HCMR -the main advisory body on aquaculture and fisheries in Greece- will participate in the project with the Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC). IMBBC aims to carry out basic and applied research on 1) aquaculture technology, reproduction, rearing, nutrition, welfare, pathology and fish quality 2) diversity of marine and freshwater life, phylogeography and genomics of marine species, development of genomic approaches in fish aquaculture, bioinformatics and interactions of organisms with their environment. IMBBC has a long-standing experience in converting accumulated knowledge to aquaculture technologies applicable to the private sector, development of genetic tools for parentage assignment, production of genetic maps and QTL analyses of aquaculture species.
Material resources: Specialized laboratories (nutrition, physiology, pathology, water quality and ethology) support any experimental study. Aqualabs are more specialized on hatchery technology, where systems with automated feeding and monitoring of environmental parameters will be applied. In Souda cages are devoted to on-growing experiments and monitoring of feeding behaviour in larger specimen of new warm-water species.
Name of the infrastructure: HCMR- Genomics-Bioinformatics
Location: Heraklion, GREECE
Website address: www.imbbc.hcmr.gr/content/institute
Contact: Costas Tsigenopoulos
Facilities
The HCMR-Genomics/Bioinformatics facility has modern equipment, essential for the design and elaboration of research projects in the fields of population genetics, molecular ecology, phylogeography, genetic improvement and genomics of Mediterranean aquaculture fish, and it is able to perform any necessary genetic analysis under the context of the proposed activity. The installations include Next Generation high-throughput genetic analysers [454 FLX & Junior (Roche) and MiSeq (Illumina)], a capillary sequence analyzer ABI 3730xl (for DNA sequencing and genotyping), an arsenal of gradient and real-time PCR machines, a microarray scanner, a TaqMan OpenArray Genotyping System, a QIAcube (Qiagen) and in general equipment which facilitates and ensures the appropriate conditions for the isolation and the qualitative and quantitative study of the genetic profile of an organism at the level of DNA, RNA and proteins.
Last, the institute operates a bioinformatics platform (BioCluster) with 13 worker nodes, 300 CPU cores, 2.5 TB RAM, 112 TB high performance storage (Lustre), 18 TB HA global storage (ZFS/NFS) /home, 40 Gbps Infiniband network.
Services currently offered by the infrastructure
The HCMR- Genomics-Bioinformatics infrastructure is a leading institution in the research for fish species for the Mediterranean aquaculture through participation to European research projects and collaborations with the industry. Round the year there is a constant flow of visitors for research and education purposes. The infrastructure pursuits research and innovation in a) phylogenetics, systematics and population genetics, b) the de novo genome analysis, transcriptome sequencing, and analysis of microbial diversity (metagenomics), and c) the development of molecular markers, parentage assignment analyses, construction of genetic maps for target species and potentially also QTL analyses.
Modality of access
The research activities of the institute (IMBBC) focus in diversity of marine and freshwater life, phylogeography and genomics of marine species, development of genomic approaches in fish aquaculture, bioinformatics and interactions of organisms with their environment. IMBBC has a long-standing experience in marker development, use of molecular genetic tools to assess population structure of natural and cultivated stocks, parentage assignment and production of genetic maps (including candidate genes and neutral markers) of species important to the aquaculture industry. The Institute was responsible for the introduction into Greece of the use of molecular genetic markers to
i) address questions of population structure of natural marine stocks and
ii) assist genetic improvement in aquaculture. Recently, the team has played a significant role in the introduction of genomic approaches in aquaculture practices and is actively contributing to practical applications of the produced results in commercial farms.
Data analysis opportunities in the HCMR- Genomics-Bioinformatics infrastructure: The bioinformatics personnel of the institute have experience in data analysis and pipeline development of various ‘omics’ fields like:
• Genomics (prokaryote and eukaryote): genome assembly, structural and functional annotation, comparative genomics (synteny, non-coding DNA, regulatory elements, genetic marker discovery), phylogenomics (orthology discovery, multiple alignment, phylogenetic reconstruction)
• Transcriptomics: Experimental design, sequencing, data pre-processing, assembly (de novo & reference-based), structural and functional annotation, genetic variant mining (SNPs and microsatellites), differential gene expression, non-coding RNA (microRNA gene and target prediction)
• Meta-genomics (microbial communities) Amplicon sequencing and analysis, taxonomy, biodiversity
• Population Genomics: SNP discovery through Genotyping by Sequencing methods (e.g. ddRAD-Sequencing) and population genomics pipelines
• Quantitative Genomics: QTL mapping, linkage maps, GWAS
• Bioinformatics expertise: pipeline/workflow design, database design and optimization, software development, software optimization (e.g. parallelization), web design, cluster development and management
Unit of Access
One week represents the access of installation. The unit of access represents the use of molecular laboratory or data analysis facilities, personnel, use of other supporting equipment and consumables (e.g. commercial kits) for one week. In the installation of Genomics-Bioinformatics, projects will be run with an average duration of 2-4 weeks. Depending on the nature of research, and although the experiments may take longer, users may spend two weeks at our institution.
After presenting a detailed description of the experimental process and requirements, users may either monitor the experiment or actively participate with hands on work, if required. Host scientists will assist visitors during their experimental work and experienced technical personnel will carry out the routine procedures.