Browsing by Author "Volckaert, F."
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- Empowering marine science through genomicsPublication . Volckaert, F.; Barbier, Michele; Canario, Adelino V. M.; Olsen, J. L.; Wesnigk, Johanna; Clark, M. S.; Boyen, CatherineMarine scientists in Europe summarize their successes with genome technologies in the marine sciences and make a plea for a concerted international effort to raise greater public education for support.
- Genomic resources for the aquaculture of European sea bassPublication . Volckaert, F.; Batargias, C.; Bonhomme, F.; Canario, Adelino V. M.; Chistiakov, D.; Choudhuri, J. V.; Galibert, F.; Georgoudis, A.; Haley, Chris; Hellemans, Bart; Kuhl, H.; Kotoulas, Georgios; Law, A.; Libertini, A.; Magoulas, A.; McAndrew, B. J.; Reinhardt, Richard; Senger, Fabrice; Souche, E.; Tsigenopoulos, C.; Whitaker, H. A.The BASSMAP consortium, funded by the European Union, has been set up to improve the understanding of the genome of European sea bass (Dicentrarchus labrax). The specific aim is to locate genes of known function on the physical map and to compare specific regions among perciforms. We have produced an F1 cross of outbred sea bass as mapping panel and a Bacterial Artificial Chromosome library (7× redundancy and 165 kb average insert size). End sequencing of the BAC library is in progress and a radiation hybrid panel is under construction.
- Genomics toolbox for farmed fishPublication . Canario, Adelino V. M.; Bargelloni, Luca; Volckaert, F.; Houston, R. D.; Massault, C.; Guiguen, YannThe last decade has seen dramatic technological developments which have resulted in massive production of genome and transcriptome sequence information from a variety of organisms, at all levels of complexity, including several fish species. While hitherto most applications of genomic data have been in biomedicine, biotechnology, and agriculture, there is a growing interest in applying genomic approaches to animal production. This review will describe the basic tools and resources that are currently available and how they are being used for advancing aquaculture. Finally, it will discuss current trends that are likely to have some impact for the benefit of aquaculture.
- Has time come for the genetic management of sea bass?Publication . Volckaert, F.; Alvarez, M. C.; Argenton, F.; Bonhomme, F.; Chatain, B.; Colombo, L.; Castilho, Rita; Chevassus, B.; Gorshkova, G.; Kohler, M.; Magoulas, A.; Martinez, G.; McAndrew, B. J.; Piferrer, F.; Vandeputte, M.; Zanuy, S.Since 1980 the industrial production of European sea bass has risen considerably up to at least 18,000 MT in 1996 ( see also Josupeit, Aquaculture Europe 20(2):-12, 1995). This growth is remarkable since few were able to culture the species in the seventies. Several "classical" stages of development can be observed; they are typical of a rapidly expanding bioindustry.
- Heritability of cortisol response to confinement stress in European sea bass dicentrarchus labraxPublication . Volckaert, F.; Hellemans, Bart; Batargias, C.; Louro, Bruno; Massault, C.; Van Houdt, Jeroen K. J.; Haley, Chris; De Koning, Dirk-Jan; Canario, Adelino V. M.In fish, the most studied production traits in terms of heritability are body weight or growth, stress or disease resistance, while heritability of cortisol levels, widely used as a measure of response to stress, is less studied. In this study, we have estimated heritabilities of two growth traits (body weight and length) and of cortisol response to confinement stress in the European sea bass.FindingsThe F1 progeny analysed (n = 922) belonged to a small effective breeding population with contributions from an unbalanced family structure of just 10 males and 2 females. Heritability values ranged from 0.54 (±0.21) for body weight to 0.65 (±0.22) for standard body length and were low for cortisol response i.e. 0.08 (±0.06). Genetic correlations were positive (0.94) between standard body length and body weight and negative between cortisol and body weight and between cortisol and standard body length (−0.60 and −0.55, respectively).ConclusionThis study confirms that in European sea bass, heritability of growth-related traits is high and that selection on such traits has potential. However, heritability of cortisol response to stress is low in European sea bass and since it is known to vary greatly among species, further studies are necessary to understand the reasons for these differences.
- Pillars of Hercules: is the Atlantic-Mediterranean transition a phylogeographical break?Publication . Patarnello, T.; Volckaert, F.; Castilho, RitaThe geological history of the Mediterranean Sea, its hydrography and connection with the Atlantic Ocean have been well documented. Despite a wealth of historical and oceanographic data, the Atlantic–Mediterranean transition remains controversial at the biological level as there are discordant results regarding the biogeographical separation between the Atlantic and Mediterranean biota. The opening of the Strait of Gibraltar at the end of the Messinian Salinity Crisis (some 5.33 million years ago), removed the land barrier that impeded the marine biota allowing it to disperse freely into the Mediterranean Sea. However, present day genetic patterns suggest a limitation to gene flow for some marine species, preventing population admixture. In the last few years, a large number of studies have challenged the hypothesis of the Strait of Gibraltar representing a phylogeographical break. A review of more than 70 papers reveals no obvious relationship between either dispersal ability or life history, and observed patterns of partial or complete genetic isolation between Atlantic and Mediterranean populations. We re-analysed a selection of this large body of data (20 studies in total) in order to provide a homogeneous and coherent view on the generality of the phylogeographical patterns and the presence of a phylogeographical barrier. This offered the opportunity to summarize the state of the art on this matter and reach some general conclusions on the evolutionary history across the Atlantic–Mediterranean range. Geographically, some species in the transition zone showed step changes of allele frequencies associated with the Almeria-Oran Front rather than with the Strait of Gibraltar itself. A major part of the data describe evolutionary events well within the time frame of the Quaternary age as very few taxa pre-date closure of the Tethys Sea. Results point to a combined signature of vicariance, palaeoclimate fluctuation and life-history traits on the Atlantic–Mediterranean phylogeographical patterns. Principal component analysis failed to show any particular association between biological traits and genetic variables. It would argue that organismal determinism may play a far less significant role than marine biogeographers have generally believed.
- The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencingPublication . Kuhl, H.; Beck, Alfred; Wozniak, Grzegorz; Canario, Adelino V. M.; Volckaert, F.; Reinhardt, RichardAbstract Background Food supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist with the removal of this bottleneck. European sea bass Dicentrarchus labrax L. (Moronidae, Perciformes, Teleostei) is one of the most important fishes in European marine aquaculture; growing genomic resources put it on its way to serve as an economic model. Results End sequencing of a sea bass genomic BAC-library enabled the comparative mapping of the sea bass genome using the three-spined stickleback Gasterosteus aculeatus genome as a reference. BAC-end sequences (102,690) were aligned to the stickleback genome. The number of mappable BACs was improved using a two-fold coverage WGS dataset of sea bass resulting in a comparative BAC-map covering 87% of stickleback chromosomes with 588 BAC-contigs. The minimum size of 83 contigs covering 50% of the reference was 1.2 Mbp; the largest BAC-contig comprised 8.86 Mbp. More than 22,000 BAC-clones aligned with both ends to the reference genome. Intra-chromosomal rearrangements between sea bass and stickleback were identified. Size distributions of mapped BACs were used to calculate that the genome of sea bass may be only 1.3 fold larger than the 460 Mbp stickleback genome. Conclusions The BAC map is used for sequencing single BACs or BAC-pools covering defined genomic entities by second generation sequencing technologies. Together with the WGS dataset it initiates a sea bass genome sequencing project. This will allow the quantification of polymorphisms through resequencing, which is important for selecting highly performing domesticated fish.