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Decoding the axolotl genome

1.2.2018 | A team of researchers led by AcademiaNet member Elly Tanaka reports that they have successfully sequenced the genome of the Mexican axolotl. The salamander is well known for its unique regenerative abilities, which – the researchers hope – will be easier to study now that the full genetic information of the axolotl is available.
Axolotl in the lab
Bild vergrößern
(© IMP)


Axolotl in the lab | After being injured, an axolotl can regrow bones, muscles and nerves in the right places. The decoding of the genome of the Mexican axolotl Ambystoma mexicanum will provide researchers with key insights into the process of tissue regeneration.

Salamanders are valuable biological models for developmental, regeneration and evolutionary studies. In particular, the Mexican axolotl Ambystoma mexicanum has received special attention due to its astounding ability to regenerate body-parts. If the cannibalistically inclined animal loses a limb, it will regrow a perfect substitute within weeks, complete with bones, muscles and nerves in the right places. Even more fascinating, the axolotl can repair severed spinal cord and retinal tissue. These qualities and the relative ease in breeding have made it a favourite biological model, cultivated in the lab for more than 150 years.


One of the largest axolotl-colonies is maintained by the team of Elly Tanaka, now at the Research Institute of Molecular Pathology (IMP) in Vienna. The Tanaka-group is studying the molecular cell biology of limb and spinal cord regeneration and how these mechanisms evolved. Over the years, the team has developed an extensive molecular toolkit for the axolotl, including comprehensive transcriptome data that reveal protein-coding sequences in the animal's genome. Using these tools, Elly Tanaka and her colleagues were able to identify the cells that initiate regeneration and describe molecular pathways that control the process.


To fully understand regeneration and to find out why it is so limited in most species, scientists need to have access to genome data to study gene regulation and evolution. So far, the axolotl genome had evaded a complete assembly, due to its sheer size: at 32 billion base pairs, it is more than ten times larger than the human genome. The sequence assembly process using existing tools had been confounded by the enormous number of large repetitive sequences in this genome.


Elly Tanaka's team – in collaboration with Michael Hiller and Gene Myers (both MPI-CBG), and Siegfried Schloissnig of the Heidelberg Institute for Theoretical Studies (HITS) – managed to achieve the feat with the help of a sequencing technology called the PacBio-platform. The tool can generate very long reads that span the large repetitive regions found in the axolotl genome.


The subsequent analysis of the assembled genome revealed features that seem to point to the uniqueness of the axolotl: The researchers found that several genes that only exist in axolotl and other amphibian species are expressed in regenerating limb tissue. Most strikingly, an essential developmental gene named PAX3 is completely missing from the genome, and its functions have been taken over by another gene termed PAX7. Both genes play key roles in muscle and neural development.


"We now have the map in our hands to investigate how complicated structures such as legs can be re-grown", says Sergej Nowoshilow, co-first author of the study and a postdoctoral fellow at the IMP. "This is a turning point for the community of scientists working with axolotl, a real milestone in a research adventure that started more than 150 years ago."


Axolotl - The Mexican salamander
Bild vergrößern
(© Vlastné dielo via wikimedia commons, licensed under CC BY-SA 4.0.)


Axolotl - The Mexican salamander | Source: Vlastné dielo via wikimedia commons

The sequence of the axolotl genome that is now publicly available is a powerful resource for researchers worldwide to study tissue-regeneration.


  (© Max-Planck-Gesellschaft / AcademiaNet)

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