Costas Tsigenopoulos

Hellenic Centre for Marine Research | hcmr · Institute of Marine Biology, Biotechnology and Aquaculture

Background Viral nervous necrosis (VNN) is a viral disease threatening the sustainability of global aquaculture, and affecting over 50 of farmed and ecologically important species. A major QTL for resistance to VNN has been previously described in European sea bass, but the underlying causal gene(s) and mutation(s) are unknown. To identify the mech...

Conserved noncoding elements in vertebrates are enriched around transcription factor loci associated with development. However, loss and rapid divergence of conserved noncoding elements has been reported in teleost fish, albeit taking only few genomes into consideration. Taking advantage of the recent increase in high-quality teleost genomes, we fo...

The greater amberjack ( Seriola dumerili ) has attracted considerable economic interest since the 1990s because it possesses traits that distinguish it as a promising candidate in aquaculture. However, the challenges of its successful rearing, combined with the need to develop proper management practices, underline the importance of research into t...

The tropical seagrass Halophila stipulacea invaded the Eastern Mediterranean Sea in the late nineteenth century and progressively spread throughout the basin ever since. Its spread is expected to continue north-westward as the Mediterranean Sea becomes warmer, potentially changing the seagrass biogeography of the basin. Given the power of genomics...

The genetic traits of seagrass populations are a crucial aspect of their ecology and evolution, influencing their adaptability and resilience. Here, we studied the genetic diversity, population structure, and connectivity of eighteen Posidonia oceanica meadows extending in the Eastern Mediterranean Sea (Aegean, Ionian and Cretan Seas, Greece), comb...

Conserved Non-coding Elements (CNE) in vertebrates are enriched around transcription factor loci associated with development. However, loss and rapid divergence of CNEs has been reported in teleost fish, albeit taking only few genomes into consideration. Taking advantage of the recent increase in high-quality teleost genomes, we focus on studying t...

Knowledge of population structure and genetic variability within and between wild and farmed populations is important to achieve sustainable aquaculture production. In this study, these features were assessed for gilthead seabream and European seabass using a combined species SNP array newly developed. Population structure analyses revealed a clear...

Devil firefish ( Pterois miles ), a member of Scorpaenidae family, is one of the most successful marine non-native species, dominating around the world, that was rapidly spread into the Mediterranean Sea, through the Suez Canal, originating from the Indian Ocean. Even though lionfishes (Scorpaenidae) are identified among the most prosperous marine...

The meagre, Argyrosomus regius, has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring...

By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while raising new ones. The latter include how different local environments influence adaptive and neutral genomic variation within and among populations, providing insights into local adaptation of natural populations and their responses to...

Objective The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algorithms, as well as the establishment of standardized...

Background: Treatment with recombinant gonadotropin hormones (rGths), follicle-stimulating hormone (rFsh) and luteinizing hormone (rLh), was shown to induce and complete vitellogenesis to finally obtain viable eggs and larvae in the flathead grey mullet (Mugil cephalus), a teleost arrested at early stages of gametogenesis in intensive captivity con...

The meagre, Argyrosomus regius, has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring...

Viral nervous necrosis (VNN) presents a significant threat to the European seabass aquaculture industry, causing extensive losses due to mortality and impaired growth of infected fish. Selective breeding presents an opportunity to develop seabass strains with increased resistance, thus reducing the impact of the disease on the industry. Knowledge o...

There is an increasing demand for the breeding programs to focus on resistance against diseases since the treatments or vaccinations increase production costs and, in some cases, they are not available at all. Most of the studies focus on virus and bacterial diseases, but limited information is available for parasitic diseases in European seabass....

Knowledge of population structure and genetic diversity within and between wild and farmed populations of gilthead sea bream (Sparus aurata) and European seabass (Dicentrarchus labrax) is important to achieve sustainable aquaculture production of these species and to assess the risk of genetic impacts of fish escaped from farms. Previous population...

The pikeperch is a freshwater/brackish water fish species with growing interest for European aquaculture. Wild populations show signs of decline in many areas of the species natural range due to human activities. The comparative evaluation of genetic status in wild and domesticated populations is extremely useful for the future establishment of gen...

Mesopelagic fishes are among the most abundant groups of vertebrates on Earth. Despite their unique biological and ecological traits, research in this group has been particularly scarce. The present study investigates the intraspecific genetic diversity of three mesopelagic fishes (Hygophum benoitι, Maurolicus muelleri, and Benthosema glaciale) in...

Meagre (Argyrosomus regius), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspect...

Viral nervous necrosis (VNN) is an infectious disease caused by the red-spotted grouper nervous necrosis virus (RGNNV) in European sea bass and is considered a serious concern for the aquaculture industry with fry and juveniles being highly susceptible. To understand the genetic basis for resistance against VNN, a survival phenotype through the cha...

The majority of the genetic studies in aquaculture breeding programs focus on commercial traits such as body weight, morphology, and resistance against diseases. However, studying stress response in European seabass may contribute to the understanding of the genetic component of stress and its future use to select broodstock whose offspring may pot...

Non-indigenous species (NIS) are one of the major threats to the native marine ecosystems of the Mediterranean Sea. Halophila stipulacea was the only exotic seagrass of the Mediterranean until 2018, when small patches of a species morphologically identified as Halophila decipiens were reported in Greece. Given the absence of reproductive structures...

This study evaluates the genetic diversity of different meagre broodstocks sampled in Greece. A multiplex of twelve microsatellite markers was used to genotype 946 fish from eleven stocks and batches used for broodstock selection, and the genetic data was used to calculate genetic population parameters as well as to investigate the genetic differen...

The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. The silver-cheeked toadfish (Lagocephalus sceleratus) is a well-known “invasive sprinter” that has invaded and spread, in less than a decade, throughout the Eastern and part of the Western Mediterranean Sea from the Red S...

Two potential candidate species for the Mediterranean aquaculture–the common dentex (Dentex dentex) and the sharpsnout seabream (Diplodus puntazzo)-are used in the present study in order to depict their genetic architecture for the first time. We have constructed the first linkage maps for both species using SNP markers derived from ddRAD sequencin...

By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while new can be asked. Such questions include how different local environments influence both adaptive and neutral genomic variation within and among populations, providing insights not only into local adaptation of natural populations, but...

High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational cha...

The European seabass is one of the main commercial fish produced in Mediterranean marine aquaculture. Recently, its production has been negatively affected by losses due to frequent and recurring outbreaks of parasitic, bacterial and viral diseases. In recent years, the gill parasites Diplectanum aequans and Lernanthropus kroyeri are increasingly b...

Increasing parentage contribution in aquaculture broodstocks is important, in order to take full advantage of the available genetic makeup of the chosen fish, and to avoid inbreeding and loss of allele diversity over subsequent production generations. European sea bass (Dicentrarchus labrax) broodstocks were evaluated over two reproductive seasons...

Scientific knowledge and methodology is undergoing transition from plain manuscript documents to multimedia-rich manuscripts linked to accompanying data. Organized datasets add value to a manuscript by being directly linked and available in reusable format [4]. The benefit of these add-on value could be multiplied once such data get repeatedly upda...

The rapid progress in sequencing technology and related bioinformatics tools is leading to disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algorithms, as well as the establishment of standardized ana...

SNP arrays are powerful tools for high-resolution studies of the genetic basis of complex traits, facilitating both selective breeding and population genomic research. The European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata) are the two most important fish species for Mediterranean aquaculture. While selective breeding...

The freshwater ichthyofauna of Greece is characterized by high diversity and endemism and faces various conservation challenges. Despite significant efforts, mainly with traditional assessment methods, the precise taxonomic status and geographic range of some of the currently acknowledged fish species remain insufficiently explored. Here, the resul...

Background In fish, minimally invasive blood sampling is widely used to monitor physiological stress with blood plasma biomarkers. As fish blood cells are nucleated, they might be a source a potential new markers derived from ‘omics technologies. We modified the epiGBS (epiGenotyping By Sequencing) technique to explore changes in genome-wide cytosi...

Wild fish assemblages that aggregate within commercial marine aquaculture sites forfeeding and shelter have been considered as a primary source of pathogenic parasites vectored tofarmed fish maintained in net pens at an elevated density. In order to evaluate whetherCeratothoaoestroides(Isopoda, Cymothoidae), a generalist and pestilent isopod that i...

Gilthead sea bream (Sparus aurata) belongs to a group of teleost which has high importance in Mediterranean aquaculture industry. However, industrial production is increasingly compromised by an elevated outbreak of diseases in sea cages, especially a disease caused by monogeneans parasite Sparicotyle chrysophrii. This parasite mainly colonizes gil...

SNP arrays are powerful tools for high-resolution studies of the genetic basis of complex traits, facilitating both population genomic and selective breeding research. The European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata) are the two most important fish species for Mediterranean aquaculture. While selective breeding...

There is a growing interest in selective breeding in European sea bass (Dicentrarchus labrax), especially regarding family selection based on growth performance. In particular, quantitative trait loci (QTL) identification in sea bass enhances the application of marker-assisted breeding for the genetic improvement of the production traits. The aims...

Microsatellite markers were used to investigate the genetic structure of the two most important cultured fish in the Mediterranean Sea, the gilthead seabream ( Sparus aurata ) and the European seabass ( Dicentrarchus labrax ), from two (one wild and one farmed) populations in Western Mediterranean (Spain) and from two (one wild and one farmed) popu...

Background: While the stress response inspired genome-wide epigenetic studies in vertebrate models, it remains mostly ignored in fish. We modified the epiGBS (epiGenotyping By sequencing) technique to explore changes in genome-wide cytosine methylation to a repeated acute stress challenge in the nucleated red blood cells (RBCs) of the European sea...

Background: While the stress response inspired genome-wide epigenetic studies in vertebrate models, it remains mostly ignored in fish. We modified the epiGBS (epiGenotyping By sequencing) technique to explore changes in genome-wide cytosine methylation to a repeated acute stress challenge in the nucleated red blood cells (RBCs) of the European sea...

Background: In fish, minimally invasive blood sampling is widely used to monitor physiological stress with blood plasma biomarkers. As fish blood cells are nucleated, they might be a source a potential new markers derived from ‘omics technologies. We modified the epiGBS (epiGenotyping By Sequencing) technique to explore changes in genome-wide cytos...

Background While the stress response inspired genome-wide epigenetic studies in vertebrate models, it remains mostly ignored in fish. We modified the epiGBS (epiGenotyping By sequencing) technique to explore changes in genome-wide cytosine methylation to a repeated acute stress challenge in the nucleated red blood cells (RBCs) of the European sea b...

The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. However, the genomic resources and especially reference assemblies are sparse for the members of the family. Ιn this study, we focus on the silver-cheeked toadfish (Lagocephalus sceleratus) a well-known 'invasive sprinter...

The emblematic sponge Spongia officinalis is currently threatened by recurrent mortality incidents in its native habitats. Elevated temperature has been indicated as a major triggering factor, but the molecular mechanisms recruited for the organism’s response to thermal shifts are yet unknown. Here, we experimentally tested the effect of exposure t...

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Objectives: We report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently separate between bacterial expressed genes from those of eukaryotic origin. The transcriptome was produced to support the assess...

Population dynamics in the marine realm can shape species' spatial structure and genetic variability between given geographical areas. Connectivity is an important factor of species' population structure. In this study, we examined the genetic diversity and structure of white seabream (Diplodus sargus, L. 1758) in the eastern Mediterranean basin, u...

Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes...

Background: Comprehensively detailed information on population dynamics for benthic species is crucial since potential admixture of individuals could shift the genetic subdivision and age structure during a full breeding period. The apparent genetic impact of the potential recruitment strategy of Norway lobster Nephrops norvegicus is still under re...

Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes...

Gilthead sea bream (Sparus aurata) is a teleost of considerable economic importance in Southern European aquaculture. The aquaculture industry shows a growing interest in the application of genetic methods that can locate phenotype–genotype associations with high economic impact. Through selective breeding, the aquaculture industry can exploit this...

Sponges are organisms with simple body plan, without true tissue differentiation. Moreover, they are notorious for hosting rich, regulated symbiotic bacterial communities, thus creating the sponge holobiont. These traits, combined with the expansive and diverse nature of the poriferan phylum and the fact that only two sponge species have been seque...