Ensembl 96: Manually annotated mouse genome available

Ensembl 96 features manually annotated mouse genome

Ensembl 96: Manually annotated mouse genome available

5 Apr 2019 - 09:20


  • Ensembl 96 contains, among other genomes, the first manually annotated version of the mouse genome
  • Mouse is the second species, after human, to be annotated in such a detailed manner
  • The mouse genome can help researchers gain valuable insights about humans and other mammals

April 9, CambridgeFor the first time, Ensembl has released a complete version of its manually annotated mouse reference genome. The project involved several years of work, during which researchers analysed every single base in the mouse genome and annotated all the identifiable genes.

Mouse is the second species, after human, to benefit from this type of manual, detailed annotation. EMBL’s European Bioinformatics Institute (EMBL-EBI) is one of the very few places in the world with the resources and dedicated expertise to perform manual genome annotation.

The mouse genome

The mouse genome is contained in 20 chromosome pairs and current research suggests that it is about 2.7 billion base pairs in size. This makes it about 15 percent smaller than the human genome, which consists of 3.1 billion base pairs spread out over 23 pairs of chromosomes.

Solid foundations

“Although manual annotation takes a lot of time and effort, it’s building a foundational resource for molecular biologists and geneticists,” explains Adam Frankish, Manual Genome Annotation Coordinator at EMBL-EBI. “We believe that it is important to represent the genes in the mouse genome as accurately as possible because any errors we make will be propagated to the research that relies on it.”

According to Frankish, the involved nature of manual gene annotation limits the number of species it can be applied to, for example to human, mouse and zebrafish in Ensembl. With tens of thousands of species being sequenced by projects such as Earth BioGenome, automatic annotation is the only feasible solution going forward.

Why does annotation matter?

Fully annotated genomes help researchers understand how different species have evolved. This can be done in a number of ways, including by comparing what genes different species have, or don’t have, in common. The mouse is a particularly useful genome to understand because mice and humans are biologically very similar and their genes show near completely overlapping functions. This makes mouse the perfect animal model for research in drug discovery, gene function and more.

Hidden genes

“There were a few interesting surprises during the manual annotation of the mouse genome,” says Emily Perry, Ensembl Outreach Project Leader. “For example, in a parallel EMBL-EBI project that sequenced 16 commonly-used lab mouse strains, our colleagues identified a new gene in one of these strains. Our manual annotators hadn’t previously had enough evidence to identify this gene in the reference genome. With this new information, they went back to the reference genome and were able to confirm that the gene was, indeed, there.

“Such situations are very uncommon these days, but they do show that there is much left to learn about the human – and mouse – genomes. As new data becomes available, we are able to create a clearer view of what is going on in the genome.”

Find out more about the other updates in Ensembl 96 on the Ensembl blog.

Contact the news team

Oana Stroe
Communications Officer
+44 (0)1223 494 369

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