Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome

Area of Science:

• Genomics
• Bioinformatics

Background:

• A new, highly contiguous Bos taurus reference genome assembly (ARS-UCD1.2) provides an opportunity to update the bovine gene set.
• Advances in graphical genome annotation tools enable collaborative gene curation using the latest sequence data.

Purpose of the Study:

• To explain the rationale behind manual gene curation decisions.
• To demonstrate the use of Bovine Genome Database (BGD) tools, like the Apollo genome annotation editor, for manual curation.
• To highlight the value of manual gene annotation for improving livestock gene sets.

Main Methods:

• Utilizing the ARS-UCD1.2 reference genome assembly.
• Employing graphical genome annotation tools, including the Apollo genome annotation editor.
• Leveraging RNA-seq and Iso-Seq data as sources of gene annotation evidence.
• Interpreting data visualizations for gene model curation.

Main Results:

• Demonstration of manual gene curation processes using BGD tools.
• Explanation of how RNA-seq and Iso-Seq data contribute to gene annotation.
• Illustrative examples of curating gene models.

Conclusions:

• Manual gene curation is valuable for enhancing livestock gene sets.
• The described process can be adapted for manual gene curation in other species.
• Encouraging researchers to contribute to gene model editing will improve bovine gene sets.