AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes

Area of Science:

• Animal Genomics
• Bioinformatics
• Comparative Genomics

Background:

• Advances in genome sequencing enable highly contiguous assemblies for non-model animals.
• Gene feature delineation in animal genomes requires further refinement.
• Existing genome browsers lack comprehensive visualization for diverse livestock species.

Purpose of the Study:

• To introduce AgAnimalGenomes, a novel resource for genome visualization and annotation.
• To support manual refinement and creation of gene models for seven livestock species.
• To provide visualization tracks for RNAseq and Functional Annotation of Animal Genomes (FAANG) data.

Main Methods:

• Development of genome browsers for bovine, chicken, goat, horse, pig, sheep, and water buffalo.
• Integration of RNAseq experiment visualization.
• Inclusion of data from the Functional Annotation of Animal Genomes (FAANG) Consortium.
• Implementation of comparative tracks for Ensembl and RefSeq gene sets to identify discrepancies.

Main Results:

• AgAnimalGenomes provides enhanced visualization and annotation tools for livestock genomes.
• The resource includes hundreds of RNAseq visualization tracks and FAANG data.
• Comparative gene tracks highlight thousands of differing protein-coding genes between Ensembl and RefSeq, aiding in gene model issue identification.

Conclusions:

• AgAnimalGenomes is a valuable resource for improving the accuracy of livestock genome annotations.
• The tool facilitates manual refinement and creation of gene models.
• Researchers can leverage AgAnimalGenomes to identify and address gene model inconsistencies, improving downstream data analysis and interpretation.