PLOS Genetics initial submission files: one PDF, separate supporting information

A PLOS Genetics initial submission can be simpler than the eventual production package, but “single PDF” does not mean “put everything into one file.” The journal allows the main manuscript, including its figures, to be submitted as one review PDF. Supporting information, the cover letter, and several submission-form declarations still have separate places.

This guide answers one narrow question: what belongs inside the PLOS Genetics initial-submission PDF, and what should stay separate? The requirements below come from the journal’s current submission guidelines. The folder and reconciliation steps are practical preparation suggestions, not extra journal rules.

Authors can review the PLOS Genetics preparation path before assembling the upload package.

Make the review PDF the center of the package

PLOS Genetics accepts initial submissions as a single PDF that may contain both manuscript text and figures. The journal says it will not request formatting changes at first submission when the file contains the information needed for editorial assessment and peer review. More detailed file separation comes later if the manuscript reaches revision.

That flexibility is useful, but the review PDF still needs to work as a complete reading copy. A practical version-freeze is to choose the author-approved manuscript source, export one PDF from it, and stop making parallel edits while the upload package is being checked. Old exports and working drafts should be moved out of the submission folder so they cannot be selected accidentally.

The initial manuscript may be DOC, DOCX, RTF, or PDF, but a LaTeX manuscript is submitted as a PDF. Word files must not be locked or protected. For the single-PDF route, check the exported PDF itself rather than assuming the editable source survived conversion.

Keep the manuscript’s reading order visible

The journal permits flexible initial formatting, while still specifying several features that make the review copy usable. Text should be double-spaced and presented in one column. Include page numbers and continuous line numbers, rather than restarting line numbering on each page. Clearly distinguish no more than three heading levels.

Most research manuscripts follow this broad order:

• Title, authors, and affiliations
• Abstract
• Author Summary
• Introduction
• Results
• Discussion
• Materials and Methods
• Acknowledgments
• References
• Supporting information captions

PLOS Genetics also allows Materials and Methods to appear before Results or before Discussion, but asks authors to explain that choice in the cover letter. Results and Discussion may be combined. Methods articles have a different supported structure, so the selected article type should match the manuscript’s organization.

The initial review PDF is not a generic shell. Confirm that its section order matches the actual article type and that every expected part is present before upload.

Put title, abstract, and Author Summary in their proper places

The first page should contain the title, author names, and affiliations. The journal asks for both a full title and a short title. The abstract follows the title page and is also entered into a separate field in the submission system. For a research article, the manuscript then includes a distinct, non-technical Author Summary immediately after the abstract.

These elements serve different readers and should not be collapsed into one repeated paragraph. The abstract may be up to 300 words and should summarize the main work without citations. The Author Summary is 150–200 words, written for a broader audience and kept distinct from the scientific abstract.

Before export, compare the PDF’s title and author information with the values ready for the portal. Confirm that the abstract pasted into the submission system matches the approved manuscript version. Authors remain responsible for the scientific meaning, claims, author order, affiliations, and summary language.

Leave tables in the manuscript file

Tables belong in the manuscript rather than in separate files. Cite them in ascending numeric order and place each table directly after the paragraph in which it first appears. Put the label and brief descriptive title above the table; legends, footnotes, and related notes go below it.

For the final PDF check, scan each first citation and then the table that follows it. Confirm that the table remains readable after export, its label matches the citation, and it has not split in a way that hides headings or notes. This is a presentation check, not permission to alter values or interpretation without author review.

Figures can stay inside the initial review PDF

At initial submission, figures may be included in the main manuscript file. Cite figures in ascending numeric order at first appearance. Figure captions may appear after their first mention or be grouped at the end of the manuscript for a new submission.

This is one of the clearest differences between the initial and revision packages. If the manuscript reaches revision, the journal asks for each figure as an individual file. Do not build the first upload around revision-stage separation unless the current submission instructions or an editorial request require it.

Review the combined PDF at ordinary reading size. Make sure every figure is present, panels are complete, captions are readable, and citations point to the intended figure. The paper’s authors must verify all scientific labels, legends, and image content.

Upload supporting information separately

Supporting information does not belong inside the single review PDF as an appended file bundle. PLOS Genetics accepts essential supporting and multimedia files alongside the manuscript, with each file smaller than 20 MB. Item names include an “S” and a number, such as S1 Appendix or S2 Table.

The captions for those supporting files stay together at the end of the main manuscript file. The journal says not to submit the captions as a separate document. Each caption needs the file number and item name; a one-line title is strongly recommended.

Create a simple reconciliation pass before upload:

1. Match every supporting file to its S-number and item name.
2. Match that same number and name to the caption in the manuscript PDF.
3. If the item is cited in the text, confirm that the citation points to the intended file.
4. Open each file and verify that it is the author-approved version and remains below the size limit.

Supporting files are published as provided and are not copyedited, which makes this file-level review especially important.

Keep the cover letter separate

The cover letter is uploaded as a separate file in the submission system. The journal asks it to explain why the manuscript is suitable for PLOS Genetics and why the study should interest and advance its field. Authors may also recommend an Academic Editor.

If the manuscript uses an alternative placement for Materials and Methods, the cover letter should explain that structural choice. Keep the cover letter out of the review PDF unless the journal specifically asks otherwise. It is available to editors and journal staff rather than functioning as another manuscript section.

Prepare portal declarations outside the PDF inventory

Several pieces of submission information belong in the online form, not in the main file. These include the financial disclosure, competing-interest declaration, related-manuscript information, editor and reviewer suggestions, and the selected PLOS Genetics section. The corresponding author is also asked to provide author contributions using the CRediT taxonomy in the submission system.

The Data Availability Statement is requested in the submission form and must reconcile with the manuscript’s data citations, repository records, DOIs, or accession numbers. Do not treat a repository URL, accession number, or portal field as “done” merely because it appears in one location. Check that the manuscript and the submission-form value describe the same approved research asset.

These are author decisions and declarations. Articlo can help surface structural and formatting gaps, but it does not choose disclosures, verify references or repositories, or decide what research information may be shared.

Run one final inside-versus-separate check

Before opening the portal, divide the package into two groups.

Inside the initial review PDF:

• Title page with authors and affiliations
• Abstract and distinct Author Summary
• Main manuscript sections
• Tables placed after first citation
• Figures included for initial review
• References
• Supporting information captions
• Page numbers and continuous line numbers

Separate from the review PDF:

• Each supporting information or multimedia file
• Cover letter
• Any required related manuscript copy
• Portal entries for funding, competing interests, data availability, author contributions, suggested reviewers and editors, and journal section

Then open the exact review PDF and every separate file once. Check filenames, S-number matches, file sizes, visible completeness, and version agreement. This small reconciliation is usually faster than discovering a mixed package after the portal has generated its compiled review copy.

Prepare the package without changing the research

PLOS Genetics gives authors a flexible initial-formatting route, but the file boundaries still matter: one coherent review PDF, separate supporting items, a separate cover letter, and accurate portal declarations.

Articlo formats author-provided manuscripts and checks them against stored journal requirements. It does not write research, verify references, choose disclosures, or guarantee acceptance. Authors remain responsible for the paper, supporting files, declarations, repository records, and submission decisions.

Run a free PLOS Genetics readiness check or revisit the journal-specific preparation guide before upload.