Article Types

Contents

Investigations return to top

Investigations are full-length research articles with no minimum or maximum length.

Genome Report return to top

G3: Genes|Genomes|Genetics is pleased to offer genome reports to enable rapid review and publication of high-quality reports describing whole genome sequence (WGS) data of organisms and/or strains.  

The editors of G3 recognize that many WGS datasets describing strain variation, comparative analysis of different model organism species, among other analyses should be made available to the community in an accessible format, even though there may not be substantial new biological insights yet associated with the study.  Genome Reports are succinct, and follow guidelines (see below) designed to make it fast and easy for authors to submit, for reviewers to rapidly assess, and for readers to easily understand the report and its results.

Criteria for acceptance in this category includes usefulness of the report (e.g. will the information provided assist future genetic investigations?), quality of the results (e.g. was the WGS well performed?), completeness (e.g. are the results comprehensive?), and the author’s interpretation of results (e.g. are the results of the WGS lucidly interpreted for the reader?). The amount of new information needed to warrant publication as a Genome Report will vary by organism/system; for example, sequencing of a couple of new isolates of Saccharomyces cerevisiae, for which there is substantial information available, would not be considered appropriate while WGS of different mouse strains would more likely fit the criteria for publication. G3 is also interested in transcriptome studies that aid in genome annotation.

The following are guidelines for the Genome Report. Authors are referred to the first published Genome Report [Morgan et al. 10.1534/g3.116.034751], as it provides a useful reference. A Genome Report submission should have the components listed below; it is acceptable to have additional subheadings or headings as appropriate. We encourage you to be as brief as possible; Genome reports are not meant to be the full length of an Investigation.

  1. Title: should include the organism and/or strain names (e.g. Genome Report: Whole genome sequence of two wild-derived Mus musculus domesticus inbred strains, LEWES/EiJ and ZALENDE/EiJ, with different diploid numbers.).
  2. Keywords: should include the relevant organism and strain names.
  3. Abstract: ~250 words. Concise summary of the results.
  4. Introduction: no more than 500 words. The introduction should discuss the rationale for the WGS of the particular organism/strain.
  5. Methods & Materials: should include the following (note: author may write additional subheadings as appropriate – the below points are not designed to be a list of complete subheadings, but rather, topics to be covered).
    • Organism/Strain origin and derivation  
    • Sequencing methods and preparation details
    • Data processing methods
    • Data availability listing where to access all raw reads, processed data, BWTs, and other relevant data. The assembly should be uploaded to NCBI or ENA.
  6. Results and Discussion: Should include a description of the genomes, coverage amount of genome sequenced, details of sequence variants ascertained, identifications of deletions, comparison of strains/genomes (if reporting WGS of multiple strains/organisms), and relevance of findings to overall organism/strain catalog.
  7. Acknowledgments
  8. Footnotes
  9. Literature Cited

Mutant Screen Report return to top

G3: Genes|Genomes|Genetics is pleased to offer a new format for quickly and easily publishing mutant screen reports. See Gazy et al. 2013 for an example of our first published Mutant Screen Report.

The Mutant Screen Report provides a useful format for describing the results of mutant screens. The format is succinct, and follows a structured template designed to make it fast and easy for authors to submit, for reviewers to rapidly assess, and for readers to easily understand the screen and its results. The Reports fulfill one of G3's goals: to make data from useful genetic screens available to the community in a timely fashion.

Criteria for acceptance in this category includes usefulness of the screen (e.g. the results of the screen will stimulate further experimentation), quality of the results (e.g. was the screen well-performed?), and completeness (e.g. are the results comprehensive?) and the author’s interpretation of results (e.g. Are the results of the screens lucidly interpreted for the reader?)

Note: We encourage you to be as brief as possible; Mutant Screen Reports are not meant to be the full length of an Investigation. Papers that go substantially beyond the screen in term of detailed phenotypic characterization will be considered on their merits as regular articles.

The Mutant Screen Reports should include the complementation test data, both within the new mutant set and with mutants in known genes, wherever possible. The usefulness of the new sets of mutants is influenced most crucially by the number of new genes identified. The complementation data greatly increases the utility of the article.

The following are guidelines for the Mutant Screen Report. Again, Gazy et al. 2013 provides a useful format to follow. Your manuscript submission should have these components, where possible; it is acceptable to have additional subheadings or headings as appropriate.

  1. Title: should include the species and relevant gene names (e.g. A Genetic Screen for supressors of Drosophila NSF2).
  2. Keywords: should include the species and relevant gene names.
  3. Abstract: ~250 words. Concise summary of the results.
  4. Introduction: no more than 500 words. The introduction should discuss the rationale for the screen.
  5. Methods & Materials: should include the following (note: author may write additional subheadings as appropriate – the below points are not designed to be a list of complete subheadings, but rather, topics to be covered).
    • Screen design, including strain/line construction and screen conditions
    • Description of phenotypes scored
    • Description of methods for classification and verification of mutants (e.g. complementation tests and test data; follow-up assays)
  6. Results and Discussion: Tables should succinctly and completely describe the results of the screens, including tables of genes and alleles, as appropriate.
  7. Acknowledgments
  8. Footnotes
  9. Literature Cited

Meeting Report return to top

G3 Meeting Reports are published by invitation only. Meeting Reports provide an overview of recent scientific meetings related to genetics and genomics and are typically authored by meeting organizers and/or select participants. Please contact the editorial office g3-gsa@thegsajournals.org for more information.

Software for Genetic Data Analyses & Database Resources

G3: Genes|Genomes|Genetics offers an article format for high quality reports describing novel software for genetic data analyses and database resources.  The editors of G3 recognize that modern genetic research requires specialized, efficient, and well-documented software, as well as access to high quality data.

The Software and Data Resources (SDR) format is succinct and follows a semi-structured template (outlined below) designed to make it easy for readers to understand the possibilities offered by the software and resource being presented.

Criteria for acceptance in this category includes the usefulness (i.e. is the tool/resource potentially useful for a broad community of researchers and not redundant with existing tools?), innovation, accessibility (including availability and quality of the documentation) and, in the case of software, scalability. Data resources must be made freely available in a public repository, and in the case of software distribution we encourage the use of Open Source. Please see the Data and Reagent Policy for full details.

SDR manuscripts have a limit of 2500 words, excluding title, abstract, tables, figures, boxes, acknowledgments and references. Content will vary depending on the nature of the software or database resource; however, articles are expected to adhere to the following structure.

Note: additional subheadings as appropriate are permitted—the below points are not designed to be a list of complete subheadings, but rather topics to be covered.

1. Title: Include the software or database resource name and make reference to the type of problem(s) addressed with the software or database.

2. Keywords: For software, include the relevant models, algorithms and language; for database resources include the organism, type of genetic data as well as phenotypes available.

3. Abstract: ~ 150 words.  Concise summary of the results.

4. Introduction: Limit of 500 words. The introduction should describe the significance of the software or resource presented, discuss novelty, provide an overview of the software or resource, and describe how researchers can access it.

5. Methods: For database resources, the authors should describe important details about the database, including the organisms, type of data available, the protocols followed in data collections and data pre-processing if any. For software, the authors should describe key elements of the algorithms implemented, and are expected to provide both the source code as well as examples illustrating the use of the software.

6. Results and Discussion: For software, the authors are expected to present a few examples that demonstrate the use of the software and benchmarks. Ideally, the examples should be simple. We encourage the use of boxes with scripts supported by a narrative. Benchmarks carried under more realistic situations than the one presented in the examples are also encouraged.

For database resources the authors are encouraged to present a limited set of analysis (e.g., PC analysis, a GWA study) that describe key features of the data.

7. Web resources: List websites providing access to the software or database and with documentation. Software or data must be accessible via a publicly accessible repository such as GitHub, figshare, Dryad, Zenodo, etc. G3 has partnered with figshare to provide a author submission portal, which authors are welcome to use. More details here.

8. Acknowledgments

9. Footnotes

10. Literature Cited

11. Supplemental data (optional): Include scripts, additional results and additional resources to help the reader to get started with the software or database. Authors must use a  publicly accessible repository such as GitHub, figshare, Dryad, Zenodo, etc. G3 has partnered with figshare to provide a author submission portal, which authors are welcome to use. More details here.

Transcriptome Analysis Studies return to top

G3 welcomes transcriptome analysis studies that report a useful or interesting objective. In addition, study design must be robust, and should meet standards for the statistical analysis of RNA-seq data, including for example at least three biological replications, which then allows for meaningful inferences about differential gene expression.
 
To help authors decide whether their manuscript is a suitable candidate for submission to G3, we provide the following questions as guidance. Regardless of the experimental system used, papers that fare well in G3 have positive responses to questions 1-4.  Authors should also consider the points outlined in question 5, in light of the state-of-the-art in the field and the system being studied.

  1. Does the transcriptome data add useful information relative to the existing literature?
  2. Does the paper present a sound rationale for choosing a particular tissue/organism/sample?
  3. Is the experimental design (sampling, number of biological replicates) sound?
  4. Is the analysis pipeline state-of-the-art?
  5. Does the paper include an additional contribution, beyond the items mentioned above? Examples include: linkage map development, demonstration of inheritance of markers, relationships among germplasm within the genus, extensive SNP discovery and annotation

Corrigenda return to top

Corrigenda correct mistakes and omissions in published manuscripts. They should be as brief as possible, and describe no new methods or results.

Companion Papers return to top

Papers that overlap in the use of primary data or share authors and consider a similar topic from a different angle are welcome to be submitted as companion papers for concurrent publication. Papers by different authors concerning the same topic may also be submitted as companions. Companion manuscripts should be submitted within two weeks of each other, and the cover letter should clearly indicate which papers are being submitted as companions. Failure to indicate which papers are companions may cause a delay in their consideration, as the editors seek to understand the relationships between papers sharing data or authors. Each companion paper should have a cover letter clearly explaining its unique and novel contributions, as well as the importance of the group of papers. Papers intended to be a companion of a paper(s) submitted for publication in another journal require full disclosure upon submission. Responsibility for adhering to publication policies in consortium groups is the sole responsibility of the authors of the paper.

Resubmissions return to top

Resubmission of manuscripts for which the decision was "reconsider pending revision" is permitted a single time (unless arranged otherwise with the Associate Editor). Authors are expected to use the reviewer's comments to revise manuscripts before submitting them anew, and should provide a detailed point-by-point response to reviewers. Manuscripts without a detailed response may be returned to the authors without review. When resubmitting a manuscript authors should fully disclose its history. Manuscripts that have been rejected can be resubmitted only with the permission of the Associate Editor.