Genetic catalogue, biological reference collections and online database of European marine fishes (original) (raw)

Visit to molecular biology laboratories at UCM and demonstrations on sampling for taxonomy, genetics and museums. At 15:30: there was a visit to the coordinating group's laboratory at the Universidad Complutense de Madrid. There was a demonstration on taxonomy sampling, for genetics and museums. Tentative protocols for sampling and molecular genetics were given to each participant. 2 nd Day 6. WP1: Standardization of Methods and Legal Aspects At 09:30 Dr Van Pelt presented the tasks covered by Wordpackage 1 (standardization) for which RIVO is the leader. In the presentation a list of subjects to standardize was shown, making special emphasis in those aspects of sampling, DNA, PCR and sequencing, data compilation, images and collection. Particular attention was given to legal aspects on public access to the database; patents and exchange flow of biological samples. The list of standardized methods of FishTrace will be available through the FishTrace web site, so all groups are able to provide identical data quality. A "legal committee" formed by Hilde van Pelt (RIVO), Guy Duhamel (MNHN), Monique Etienne (IFREMER) and Philippe Carreau (EJC) will help and research to advise on legal questions related to data releasing from FrishTrace. During the discussion it was agreed that the protocols for standardization must circulate form the Workpackage leader of each standardized tasks to the other contributors in the same Worpackage. Finally, RIVO will act as a referee for all method standarization and produce the definitive standardized protocol. 7. WP2: Sampling and Taxonomy. At 10:15 Dr Kullander presented the tasks covered by Workpackage 2 (Sampling + Taxonomy) for which NRM is the Workpackage leader. Within the objectives of this Workpackage it was described the sampling procedure and the corresponding data and material to be obtained from each sample. Particular emphasis was given to the systematic work, and the relationship with possible different haplotypes detected in Workpackage 4 from the different geographical locations. The need for a standardization and agreement on the systematic by all groups contributing was clear during the discussion, in particular related to the fields in the database. Issues related to regional data compilation and literature was also raised. This is expected to maintain a certain degree of originality in terms of discovering the most local particularities and not to download from other databases. It was also mentioned that fish photos must retain the copyright of the photographer but them will be freely released among the participants of the project. The need for agreements on what to do with excess of samples and the interchange of them among institutions was also foreseen at the discussion. 8. WP3: Molecular Genetic Identification. At 11:20 Dr. Bautista presented the tasks covered by Workpackage 3 (Molecular Genetics Identification) for which UCM is the Workpackage Leader. Within the scope of the essential information of this Workpackage it was defined the requirements for a sound molecular genetic identification of the samples received by the groups contributing to this Workpackage. Topics covered included the methodology for DNA, extraction, PCR and sequencing. Tentative protocols will be released to the groups participating and a review based on previous experience from all groups will help to define a definitive protocol. Emphasis was given to the quality control of the sequences obtained through a dichotomy scheme that has been working in previous regional projects. Exceptions to the general protocol must be considered since it was pointed out that experimental difficulties could arise in some samples (10-15% of the samples) due to DNA quality, mislabelling, misidentified, technical sequencing error, etc… A brief discussion helped to explain the use of sequencing both genes (Rhodopsin and cytochrome b) for a precise genetic characterization, and how sequences from both genes act as an internal quality control for taxonomic and genetic procedures. 9. WP4: Biogeographical Molecular Haplotyping. At 12:05 Dr. Krey presented the tasks covered by Workpackage 4 (Biogeographical Molecular Haplotyping) for which NAGREF is the Workpackage leader. Within the pursued objectives it was pointed out the need to establish if cyt b and rhodopsin would be efficient markers for polymorphisms studies. Emphasis was given to intraspecies polymorphism detection as a result of the mutation rate, the sample size and the biology of the species examined. An estimation of the number of the species represented in one or more than one geographical location, suggested trying to balance the number of species in which it would be possible to do haplotyping at the cyt b gene using a high number of specimens at each geographical location. Also the life history of each species would be considered, in terms of genetics variability, established populations (pelgic/migratory verses demersal/benthic). It was also mentioned the methodology to be employed and the data analysis for individual sequence and consensus as well as for haplotype diversity annotation. 10. WP5: Biological Reference Collections. At 15:30 Dr. Freitas presented the methods and procedures included in WP 5 (Biological reference collections) for which IMAR is the Workpackage leader. It was examined within the objectives the way to coordinate the collections of biological material obtained in the project, at each institution (because of the hetereogeneity interests and possibilities) and among participating institutions, including exchange, loan and access to the biological collections. Dr Freitas also anticipated some difficulties regarding critical revision of species lists, size and intra-specific morphological variations. An issue was raised during the discussion on what the most adequate number of vouchers would be for systematic, taken into account the high number of species to be collected and sampled. It was also mentioned the great scientific opportunity with FishTrace to afford a wide characterization of species from taxonomy to genetics compiled with the storage of reference biological samples, all compiled in a new database. For this reason it was found convenient to try to get a significant number of specimens for future analysis. 11. WP6: Database Development. 16:30: Philippe Carreau presented the JRC group since it was not done at the day of the presentations. After that Mr Carreau presented Workpackage 6 (Database development) for which JRC is the Workpackage leader. Architecture of the FishTrace database will be based on the present Fishgen database. The database will be extended for many new species from FishTrace and will contain a new date structure with new tables related to the new data provided and new user specifications. Improvements will be done on: a) Taxonomy database structure through the participants input, b) Data quality by describing more precise sample acquisitions process, and analysis procedure. 14. WP 9: Dissemination and Applicability. At 9:30, Dr. Verrez-Bagnis presented Workpackage 9 (Dissemination and Applicability.) for which IFREMER is the Workpackage leader. Expected users who could be interested in the FishTrace database are scientists, technical centres, seafood processors, seafood wholesalers and retailers, consumer associations, administration and regulatory bodies, and control laboratories. Various means of disseminations are foreseen, as articles in scientific, technical and professional journals, brochures to promote the network, booklets presenting a detailed description of the database and the reference collection and genetic catalogue, communications in seminars and specialized symposia (WEFTA: West European Fish technologist association, FASIS: Food Authenticity and Safety International Symposium, etc…, communications at exhibitions like Seafood (Bruxelles), SIAL (Paris), Fisk Seafood International Europe (Bremen)…etc. The importance of links from web sites of each institution to the FishTrace web site, as well as the links with other databases as FishBase or GenBank was mentioned. It was also pointed out that a FishTrace logo could be designed as a kind of brand for our project. The agreed lists of species for the project could be released on the web so to help promote and disseminate the work expectations. It was also discussed the possibility of designing a brochure to send to a mailing list compiled by each participant. Two formats were suggested, either electronic (in the web site) or paper (to send by post). 15. Organization of practical work and information flow (Taxonomic, genetic and Collections Data Blocks: Research teams involved and flow). A brain storming session about the organization of the practical work allowed establishing the following general agreements to follow by the FishTrace participants regarding the main data and sampling collection work: