Ensembl - adding value to animal genomes through high quality annotation

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High quality annotated genomes are essential resources for life sciences research.

Draft reference genome sequences have been established for several farmed and domesticated animals: cattle, goat, pig, sheep; chicken, duck, turkey; dog, horse; rainbow trout, salmon, tilapia. Substantially improved genome assemblies have been established for goat, pig, cattle, sheep, water buffalo, chicken) using long read sequencing technologies. There are gaps in the annotation of these genomes in terms of transcript complexity, non-coding genes, pseudogenes and regulatory sequences. Moreover, the pseudo haploid genome sequence of one individual provides an incomplete view of a species' genome.
Scientists are generating more and better genome sequences for additional species and individuals within a species. Researchers, especially in the FAANG and FAASG consortia are generating functional data for annotation of coding, non-coding and regulatory sequences.

We will analyse and annotate farmed and domesticated animal genomes as they are released, exploiting the growing volumes of functional data (short and long read RNA-seq / transcript sequences; ChIP-seq; ATAC-Seq; CAGE; bisulfite sequence) to identify coding genes, non-coding genes and regulatory sequences. We will acquire data from re-sequencing projects to characterise genetic variation within species (SNPs, indel, structural variants) and display this variation in its genomics context. We will run comparative genomics analyses both between species and within species.

We will disseminate the resulting richly annotated genome sequences freely via the Ensembl Genome Browser and via an API for power users. These annotated genomes will provide an integrated view of functional sequences (coding, non-coding and regulatory) and sequence variation for a single or multiple individuals for key farmed and domesticated animals.

To maximise use of this resource we will provide demonstrations, on-line and face-to-face training.

Who will benefit?
We anticipate the beneficiaries of the Ensembl genome portal for farmed and companion animals to be:
(i) the academic research community
The primary beneficiaries from this proposal for development and maintenance of Ensembl resources for farmed and companion animals will be researchers in academia and industry in the UK and across the globe.
(ii) animal breeding companies
The world's leading animal breeding and aquaculture breeding companies, of which some of the largest are UK companies, have in-house genetics expertise. Thus, these companies have the expertise to exploit the information captured and disseminated through Ensembl resources.
(iii) owners of farm and companion animals and other stakeholders
Research on domesticated animals has important socio-economic impacts, including underpinning and accelerating improvements in veterinary research and agriculture and improving animal health and welfare. Suppliers of species specific 'omics tools such as expression arrays and SNP chips will also benefit from access to annotated genomes sequences.
(iv) science infrastructure and capacity
The Ensembl project is one of three systems worldwide concerned with delivering annotated genome sequences for a large number of species to the scientific community. As such the Ensembl genome portal makes a considerable and continuing contribution to maintaining science infrastructure and capacity.
(v) society
The Ensembl portal provides direct benefits to specific demographics of society through the provision of out-reach activities and training, as well as to society more widely.

How will they benefit?
(i) the academic research community
The Ensembl genome portal adds value to animal genomes via high quality annotation. High quality annotated reference genome sequences are essential resources for contemporary research in the biological sciences. The Ensembl browser and associated annotation tools and database have been shown to be robust and effective means for making genomic information useful to a wide range of users.
(ii) animal breeding companies
The proposed Ensembl resources, especially the genetic variation resources, will enable researchers to dissect the genetic control of economically important (and complex) traits in farmed animals including feed efficiency and susceptibility to infectious diseases. This enabling of genetics research in farmed animals and aquaculture species will facilitate advanced genetic improvement. Genetic improvement of farmed animal species is a key means of addressing sustainable food production for the animal agriculture and aquaculture sectors.
(iii) owners of farm and companion animals and other stakeholders
In companion animals the benefits will be improved tools for selective breeding to minimise inherited diseases and inbreeding and to improve animal welfare. The utility of 'omics technology products for this purpose such as expression microarrays and SNP chips is greatly enhanced when the features on these products can be linked to a high quality annotated genome sequence and other information sources.
(iv) science infrastructure and capacity
The Ensembl genome portal for farmed and companion animals itself provides a valuable resource underpinning science infrastructure and capacity. In addition, Ensembl has developed a training programme including demonstrations, online tutorials and workshops in the use of the genome portal. This programme trains PhD students, Post Docs and research scientists to develop their skills in genome annotation, genome browsing and importantly how to interpret and understand their own data.
(v) society
The demographic of society most likely to benefit from the training opportunities the Ensembl project can provide are students who are interested in developing skills in bioinformatics. The project will benefit society more widely by providing a resource that contributes to enhancing sustainable food production.