The International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG), a $10M USD investment by the partners in Chile, Norway and British Columbia, Canada resulted in a landmark paper published in Nature in April 2016. Thanks to this, functional annotation of salmonids is now possible based on the completion of a very high quality reference genome for Atlantic salmon.
This website is to inform and engage you in the development of an emerging initiative taken by the ICSASG-collaboration, focused on the Functional Annotation of All Salmonid Genomes (FAASG).
The idea for the initiative stems from discussions at the International Conference on Integrative Salmonid Biology (ICISB) meeting in Puerto Varas earlier this year, and follows in the tradition of functional annotation initiatives in human and mouse (ENCODE) and, more recently, terrestrial animals (FAANG).
At the meeting in Puerto Varas, ICSASG funders and scientists invited the international community to come together and consider new work based on salmonid knowledge, reference sequences and stakeholder's needs, that could be constructively taken forward in an international collaboration. Discussions identified functional annotation as a possible focus for new work and the ICSASG leaders agreed to convene a workshop in Toronto (June 2016) with key international stakeholders to discuss the idea.
The Toronto workshop included scientists and funders from 19 institutions in ten countries and provided a forum to discuss opportunities for an international collaboration on functional annotation afforded by the availability of the reference salmon genome. The workshop report is attached.
The following key messages arose during the workshop:
- Salmonids are the focus of a great amount of research, however much of this data is housed in private databases and websites. This fragmentation along with lack of standards (e.g. transcriptomics and chromosome nomenclature) is limiting advances in salmonid research and development.
- There is interest in the salmonid community to take forward work on functional annotation of salmonids: to identify gene variants and their location and link this to their function or physical traits.
- The FAANG initiative provides a framework for possible collaboration on FAASG.
- Functional annotation work in salmonids should be harmonized or aligned with FAANG to the extent possible, however it is not clear whether FAANG core assays will work well for salmon, or whether new assays need to be developed.
- Given the breadth of salmonid species (70-200) collaboration on the functional annotation of salmonids could provide a depth and richness to the understanding of salmonid biology not possible for commercial terrestrial species.
- There is a need to engage the broader salmonid community in thinking about functional annotation of salmonids
- Scientists agreed on the need for an international initiative to support functional annotation of salmonids and agreed on a plan of work to lay the foundation for the initiative and engage the larger salmonid community in its development and operation.
- Industry engagement is needed and initiatives will be taken.
Workshop participants agreed to (i) develop a Functional Annotation of All Salmonid Genomes (FAASG) Initiative and (ii) engage the international salmonid community and industries.
We hope to engage the wider salmonid research community along with end-users of this knowledge in the development of this initiative. To learn more, or to be come involved, please check back on the website which will be updated as more information becomes available.
As a result of the interactions, several working groups have been identified. Please follow the link to learn more about the organizational structure of FAASG.