Accessing Livestock Resources in Ensembl.

Area of Science:

• Genomics
• Bioinformatics
• Comparative Genomics

Background:

• Genome assembly technologies have advanced significantly in cost, accuracy, and automation.
• The livestock research community has pioneered high-quality vertebrate genome sequencing.
• Ensembl aims to enhance these genomes with functional and comparative annotation.

Purpose of the Study:

• To describe the livestock data available within the Ensembl resource.
• To provide protocols for accessing and utilizing Ensembl's livestock genomic data.
• To highlight Ensembl's unique support for non-reference and breed-specific assemblies.

Main Methods:

• High-throughput computational analyses for gene annotation, genomic alignments, gene trees, regulatory, and variation data.
• Continuous annotation updates for reference and non-reference livestock genome assemblies.
• Development and maintenance of Ensembl's genome browser, FTP site, tools, and REST API.

Main Results:

• Ensembl offers extensive functional and comparative annotation for livestock genomes.
• The resource supports 13 pig breeds, hybrid cattle haplotypes, and wild-type assemblies.
• Ensembl is a unique resource for breed-specific and non-reference genome annotation.

Conclusions:

• Ensembl significantly accelerates livestock research by providing comprehensive, accessible genomic data and analysis tools.
• The platform supports a growing range of livestock species and breeds, including non-reference assemblies.
• Researchers can leverage Ensembl for detailed genomic insights through its browser, download, and programmatic access options.