Abstract
Genome assembly is cheaper, more accurate and more automated than it has ever been. This is due to a combination of more cost-efficient chemistries, new sequencing technologies and better algorithms. The livestock community has been at the forefront of this new wave of genome assembly, generating some of the highest quality vertebrate genome sequences. Ensembl’s goal is to add functional and comparative annotation to these genomes, through our gene annotation, genomic alignments, gene trees, regulatory, and variation data. We run computationally complex analyses in a high throughput and consistent manner to help accelerate downstream science. Our livestock resources are continuously growing in both breadth and depth. We annotate reference genome assemblies for newly sequenced species and regularly update annotation for existing genomes. We are the only major resource to support the annotation of breeds and other non-reference assemblies. We currently provide resources for 13 pig breeds, maternal and paternal haplotypes for hybrid cattle and various other non-reference or wild type assemblies for livestock species. Here, we describe the livestock data present in Ensembl and provide protocols for how to view data in our genome browser, download via it our FTP site, manipulate it via our tools and interact with it programmatically via our REST API.
Highlights
Efficient management of livestock resources is key to global food security
Livestock production is critical to developing countries, as it acts both as a major source of income and a means to escape poverty (Otte and Upton, 2005) and as a backup food source in the case of crop failures (Kabubo-Mariara, 2009; Rota and Sperandini, 2009)
Ensembl contains a large variety of livestock species ranging from cow, pig, and chicken to Arabian camel, African ostrich, and Siberian musk deer
Summary
Efficient management of livestock resources is key to global food security. Livestock production represents the largest land use sector worldwide and employs almost a billion people globally (Hurst et al, 2005; Abu Hatab et al, 2019). The average per capita meat consumption is projected to grow from 34 kg in 2015 to 49 kg in 2050 (Yawson et al, 2017). There is increasing competition for the use of key resources such as land and water and a need to move to less carbon intensive LSF production, especially in the face of climate change (Thornton, 2010; Yawson et al, 2017). Genomics has emerged as a key tool in the effort to create more efficient LSF production, the use of genomic selection to improve breeding programs (Hayes et al, 2009; Christensen et al, 2012; Cleveland and Hickey, 2013)
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