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Your final, polished GenomeA will be due at the end of the semester. Don’t let it creep up on you!
Genome Announcements is a peer-reviewed, Open Access journal published by the American Society for Microbiology. For a GenomeA paper to be published, one of the pre-requisites is the deposition of your phage’s genome in the NCBI GenBank database.
This is a short paper (limit of 500 words) and there is a lot that we need to jam in there, so your writing needs to be clear, concise, and scientific. You will have no problem writing 500 words of text about your phage; in fact the challenge will be for you to describe your phage in only 500 words!
Be clear: Don’t use flowery writing–you don’t need to use phrases like “first and foremost”. You don’t need fancy sentence or paragraph transitions. Keep it simple.
Be concise: Do not use nine words when 3 will do. You want to be precise and deliberate with your sentences.
Be scientific: Do not use pronouns or descriptors of inanimate things-we had someone a few years ago refer to the bacterial cells being lysed as “those poor little guys”. Do not use words like plethora, really, very, and a lot. They are not descriptive, have no defined quantity, and as a result, have no scientific value. Also, don’t use words like “cool” or “neat”.
Keep in mind gene versus protein notation, genes are always italicized while proteins are not. For example, ”...phage Aggie gene 14 encodes a predicted DNA helicase. Aggie gp14 is 81% identical the gp25 DNA helicase of phage Sarge.”
Remember that your audience is members of the scientific community, including the phage community. You do not need to explain what a portal protein does or how the T7 polymerase works. The purpose of this paper is to inform readers about the features of your genome, not teach them phage biology.
Finally, we suggest reading your writing out loud to yourself. If it sounds funny to you, chances are it will read that way as well.
We have provided a few published GenomeA papers from previous years’ classes in the class Google Drive. You may also visit the journal’s website at http://genomea.asm.org/ if you want to look at more writing samples.
The GenomeA manuscript and drafts should be submitted via email as MS Word or compatible documents in single-spaced, 11-point Arial, Helvetica or Times New Roman font on an 8.5” x 11” page size with 1” margins. Page numbering and line numbering for the manuscript should be turned on. Line numbers are controlled under the Layout tab in newer versions of MS Word.
The first page of your GenomeA manuscript will be the title page. Near the top of this page, the first lines of your manuscript will be the title. This is an announcement, so this usually reads something like “The complete genome of the novel Escherichia coli phage Z”. Make sure to properly italicize species names. Manuscript titles are traditionally typed in bold font.
A few blank lines will separate the title from the manuscript authors. Here you would normally list all the paper’s authors and their affiliations in order, but you should list only your own name here for now. We will add appropriate affiliations and co-authors later. Your co-authors may include the original isolator of the phage, anyone else who has done substantial work on its sequencing or annotation, and at least one PI who was in charge of the project.
Below your name you should provide a permanent (i.e., non-TAMU) email address so we can contact you again after you graduate. You can provide two such email addresses if you have them. You can also provide an ORCID here if desired (see below).
All of the text on the title page is traditionally aligned to the center.
The next page of the the GenomeA manuscript will contain an Abstract of 50 words or less that summarizes the entire work. Here you should describe the host bacterium and the phage, and its general relationship to other phages. Because this is a summary of the rest of the paper, this section is usually written last. The Abstract should appear on its own page.
Like any paper, yours will start off with an introduction. In these first few sentences, you must communicate why anyone should care that you have sequenced this genome, and we typically begin by talking about the bacterial host. Is it Gram-positive or Gram-negative? What is its importance? The phage’s host could be of interest for any number of reasons: it could be an important human or animal pathogen, it could be a well-studied model organism, or it could have industrial or biotechnological applications. Once you know your phage’s host, it is up to you to dive into the literature to find out more about it and formulate a brief and interesting introduction. We also care about the phage–why was it isolated? What are the possible downstream applications? We’d also like to know briefly if your phage is similar to another one out there, or if it belongs to a larger family of phages. You won’t know much about that until later in the course, but this should be included in the final draft of your GenomeA.
An important aspect of any scientific paper is that the methods be clearly outlined. The idea is that someone could follow exactly what you did. Since you were probably not involved in the isolation or sequencing of the phage you are annotating, we will provide you with all the information you need to write this section as tables of data or bullet-point lists. It will be up to you to arrange this information into prose; you can look at published GenomeA papers to see how other authors have done this. There are several major areas to cover here:
Phage isolation source: You need to mention the type of sample the phage was isolated from (soil, sewage, etc.), the location and time of the sample collection, and the bacterial host.
Sequencing method: The sequencing method and run paramters, genome assembly and genome closure.
Annotation method: The tools used and general annotation steps should be concisely described.
Phage morphology: Describe breifly how morphology was determined by TEM. These images are important for defining the morphology of your phage but will not be included in the paper. Since this is a short announcement, no figures are accepted.
The next section will include general statistics of your genome. Your reader would like to know:
Genome size in bp
Genomic termini (if known)
Number of protein-coding genes and tRNAs
Coding density
G+C content, and how the phage G+C content compares to that of the host
Gene relationships (number of novel and conserved proteins)
The bulk of your paper will be about the content of your phage’s genome, and this is were you can be most creative. We would like to know if your phage is similar to other phages. For example, if your BLAST results show a large number of hits for N4 or T4, you would say that your phage is N4 or T4-like. If a majority of your genome is novel, this is also significant. If your phage can be classified to a known phage type, we’d like to know if it is syntenic (in a similar gene order) with that phage. We will cover these topics as the semester progresses.
We would like to know what general features you’ve identified. This is straight forward! You will basically list (in sentence form) what replication genes you found, what genes for structural proteins you found. You can describe your lysis genes in a bit of detail (what class of holin did you find/ what class does you endolysin belong to?).
If any genes are missing (tail fibers for example, or if you have a T4-like phage but cannot locate RIIA or RIIB genes), we’d like to know that also.
Finally, keep an eye out for unusual finds. By now, you have had a thorough treatment of phage biology so you know what should be in phages and what is unique. If you think something is cool, but you’re not sure, contact your herd leader for guidance.
The genes in your genome will not be numbered until we finalize and export your annotation from Apollo for submission to GenBank, which will happen sometime after the class is over. In your GenomeA manuscript, however, you may need to refer to a specific gene (e.g., “the gene 73 HNH endonulease...”). In these cases, you should refer to the gene by its coordinates in the genome, in the format (start..stop), e.g., “the gene (63450..64225) HNH endonulease...”. We will convert these coordinate references to gene numbers once the genome is deposited in GenBank.
Before these papers are submitted to the journal, we must have an accession number for your genome. This means that your annotation must be complete and sent off to NCBI for approval. Typically it takes 8-12 weeks from the initial submission date for a genome to appear in the database. We will add your genome’s accession number to your manuscript and submit it to the journal for you.
Your manuscript will also have a brief acknowledgements section, we will provide this as well. This section is mostly to describe funding for the project.
Finally, be sure your references are in the correct format. The journal’s Instructions to Authors describes the correct format in detail. We strongly suggest you use EndNote or a similar reference manager to keep track of your citations and generate your bibliography.
ORCIDs are persistent digital identifiers which identify you as a person. They help disambiguate researchers with identical names by assigning you a unique number.
If you have an ORCID, please make us aware of it by noting it on the title page below your name. Graduate students may already have one. If you would like to get an ORCID, you may do so at their website. If you get an ORCID, please let the library know.