Structural variant landscape provides insights into genome organisation and domestication in European seabass

Starry flounder (Platichthys stellatus) is an important sport and food fish found around the margins of the North Pacific. Aquaculture production of this species in Korea has increased because of its commercial value. Microsatellite DNA markers are a useful DNA-based tool for monitoring the genetic variation of starry flounder populations. In this study, 12 polymorphic microsatellite DNA markers were identified from a partial genomic starry flounder DNA library enriched in CA repeats, and used to compare allelic variation between wild and hatchery starry flounder populations in Korea. All loci were readily amplified and demonstrated high allelic diversity, with the number of alleles ranging from 6 to 18 in the wild population and from 2 to 12 in the farmed population. A total of 136 alleles were detected at the 12 microsatellite loci in the two populations. The mean observed and expected heterozygosities were 0.62 and 0.68, respectively, in the hatchery samples and 0.67 and 0.75, respectively, in the wild samples. These results indicate lower genetic variability in the hatchery population as compared to the wild population. Significant shifts in allelic frequencies were detected at eight loci, which resulted in a small but significant genetic differences between the wild and hatchery populations (FST = 0.043, P < 0.05). Further studies with additional starry flounder sample collections are needed for comprehensive determinations of the genetic varieties between the wild and hatchery populations. These microsatellite loci may be valuable for future population genetic studies, monitoring the genetic variation for successful aquaculture management and the preservation of aquatic biodiversity.

Gene function conservation is crucial in molecular ecology, especially for key traits like growth and maturation in teleost fish. The vgll3 and six6 genes are known to influence age-at-maturity in Atlantic salmon, but their impact on other fish species is poorly understood. Here, we investigated the association of vgll3 and six6 in the domestication of gilthead seabream and European seabass, both undergoing selective breeding for growth-related traits in the Mediterranean. We analysed two different sets of samples using two different genotyping approaches. The first dataset comprised farmed and wild populations from Greece, genotyped for SNPs within the two genes ('gene-level genotyping'). The second dataset examined 300-600 k SNPs located in the chromosomes of the two genes, derived from a meta-analysis of a Pool-Seq experiment involving farmed and wild populations distributed widely across the Mediterranean ('chromosome-level genotyping'). The gene-level analysis revealed a statistically significant allele frequency differences between farmed and wild populations on both genes in each species. This finding was partially supported by the chromosome-level analysis, identifying highly differentiated regions may be involved in the domestication process at varying distances from the candidate genes. Noteworthy genomic features were found, such as a CpG island in gilthead seabream and novel candidate genes in European seabass, warranting further investigation. These findings support a putative role of vgll3 and six6 in the maturation and growth of gilthead seabream and European seabass, emphasizing the need for further research on their conserved function.

Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re-introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re-introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re-introduced population's genetic diversity could have significant consequences for the long-term persistence of the population in the Negev. The stochastic modelling approach and the use of allele-frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited.

Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata)

Socio-economic value of genetic crop improvement in the European Union

Transgenerational regulation of cbln11 gene expression in the olfactory rosette of the European sea bass (Dicentrarchus labrax) exposed to ocean acidification

BackgroundCacao swollen shoot virus (CSSV), Cacao swollen shoot CD virus (CSSCDV), and Cacao swollen shoot Togo A virus (CSSTAV) cause cacao swollen shoot disease (CSSD) in West Africa. During 2000–2003, leaf and shoot-swelling symptoms and rapid tree death were observed in cacao in Cote d’Ivoire and Ghana. Molecular tests showed positive infection in only ~50–60% of symptomatic trees, suggesting the possible emergence of an unknown badnavirus.MethodsThe DNA virome was determined from symptomatic cacao samples using Illumina-Hi Seq, and sequence accuracy was verified by Sanger sequencing. The resultant 14, and seven previously known, full-length badnaviral genomic and RT-RNase H sequences were analyzed by pairwise distance analysis to resolve species relationships, and by Maximum likelihood (ML) to reconstruct phylogenetic relationships. The viral coding and non-coding sequences, genome organization, and predicted conserved protein domains (CPDs) were identified and characterized at the species level.ResultsThe 21 CSSD-badnaviral genomes and RT-RNase H sequences shared 70–100% and 72–100% identity, respectively. The RT-RNase H analysis predicted four species, based on an ≥80% species cutoff. The ML genome sequence tree resolved three well-supported clades, with ≥70% bootstrap, whereas, the RT-RNase H phylogeny was poorly resolved, however, both trees grouped CSSD isolates within one large clade, including the newly discovered Cacao red vein virus (CRVV) proposed species. The genome arrangement of the four species consists of four, five, or six predicted open reading frames (ORFs), and the CPDs have similar architectures. By comparison, two New World cacao-infecting badnaviruses encode four ORFs, and harbor CPDs like the West African species.ConclusionsThree previously recognized West African cacao-infecting badnaviral species were identified, and a fourth, previously unidentified species, CRVV, is described for the first time. The CRVV is a suspect causal agent of the rapid decline phenotype, however Koch’s Postulates have not been proven. To reconcile viral evolutionary with epidemiology considerations, more detailed information about CSSD-genomic variability is essential. Also, the functional basis for the multiple genome arrangements and subtly distinct CPD architectures among cacao-infecting badnaviruses is poorly understood. New knowledge about functional relationships may help explain the diverse symptomatologies observed in affected cacao trees.

Stable isotope data are often used to assess diet, trophic level, trophic niche width and the extent of omnivory. Notwithstanding ongoing discussions about the value of these approaches, variations in isotopic signatures among individuals depend on inherent variability as well as differences in feeding habitats. Remarkably, the relative contributions of diet variation and inherent variability to differences in delta(15)N and delta(13)C among individuals have not been quantified for the same species at the same life history stages, and inherent variability has been ignored or assumed. We quantified inherent variability in delta(13)C and delta(15)N among individuals of a marine fish (the European sea bass, Dicentrarchus labrax) reared in a controlled environment on a diet of constant isotopic composition and compared it with variability in delta(13)C and delta(15)N among individuals from wild bass populations. The analysis showed that inherent variability among reared individuals on a controlled diet was equivalent to a large proportion of the observed variability among wild individuals and, therefore, that inherent variability should be measured to establish baseline variability in wild populations before any assumptions are made about the influence of diet. Given that inherent variability is known to be dependent on species, life history stage and the environment, our results show that it should be quantified on a case-by-case basis if diet studies are intended to provide absolute assessments of dietary habits.

Using breeding programs to improve feed efficiency, the ratio between fish body weight gain (BWG) and feed intake (FI), could increase aquaculture sustainability through reduced feed costs and environmental impact. To this end, individual phenotypic information is required. Individual FI can be measured by isolating each fish. Under these conditions, restricting the feeding rate has proved relevant to improve feed efficiency indirectly by selecting faster-growing animals. Moreover, a restricted feeding rate reduces the work load of collecting uneaten pellets after each meal. The approach assumes the most efficient fish at high and low feeding rates are the same, but this assumption remains untested. In European sea bass (Dicentrarchus labrax), feed efficiency is likely to be impacted also by population, temperature, and their interaction, as already demonstrated for growth in this species. To investigate these issues, 200 European sea bass from three wild populations, Atlantic (AT), West Mediterranean (WM) and East Mediterranean (EM), were reared individually at two temperatures, 18°C and 24°C. Their BWG and FI were measured at six different feeding rates, from ad libitum (100% ADL) down to fasting. A trade-off between performance at 100% ADL and at fasting was observed: more efficient fish at 100% ADL showed a stronger decrease in BWG (standardized to metabolic weight) when the feeding rate was progressively lowered and lost more weight at fasting. The most efficient fish were not the same depending on the feeding rate, suggesting the feeding rate used to phenotype fish in selective breeding programs must be the same as that used in commercial practices. The slope in the linear relationship between BWG and FI (both standardized to metabolic weight) was similar among populations and temperatures. However, EM fish had a higher intercept than others, suggesting this population grew more and thus was more efficient for an equal feeding rate. Similarly, fish reared at 18°C were more efficient for an equal feeding rate. When feed efficiency was studied in fish fed at 100% ADL, the temperature effect disappeared but the population effect remained. This highlights the complex interplay between population, temperature and feeding rate when evaluating individual feed efficiency.

Genetic variation of resistance to Viral Nervous Necrosis and genetic correlations with production traits in wild populations of the European sea bass (Dicentrarchus labrax)

Hemoglobins (Hb) play a critical role in satisfying the oxygen demand of vertebrate aerobic metabolism. The present study reports the characterization of the European sea bass (Dicentrarchus labrax) Hb genes, including genomic organization, phylogeny, and spatio-temporal gene expression. These Hb genes are divided into two unlinked clusters, the “MN” cluster containing eleven genes (five Hbα genes named MN-Hbα1-5 and six Hbβ genes named MN-Hbβ1–6) and the “LA” cluster consisting of three genes (two Hbα genes named LA-Hbα1-2 and one Hbβ gene named LA-Hbβ1). Comparative analysis of Hb amino acid sequences indicates that most of the important amino acid residues involved in hemoglobin-oxygen binding, particularly in the Bohr and Root effects, are generally well conserved, except in MN-Hbβ3. Six genes were mainly expressed during early life (MN-Hbα3-5, MN-Hbβ4–6), while the others were predominantly expressed at juvenile–adult stages. Adult fish expressed Hb genes at high levels in the head kidney and spleen; the main organs involved in blood formation. The Hb genes expressed in non-hematopoietic organs (intestine, gills, heart, brain, and liver) may facilitate oxygen homeostasis or be involved in antimicrobial defense. Stage- and tissue-specific gene expression patterns, together with the sequence features of the different Hb proteins, suggest a broad range of roles in European sea bass.

Population structure and genetic variability in wild and farmed Mediterranean populations of gilthead seabream and European seabass inferred from a 60K combined species SNP array

Are Complex Behaviors Specified by Dedicated Regulatory Genes? Reasoning from Drosophila

Fatty acids in liver and muscle of farmed and wild sea bass ( Dicentrarchus labrax L.)

European sea bass, Dicentrarchus labrax , is a highly valuable species in Europe, both for aquaculture in the Mediterranean Sea and for commercial and recreational fisheries in the North East Atlantic Ocean. Subjected to increasing fishing pressure, the wild population has recently experienced significant recruitment fluctuation as well as a northward extension of its distribution area in the North Sea. While the nature of the ecological and/or physiological processes involved remains unresolved, ontogenetic habitat shifts and adult site fidelity could increase the species’ vulnerability to climate change and overfishing. As managers look for expert information to propose management scenarios leading to sustainable exploitation, exploratory modelling appears to be a cost-efficient approach to enhance the understanding of recruitment dynamics and the spatio-temporal scales over which fish populations function. A conceptual modelling framework and its specific data requirements are discussed to tackle some sound ecological questions regarding this species. We consequently provide an updated review of current knowledge on bass population structure, biology and ecology. This paper will hence be particularly valuable to develop spatially-explicit models of European sea bass dynamics under environmental and anthropogenic forcing. Knowledge gaps requiring further research efforts are also reported.