MRA Genome Announcement Template Narrative - Isolates v0.3
Zach Crockett
Generated July 11, 2023

Introduction to the template Narrative

Background

KBase and the American Society for Microbiology have created a Narrative template to assist KBase users in publishing genomes as data sets in Microbiology Resource Announcements (MRA). The template follows the MRA Author Checklist for prokaryotic or eukaryotic genome sequences.

For full submission information, please refer to the MRA website. We also recommend reading MRA Best Practices editorial for advice directly from the MRA editors, and which has been used to provide guidance in this Narrative.

For general advice on creating genome announcement Narratives, see this KBase News post by Ben Allen, Miriam Land, and Elisha Wood-Charlson.

Purpose

The goal of this template Narrative is to help you organize your analysis and ensure your documentation matches what is required for MRA submission. It is only meant to provide a guideline for creating a genome announcement publication; you should use it however best works for you - alongside your analysis, copied and pasted into a work document to serve as a template, or in-line with your analysis. You can use the template as it is from the beginning of your analysis, or you can start your analysis in a blank Narrative and add Markdown cells matching these after you have run the apps. You should also feel free to delete any of the text or checkboxes out of the Markdown cells, but keep in mind that these are MRA's requirements for submission, so be sure to include them in your manuscript.

Using the Narrative

This Narrative is a template only. To start, make a copy of this Narrative and follow the organizational structure provided below. You can delete this cell and any extraneous text, including the check boxes, prior to submission.

Apps have not been added to the Narrative. Each section provides recommendations in the "Note to Author" sections, which can also be removed prior to submission. These provide tips for performing the relevant steps in KBase.

Any bold text denotes tips from the MRA Best Practices editorial or the MRA article template. These are required for the resource announcement publication but not the Narrative; however, they can only help to make the Narrative more user-friendly, so we recommend including them here as well once the text has been written. As these are required to submit the article, you can use this Narrative to begin the publication in parallel with your analysis in KBase.

At the end of the analysis sections there are instructions for submission and next steps after completing the analysis in the Narrative.

We've included a list of resources below for working with markdown cells and for creating high-quality MRA publications.

For an example of a previous MRA submission with associated Narrative, see Jennifer Goff et al, Complete Genome Sequence of Bacillus cereus Strain CPT56D-587-MTF, Isolated from a Nitrate- and Metal-Contaminated Subsurface Environment and the Narrative.

This template is currently in a beta state, and as such we would love to hear any feedback or suggestions you have.

Table of contents

  1. Tips, Help, and Resources: links to guides and other help resources with Markdown/HTML formatting, MRA Best Practices Guide, etc.
  2. Analysis: the sections of the Narrative to keep in the final product
    1. Introduction - Markdown cell for the introductory part of the core MRA Narrative
    2. Background and Experimental Methods
    3. Import
    4. QC, Assembly, and Annotation
    5. Taxonomic Identification
    6. Metabolic Modeling and Flux Balance Analysis
    7. References
  3. Final Steps: the next steps for progressing toward an MRA publication, including advice for the non-KBase requirements.

Tips, Help, and Resources

Title

Publication Title should not exceed 54 characters. Narratives and articles should have related but different names for enhanced findability.

Abstract

Abstracts for MRA announcements should be limited to 50 words or fewer.

Introduction

Include an introduction to the Narrative including background information on the organism's relatives and where the organism was collected. The publication by [author list] can be found here: [URL]

Table of Contents

  1. Background and Experimental Methods
  2. Import and annotation
  3. QC, Assembly, and Annotation
  4. Taxonomic Classification
  5. Metabolic Modeling and Flux Balance Analysis
  6. References
Narrative created by: [Narrative owner's name and contributors]

Note to Authors

The publication may not be available at the time of the static Narrative creation. This can be added after the fact; please contact engage@kbase.us to update the DOI landing page when this is done.

Background and Experimental Methods

Authors should use this space to detail the experimental methods used to collect, isolate, and sequence the samples.

Genome announcements should include a description of how, when, and where (with latitude and longitude, if possible) the organism was isolated. A brief description of the isolation procedure can be included with a citation of the full peer-reviewed manuscript of the procedure.

For Illumina sequencing, the platform should be described, along with read pairing status, the length of the reads, the number of raw reads in total and/or the sequencing depth, and the methods for quality control and trimming, if applicable. For Pacific Biosciences (PacBio) sequencing, the platform should be described, preferably with the chemistry, along with the library construction method, whether and how DNA was sheared, whether and how DNA was size selected, the read N50, the number of raw reads, and, if applicable, a description of read quality control, error correction, and adapter trimming. For Oxford Nanopore Technologies sequencing, the device and flow cell should be described, along with the library construction methods, the read N50 and number of raw reads, the base caller, read quality control, error correction, and, if applicable, adapter trimming.</b>

If beginning with reads in KBase, you can find stats like N50 and number of reads in the object info for the PairedEndLibrary object.

Author Checklist












Sample Collection

Isolation

Genome Sequencing

For Illumina sequencing, please include






For Pacific Biosciences (PacBio) sequencing, please include








For Oxford Nanopore Technologies sequencing, please include









Import

Note to authors

Reads or assemblies should be imported through the staging area. See the upload and download guide on the KBase documentation site for details instructions.

QC, Assembly, and Annotation

Assembly and annotation should include software cited by including version number, even for common software like PGAP. MRA requires settings or options to be provided, but can be commmented as "default parameters were used, except where otherwise noted." Genome quality assessment using a conserved set of markers can be a useful and important metric for evaluating whether the genome is complete, particularly for large genomes.

Author Checklist









Note to authors

The recommended app for quality control is FastQC. There are multiple apps for assembly.

There is no "best" assembler, and assembly tools should be evaluated on a case-by-case basis. You are welcome and encouraged to use multiple apps and compare the results.

Annotation can be performed using Prokka or RAST. Again, comparison of multiple tools is encouraged. For downstream steps such as metabolic modeling, however, RAST-annotated genomes perform better with KBase modeling tools.

If you perform these steps in KBase, you can see the software version number both in the app cell and in the citations tab of the static Narrative page when you create it.

For statistics such as number of contigs or N50 values, all KBase assemblers will return a QUAST report. You can create a separate report by running the standalone QUAST app if you feel that it makes your Narrative more immediately readable.

Taxonomic Identification


MRA requires taxonomic designation at the genus level, but does not allow for descriptions of the isolate as a new species. If there is no known species, the isolate can be designated as a member of an existing genus, for instance Larkinella sp. Strain BK230.

Note to Authors

One common way is to use the GTDB-Tk classify app. We recommend adding a phylogenetic tree using the Insert Genome into SpeciesTree app.

Metabolic Modeling and Flux Balance Analysis (optional)

Note to Authors

Metabolic modeling is not listed on the MRA checklist; however, many MRA authors using KBase have included a metabolic model in their Narrative. If you are new to metabolic modeling, we have tutorials and webinars on the docs site and on YouTube.
If you do not use this section, delete this Markdown cell, and remove it from the table of contents at the top of the Narrative.

References


Note to authors

The KBase static Narrative service automatically generates a list of citations for apps used. If you provide any citations for literature or outside tools within the markdown cells, those should be included here.

Final Steps

Requesting a DOI

Once you have completed the analysis steps in KBase and are ready for a public Narrative DOI, send an email to Zach Crockett (crockettzr@ornl.gov) and CC Elisha Wood-Charlson. You should delete the top two cells (Introduction to the Narrative and Resources) and this cell before finalizing the Narrative, and remove any pre-filled text from the other Markdown cells. To get a DOI, we will need a public landing page in the form of static Narrative. To create a static Narrative, make the Narrative public, then select the "Manage Static Narratives" option under the Share menu (see documentation for more information). We will also need some additional metadata not captured in the Narrative, which we will request through the email. If you are not ready to make the Narrative public but do want to start the DOI process, we can reserve a DOI which you can use as when writing the manuscript, but which is not publicly available. Please reach out to us if you have any questions and/or are ready to create or reserve a DOI.

Using a "Dataset" DOI

The external infrastructure that tracks and records relations between citable scientific products only includes the references section, which is sent as structured metadata from the publishers. As such, you must include your Narrative DOI in the references for the bibliometrics infrastructure to recognize it.

This requirement is to enable the machine-readability of the references, but in general the intuitive place to provide a link to the Narrative is in data availability statement. It is perfectly acceptable and even recommended to provide the Narrative DOI in both places as there is no risk of duplicating citation counts between the human- and machine-readable references.

When referring to the Narrative, use the DOI instead of the URL for the static Narrative. We can and will edit the DOI so that it resolves to the most recent version, and this provides forward compatibility in case we ever need to change the URL format for static Narratives.

Depositing in NCBI

Most users deposit reads in the NBCI Sequence Read Archive (SRA). To submit at SRA, login to their Submission Portal. The portal walks users through the steps required for submission, but the metadata submission can be difficult to format correctly. NCBI uses the Minimum Information about any (x) Sequence (MIxS) templates for submission. MIxS is not single template but a collection of templates for different sequence types, such as genomes (MIGS) or metagenomes (MIMS). We recommend reading the MIxS publication to learn more about formatting metadata for the templates. The SRA Submission Portal will help choose which template fits your data.