Tutorial: I have a genome belonging to a novel taxon, how can I register it?

About this tutorial

Please note that the steps below (in particular 1-3) do not capture all the complexities behind genomics and systematics. Instead, the objective of this tutorial is to guide users on the registration process in the SeqCode Registry, assuming they already have a solid background on genome-based taxonomic analyses.

1. Review the quality of your genome

The first step when considering to register a genome as the type material for a novel taxon under the SeqCode is to evaluate the quality. You can see the minimum quality requirements here: SeqCode Appendix I.

You can use any of the many methods to evaluate quality, so long as you document which method was used. Internally, the Registry revises estimates using MiGA, but that's only to ensure quality-control.

For additional details on how these genomes are evaluated, see How are names internally curated?

2. Determine the degree of taxonomic novelty

The next step, is to determine up to which rank the new taxon is novel. For example, if the genome can be confidently classified into a genus, but not a species, you might consider proposing a novel species within that known genus. If, instead, the genome cannot be classified confidently to genus, family, or class, but it can be classified confidently to order, the novelty will be up to the class level. In the extreme case, when the only confident classification is at the domain level, phylum-level novelty might be warranted. This determination should be made carefully, and in many cases conservatively, but ultimately the decision is left for the authors and the peer-review process of the effective publication to evaluate.

3. Create the name/s for the novel taxon/a

If the novelty in step 2 is determined to be just at the species level, you'll only need a new specific epithet. If the novelty is at the rank of genus or above, you'll also need a new name for the genus. All other taxa (above genus) will be named on the basis of the genus, and the Registry will help you with their spelling.

For additional resources on name creation, see How do I Fill the Etymology Table?

4. Create a guided registration

The easiest way to register your names now is to follow a guided registration. Select "New species and parent taxa" and initialize this register list: Fill the species name and the most specific classification (both defined above). For example, if you determined that the genome belongs to a novel class of a known phylum, fill-up the species name and the phylum to which you believe the species belongs.

5. Follow the guided registration

You can simply follow the guided registration. Briefly:

  1. Review the proposed new names for all intermediate ranks (if any) and continue.
  2. Click again "continue" and define the type material of the species, which is the genome you characterized above. Make sure it's available in INSDC Nucleotide or Assembly databases; select the appropriate database, and then pick the accession. Include the reference strain only if the genome is derived from a culture. For MAGs and SAGs, leave this field empty.
  3. Continue, fill-up additional details, and continue.
  4. Add a description for the proposed species. Note that this refers to properties of the species and the circumscription, not the etymology.
  5. Fill the etymology (refer to the in-page documentation for more details).
  6. Continue the registration for all remaining names. For the most part, you will only need descriptions and etymologies (most of which might be automatically filled, with the exception of genus names).
  7. Finally, all names will be added to a single Register List. Make sure to select "Create a new Register" if this lineage stands alone in an effective publication, or to select the appropriate register list if it belongs to a collection of lineages for which you already have an existing register.

6. Submit the list

You can repeat steps 1-5 for all the lineages that you report in the effective publication. Once you're done with these, you can submit it. If you are currently working on your manuscript or undegoing peer-review, click on "Submit register list for evaluation" in the Register List page (this is called Path 1). If you are registering names from an effective publication that is already published, click on "Notify about effective publication" (this is called Path 2).