AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes

Abstract

Current genome sequencing technologies have made it possible to generate highly contiguous genome assemblies for non-model animal species. Despite advances in genome assembly methods, there is still room for improvement in the delineation of specific gene features in the genomes. Here we present genome visualization and annotation tools to support seven livestock species (bovine, chicken, goat, horse, pig, sheep, and water buffalo), available in a new resource called AgAnimalGenomes. In addition to supporting the manual refinement of gene models, these browsers provide visualization tracks for hundreds of RNAseq experiments, as well as data generated by the Functional Annotation of Animal Genomes (FAANG) Consortium. For species with predicted gene sets from both Ensembl and RefSeq, the browsers provide special tracks showing the thousands of protein-coding genes that disagree across the two gene sources, serving as a valuable resource to alert researchers to gene model issues that may affect data interpretation. We describe the data and search methods available in the new genome browsers and how to use the provided tools to edit and create new gene models.

Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities

“…Many analysis tools built for model organisms are expanding to become species-agnostic, which provides substantial opportunities for livestock researchers to utilize these with annotation from their own genomes. The quality and utility of ruminant livestock genomes and annotation are advancing rapidly driven by community efforts, including pangenome construction [ 47 , 48 , 49 , 50 ], complete telomere-to-telomere assemblies [ 84 ], and sophisticated annotation pipelines and resources [ 85 ]. These efforts will enhance the ability to precisely differentiate cell clusters based on gene expression, providing even greater insights into cellular heterogeneity and gene expression patterns within tissues important for the understanding of economically important traits in ruminant livestock.…”

Research Progress and Applications of Bovine Genome in the Tribe Bovini

“…These datasets provide valuable resources to enable the animal resource research community to gain more genomic variants in genomics applications. To accommodate the increasing amount of genomics data, AgAnimalGenomes, a cross-species database, was built to mine the gene features of massive public data and improve the refinement of gene models [80].…”