editorial Procedure and Policy
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.
Open Access fees—All APPS papers are Open Access. Non-BSA members will be charged $1200 per article. BSA members will be assessed a reduced fee of $350 for each published article. This policy applies to all articles accepted, 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 online publication. Note: As an Open Access journal, APPS does not provide free pages for BSA members, and papers published in APPS do not count against an author’s annual allotment of free pages in AJB.
Indexing Information—ISI impact factor: 0.911 (2015 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 Information—APPS operates under a Creative Commons Attribution 3.0 license (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. The license ensures wide availability of the article and that the article can be included in any scientific archive. Those wishing to use material for commercial purposes should contact the author. 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. 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) (www.botany.org/governance/ethics.php). 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 Access—APPS 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 (http://datadryad.org/). 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 (http://figshare.com/). 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.
Nomenclature—APPS 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 (http://www.ipni.org/index.html) or Tropicos (http://www.tropicos.org/) 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.
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. 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.
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.
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.
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).
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.
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 will generally not be considered for Primer Notes as their nature complicates broad applicability across multiple taxa.) Markers developed using novel techniques are especially welcome. Please note the specific criteria below.
Exceptions to any of the above criteria will be considered on a case-by-case basis, with adequate justification provided in the cover letter.
A cover letter, an author agreement form, a manuscript file, and separate files for figures should be uploaded at http://apps.edmgr.com. 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:
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.
1. Title and Footnotes
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:
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 (Abstract, 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.
For Genomic Resources and Application Articles, the format should be:
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.
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 Template, Software 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
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.
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.
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.
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 http://www.r-project.org/ [accessed 13 July 2012].
Websites (no print version):
Joint Genome Institute. 2012. JGI Plant Genomics Program—Home [online]. Website http://genome.jgi.doe.gov/genome-projects/ [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 http://www.morphobank.org.
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. Tables—include in manuscript file
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.
6. Appendices—include in manuscript file
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.
7. Figure/Illustration—upload as separate files (do not include in the manuscript file)
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.
8. Figure Legend—include in manuscript file and place immediately after the Appendices (or after the tables if there are no appendices)
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.
9. Multimedia Content—upload as a separate file (do not include in the manuscript file)
10. Supplemental Materials—upload as a separate file (do not include in the manuscript file)
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.
Author Agreement Form
Questions? Contact the Editorial Office