Tutorial: annotation of animal genomes.

As DNA sequencing technologies improve, it is becoming easier to sequence and assemble new genomes from non-model organisms. However, before a newly assembled genome sequence can be used as a reference, it must be annotated with genes and other features. This can be conducted by individual laboratories using publicly available software. Modern genome annotations integrate gene predictions from the assembled DNA sequence with gene homology information from other high-quality reference genomes and take into account functional evidence (e.g., protein sequences and RNA sequencing information). Many genome annotation pipelines exist but have varying accuracies, resource requirements and ease of use. This genome annotation Tutorial describes a streamlined genome annotation pipeline that can create high-quality genome annotations for animals in the laboratory. Our workflow integrates existing state-of-the-art genome annotation tools capable of annotating protein-coding and non-coding RNA genes. This Tutorial also guides the user on assigning gene symbols and annotating repeat regions. Finally, we describe additional tools to assess annotation quality and combine and format the results.