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Genomic in fish and shellfish: From research to aquaculture

Final Report Summary - AQUAGENOME (Genomic in fish and shellfish: From research to aquaculture)

Numerous European research projects investigated the biology of aquaculture species through genomic approaches and generated useful tools; however, their coordination was insufficient and knowledge was not transferred effectively to the industry. The AQUAGENOME project aimed to fill these gaps so as to improve coordination of the ongoing and future national and international research efforts, as well as to enhance the transfer of information to stakeholders.

The following activities were undertaken to achieve AQUAGENOME objectives:
1. inventory of existing genomic resources on order to identify and evaluate innovative bioinformatic resources, information and tools;
2. development of new instruments to improve the poor quality of the annotation of fish and shellfish genomic resources;
3. elaboration of a transcriptome analysis in various using conventional microarray and new high-throughput sequencing technology;
4. identification of specific research domains in which genomic approaches should be developed to support European aquaculture industry;
5. improvement of the transfer of information to the industry via the establishment of a network of contact, the organisation of two workshops and the development of a document prioritising research and knowledge exchange needs;
6. support of the mobility of experts and knowledge between network members through the distribution of grants;
7. formulation of recommendations that were disseminated to the European Community through the participation of AQUAGENOME members to related research platforms.

Firstly, all genomic tools that could be developed were identified, regardless of the species. The selection among different species was then based on their importance for aquaculture. As a result, a table combining species and potential resources was developed and completed with available data. The matrix was accessible by stakeholders via the Internet. Genetic maps were also produced, but their quality depended highly on available markers; thus, they were not exploitable during the project lifetime. The process indicated that the principal gap for all species was the lack of complete genome sequences.

Innovative methods were subsequently examined to improve gene annotation. The potential of high throughput phylogenomics to annotate fish genes was investigated and promising results were produced. However, the proposals were not yet applicable on a large scale. The gene annotation quality in the common carp was also analysed, along with the impact of new sequencing approaches on this annotation. The lack of proper gene annotations was apparent in many cases; nevertheless significant improvements could be easily made.

In addition, the state of the art of functional genomics in sustainable aquaculture was surveyed based on the findings of recent European projects, so as to highlight specific research priorities. An international meeting was organised for this purpose, resulting in a synthesis document which was supplied to the European Commission. The document contained general and specific recommendations for aquaculture and its components as well as suggestions for resources' development and maintenance.

Furthermore, the need for a more systematic and extensive approach to gathering and integrating data, feasible through the collaboration of experts towards a common base, was discussed. The establishment of benchmarks, i.e. best practices leading to superior performance, was crucial. The selected approach was to apply a technique, microarray, instead of implementing standardisation to a group of organisations. The multi-species character of aquaculture formed a major technical and economic challenge for microarrays' development. Three technologies, allowing for the analysis of the transcriptome, were evaluated. Oligoarrays were the best performing method, with notable advantages for aquaculture research.

AQUAGENOME facilitated exchange and dissemination of resources, materials, experts and information via the development of relevant programmes. Numerous students were provided with mobility grants and produced interesting research results that enhanced knowledge in the field. In addition, grants for the exchange of resources were allocated. The dissemination of information to the industry via the establishment of a contacts' network and the development of a website was among the project priorities. Numerous workshops were also organised and documentation, relevant to the project findings, was published and supplied to policy makers and other involved parts.

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