AgAnimalGenomes

AgAnimalGenomes provides genome visualization and annotation for livestock species to support exploration and refinement of gene models and integration of functional genomic data.

Key Features:

• Visualization Tools: Uses JBrowse to display tracks including genes, gene expression profiles, functional annotations, quantitative trait loci (QTL), single nucleotide polymorphisms (SNP), and repetitive sequences.
• Annotation Capabilities: Integrates Apollo to enable manual refinement and creation of gene models on genome assemblies.
• Data Integration: Visualizes hundreds of RNAseq experiments and incorporates datasets from the Functional Annotation of Animal Genomes (FAANG) Consortium.
• Comparative Gene Analysis: Provides tracks that highlight discrepancies between Ensembl and RefSeq protein-coding gene predictions to identify potential gene model issues.
• Assembly Support: Targets highly contiguous genome assemblies generated using current genome sequencing technologies.
• Supported Species: Includes genomic resources for bovine, chicken, goat, horse, pig, sheep, and water buffalo.

Scientific Applications:

• Gene Model Refinement: Manual editing in Apollo enables adjustment and improvement of gene models derived from assemblies and annotations.
• Transcriptomic Studies: Integration of hundreds of RNAseq experiments supports analysis of gene expression patterns across tissues and conditions.
• Functional Genomics: Inclusion of FAANG datasets facilitates functional annotation and investigation of regulatory features.
• Comparative Genomics: Direct comparison of Ensembl and RefSeq predictions aids identification of annotation inconsistencies and potential model errors.

Methodology:

Uses JBrowse for genomic visualization and Apollo for manual annotation; displays tracks for genes, expression, functional annotations, QTL, SNPs, and repeats; integrates hundreds of RNAseq experiments and FAANG datasets; provides comparative tracks between Ensembl and RefSeq; targets highly contiguous assemblies from current genome sequencing technologies.