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Integrated knowledge on functional genomics in sustainable aquaculture

Final Report Summary - AQUAFUNC (Integrated knowledge on functional genomics in sustainable aquaculture)

Numerous research projects were elaborated during the past years, in order to improve sustainability of European aquaculture by developing molecular technologies, gene mapping and functional genomics approaches. AQUAFUNC aimed to integrate the outcome of these projects in order to identify specific needs in the area, to reduce repetition and to prepare a solid basis by integrating previous investment and investigation results.

The project combined various alternative techniques to construct a common knowledge base for both the scientific community and the public. The need for information and development of additional tools for use by scientists in the research area was thoroughly examined. In addition, the way in which research could respond to emerging problems was investigated. The necessity for common bioinformatics facilities and resources was outlined, along with the provision of a European management context for such facilities.

Scientific coordinators of previous projects were invited to join AQUAFUNC working group so that a forum for discussion and integration of outcomes could be created. An open meeting of this group along with several workshops were then organised, to motivate and increase communication. This approach allowed for the project to be further disseminated.

Moreover, scientific publications on selected AQUAFUNC components were prepared and a journal of significant impact factor was selected as a means of dissemination. The manuscripts were internally reviewed prior to their publication. A journal issue containing AQUAFUNC reviews was subsequently published.

A large variety of tools related to fish or shellfish were developed as part of the previously elaborated research. The project aimed to integrate these tools in a common database and to achieve collaboration of the laboratories which created them, so as to improve spreading of these tools and increase the approaches' efficiency. An important parameter of the undertaken work was to analyse the accessibility, the quality and the sustainability of genomics resources and to identify potential bottlenecks for access by the scientific community in Europe.

The complexity of interrelations between different tools along with their significant number did not allow for completion of the database during the project lifetime. The project webpage contained an inventory of all projects related to AQUAFUNC; however, it was not possible to provide extensive information on all species. It was decided to focus on analysis of resources in trout species, which were rich with regards to genomic resources. The relevant table was elaborated and served as a model situation for the approach developed in AQUAFUNC for integration of bioinformatics tools and resources.

Finally, the needs for development of new bioinformatics resources became apparent during the investigation of available trout resources. Thus, a new strategy based on phylogenic analysis was proposed to improve the available annotation.