A community-curated GTF file for the Platynereis dumerilii genome. The idea is that each expert in the community can add, refine, or amend gene models and the corresponding metadata starting from the most current Ensembl Metazoa version of the genome.

1. Find your gene(s) of interest on the genome, e.g. by a combination of BLAST/MMseqs2/DIAMOND searches and phylogenetic trees.
2. Make a fork of the repository.
3. Edit the GTF file to reflect your new insights (e.g. propose a name for an XLOC, improve the annotation of the 5' UTR for another locus), save, and commit.
4. Propose your commit as a pull request to the main repository.
5. In the pull request, try to explain how you arrived at the proposed change; try to upload any relevant results so that others can judge.
6. Wait for consensus to build; ideally your contribution is widely accepted. The pull request is merged, and the version of the genome goes up slightly.

Every once in a while (depending on NCBI/Ensembl Metazoa update cycles) a new GTF version will be uploaded. This will trigger a minor version bump.

Sweeping changes to the assembly (like re-assemblies or similar) will be communicated via appropriate channels (spiraliabase, Platy community meetings, lab emails?).

The latest release will contain the consensus up-to-date version of the genome annotation. If this doesn't include your favorite gene feel free to use the version specified by the commit of the corresponding pull request. To avoid misunderstandings in publications, always refer to the genome by full version string and commit ID.

Recent changes to the genome are documented in the changelog.

• Find official GTF/GFF.
• Add a DOI to the repository.
• Tutorial on how to make changes.
• Automate version bumping.
• Automate DOI generation upon new release (zenodo?).
• Link to other resources:
  • SpiraliaBase
  • Ensembl Metazoa
  • NCBI
  • platynereis.com