Introduction

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.

HCMR Genomics-Bioinformatics

Infrastructure: HCMR- Genomics-Bioinformatics

Location: Heraklion, GREECE

Web site address: www.imbbc.hcmr.gr

Contact: Costas Tsigenopoulos (tsigeno@hcmr.gr)

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 [a MiSeq (Illumina) and two Oxford Nanopore (MinION and MinION-Mk1C) sequencing devices], a capillary sequence analyzer ABI 3730xl (for DNA sequencing and genotyping)(https://imbbc.hcmr.gr/infrastructures/facilitiesimbbc/dna-sequencing-platform/), an arsenal of gradient and real-time PCR machines (including two Magnetic Induction Cycler qPCRs), 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. (https://imbbc.hcmr.gr/infrastructures/facilitiesimbbc/genetics-molecular-biotechnology-lab/).

The High-Performance Computing (HPC) facility of IMBBC/HCMR was launched in 2009 to address computational challenges over a range of scientific fields in marine biology, with a focus on non-model taxa. The bioinformatics platform (Zorba) currently consists of 328 cores and 2.3 TB total memory. Job submission takes place to the four available computing partitions, or queues, and at its current state achieves a peak performance of 8.3 trillion double-precision floating-point operations per second (8.3 Tflops). On top of these, a total 7.5 TB is distributed to all servers for the storage of environment and system files.

(https://imbbc.hcmr.gr/infrastructures/facilitiesimbbc/high-performance-computing/)

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 longstanding 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. ddRADSequencing) 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.

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