Characterization of polymorphic microsatellite loci in the Antarctic krill Euphausia superba - Candeias, Rui; Teixeira, Sara; Duarte, Carlos M.; Pearson, Gareth A.
Background: The Antarctic krill, Euphausia superba is a pelagic crustacean, abundant in high-density swarms (10 000 – 30 000 ind/m2) with a circumpolar distribution and a key role in the food web of the Southern Ocean. Only three EST derived microsatellite markers have been used in previous genetic studies, hence we developed additional highly polymorphic microsatellite markers to allow robust studies of the genetic variability and population differentiation within this species. Findings: The microsatellite markers described here were obtained through an enriched genomic library, followed by 454 pyrosequencing. A total of 10 microsatellite markers were tested in 32 individuals from...
Sex-biased gene expression in the brown alga Fucus vesiculosus - Martins, Maria João F.; Mota, Catarina F.; Pearson, Gareth A.
The fucoid brown algae (Heterokontophyta, Phaeophyceae) are increasingly the focus of ecological genetics, biodiversity, biogeography and speciation research. The molecular genetics underlying mating system variation, where repeated dioecious – hermaphrodite switches during evolution are recognized, and the molecular evolution of sex-related genes are key questions currently hampered by a lack of genomic information. We therefore undertook a comparative analysis of male and female reproductive tissue transcriptomes against a vegetative background during natural reproductive cycles in Fucus vesiculosus.
Over 300 k reads were assembled and annotated against public protein databases including a brown alga. Compared with the vegetative tissue, photosynthetic and carbohydrate metabolism...
Characterization of ten highly polymorphic microsatellite loci for the intertidal mussel Perna perna, and cross species amplification within the genus - Coelho, Nelson Alexandre Castilho; Zardi, Gerardo I.; Pearson, Gareth A.; Serrão, Ester; Nicastro, Katy R.
The brown mussel Perna perna (Linnaeus, 1758) is a dominant constituent of intertidal communities and a strong invader with multiple non-native populations distributed around the world. In a previous study, two polymorphic microsatellite loci were developed and used to determine population-level genetic diversity in invasive and native P. perna populations. However, higher number of microsatellite markers are required for reliable population genetic studies.
In this context, in order to understand P. perna origins and history of invasion and to compare population genetic structure in native versus invaded areas, we developed 10 polymorphic microsatellite markers.
Described microsatellite markers were developed from an enriched...
Development and characterization of 35 single nucleotide polymorphism markers for the brown alga Fucus vesiculosus - Cánovas, Fernando G.; Mota, Catarina F.; Ferreira-Costa, Joana; Serrão, Ester; Coyer, Jim; Olsen, Jeanine; Pearson, Gareth A.
We characterized 35 single nucleotide polymorphism (SNP) markers for the brown alga Fucus vesiculosus. Based on existing
Fucus Expressed Sequence Tag libraries for heat and desiccation-stressed tissue, SNPs were developed and confirmed by
re-sequencing cDNA from a diverse panel of individuals. SNP loci were genotyped using the SEQUENOM single base
extension iPLEXTM system for multiplex assays on the MassARRAY platform, which uses matrix-assisted laser desorption/
ionization time-of-flight mass spectrometry (MALDI-TOF MS) to discriminate allele-specific products. The SNP markers
showed a wide range of variability among 16 populations from the south-west of the UK, northern Portugal and Morocco.
The analysis of the information provided by these markers...
Proteomics in aquaculture: applications and trends - Rodrigues, Pedro; Silva, Tomé S.; Dias, Jorge; Jessen, Flemming
Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come.
Aquaculture is, though, a very competitivemarket, and a globalawareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organismthrough a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful...
Feeding and the rhodopsin family G-Protein Coupled Receptors (GPCRs) in nematodes and arthropods - Cardoso, João
In vertebrates, receptors of the rhodopsin G-protein coupled superfamily (GPCRs) play an important role in the regulation of feeding and energy homeostasis and are activated by peptide hormones produced in the brain-gut axis. These peptides regulate appetite and energy expenditure by promoting or inhibiting food intake. Sequence and function homologues of human GPCRs involved in feeding exist in the nematode roundworm, Caenorhabditis elegans (C. elegans) and the arthropod fruit fly, Drosophila melanogaster (D. melanogaster), suggesting that the mechanisms that regulate food intake emerged early and have been conserved during metazoan radiation. Nematodes and arthropods are the most diverse and successful...
Effects of genotype and dietary fish oil replacement with vegetable oil on the intestinal transcriptome and proteome of Atlantic salmon (Salmo salar) - Silva, Tomé; Cordeiro, Odete; Rodrigues, Pedro; Guy, Derrick R.; Bron, James E.; Taggart, John B.; Bell, J. Gordon; Tocher, Douglas R.
Expansion of aquaculture requires alternative feeds and breeding strategies to reduce dependency on fish oil (FO) and better utilization of dietary vegetable oil (VO). Despite the central role of intestine in maintaining body homeostasis and health, its molecular response to replacement of dietary FO by VO has been little investigated. This study employed transcriptomic and proteomic analyses to study effects of dietary VO in two family groups of Atlantic salmon selected for flesh lipid content, 'Lean' or 'Fat'.ResultsMetabolism, particularly of lipid and energy, was the functional category most affected by diet. Important effects were also measured in ribosomal proteins and...
Heritability of cortisol response to confinement stress in European sea bass dicentrarchus labrax - Volckaert, Filip AM; Hellemans, Bart; Batargias, Costas; Louro, Bruno; Massault, Cécile; Van Houdt, Jeroen KJ; Haley, Chris; De Koning, Dirk-Jan; Canario, Adelino V. M.
AbstractBackgroundIn 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...
Driving south: a multi-gene phylogeny of the brown algal family Fucaceae reveals relationships and recent drivers of a marine radiation - Cánovas, Fernando G.; Mota, Catarina F.; Serrão, Ester; Pearson, Gareth A.
Understanding the processes driving speciation in marine ecosystems remained a challenge until recently, due to the unclear nature of dispersal boundaries. However, recent evidence for marine adaptive radiations and ecological speciation, as well as previously undetected patterns of cryptic speciation is overturning this view. Here, we use multi-gene phylogenetics to infer the family-level evolutionary history of Fucaceae (intertidal brown algae of the northern Pacific and Atlantic) in order to investigate recent and unique patterns of radiative speciation in the genus Fucus in the Atlantic, in contrast with the mainly monospecific extant genera. Results We developed a set of markers from...
Neogastropod phylogenetic relationships based on entire mitochondrial genomes - Cunha, Regina L.; Grande, Cristina; Zardoya, Rafael
The Neogastropoda is a highly diversified group of predatory marine snails (Gastropoda: Caenogastropoda). Traditionally, its monophyly has been widely accepted based on several morphological synapomorphies mostly related with the digestive system. However, recent molecular phylogenetic studies challenged the monophyly of Neogastropoda due to the inclusion of representatives of other caenogastropod lineages (e.g. Littorinimorpha) within the group. Neogastropoda has been classified into up to six superfamilies including Buccinoidea, Muricoidea, Olivoidea, Pseudolivoidea, Conoidea, and Cancellarioidea. Phylogenetic relationships among neogastropod superfamilies remain unresolved. Results The complete mitochondrial (mt) genomes of seven Neogastropoda (Bolinus brandaris, Cancellaria cancellata, Conus borgesi, Cymbium olla, Fusiturris similis, Nassarius...
Analysis of the asymmetrically expressed Ablim1 locus reveals existence of a lateral plate Nodal-independent left sided signal and an early, left-right independent role for nodal flow - Stevens, Jonathan; Ermakov, Alexander; Braganca, José; Hilton, Helen; Underhill, Peter; Bhattacharya, Shoumo; Brown, Nigel A.; Norris, Dominic P.
Abstract Background Vertebrates show clear asymmetry in left-right (L-R) patterning of their organs and associated vasculature. During mammalian development a cilia driven leftwards flow of liquid leads to the left-sided expression of Nodal, which in turn activates asymmetric expression of the transcription factor Pitx2. While Pitx2 asymmetry drives many aspects of asymmetric morphogenesis, it is clear from published data that additional asymmetrically expressed loci must exist. Results A L-R expression screen identified the cytoskeletally-associated gene, actin binding lim protein 1 (Ablim1), as asymmetrically expressed in both the node and left lateral plate mesoderm (LPM). LPM expression closely mirrors that of...
Microplate-based high throughput screening procedure for the isolation of lipid-rich marine microalgae - Pereira, Hugo; Barreira, Luísa Paula Viola Afonso; Mozes, Andre; Florindo, Claudia; Polo, Cristina; Duarte, Catarina V; Custódio, Luísa Margarida Batista; Varela, Joao
Abstract We describe a new selection method based on BODIPY (4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene) staining, fluorescence activated cell sorting (FACS) and microplate-based isolation of lipid-rich microalgae from an environmental sample. Our results show that direct sorting onto solid medium upon FACS can save about 3 weeks during the scale-up process as compared with the growth of the same cultures in liquid medium. This approach enabled us to isolate a biodiverse collection of several axenic and unialgal cultures of different phyla.
The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing - Kuhl, Heiner; Beck, Alfred; Wozniak, Grzegorz; Canario, Adelino V. M.; Volckaert, Filip A. M.; Reinhardt, Richard
Abstract 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...
Gill transcriptome response to changes in environmental calcium in the green spotted puffer fish - Pinto, Patricia; Matsumura, Hideo; Thorne, Michael A. S.; Power, Deborah; Terauchi, Ryohei; Reinhardt, Richard; Canario, Adelino V. M.
Abstract Background Calcium ion is tightly regulated in body fluids and for euryhaline fish, which are exposed to rapid changes in environmental [Ca2+], homeostasis is especially challenging. The gill is the main organ of active calcium uptake and therefore plays a crucial role in the maintenance of calcium ion homeostasis. To study the molecular basis of the short-term responses to changing calcium availability, the whole gill transcriptome obtained by Super Serial Analysis of Gene Expression (SuperSAGE) of the euryhaline teleost green spotted puffer fish, Tetraodon nigroviridis, exposed to water with altered [Ca2+] was analysed. Results Transfer of T. nigroviridis from...
Skin healing and scale regeneration in fed and unfed sea bream, Sparus auratus - Vieira, Florbela A.; Gregório, Sílvia F.; Ferraresso, Serena; Thorne, Michael A. S.; Costa, Rita Alves; Milan, Massimo; Bargelloni, Luca; Clark, Melody S.; Canario, Adelino V. M.; Power, Deborah
Abstract Background Fish scales are an important reservoir of calcium and phosphorus and together with the skin function as an integrated barrier against environmental changes and external aggressors. Histological studies have revealed that the skin and scales regenerate rapidly in fish when they are lost or damaged. In the present manuscript the histological and molecular changes underlying skin and scale regeneration in fed and fasted sea bream (Sparus auratus) were studied using a microarray 3 and 7 days after scale removal to provide a comprehensive molecular understanding of the early stages of these processes. Results Histological analysis of skin/scales revealed...
Global analysis of gene expression in mineralizing fish vertebra-derived cell lines: new insights into anti-mineralogenic effect of vanadate - Tiago, Daniel M.; Laizé, Vincent; Bargelloni, Luca; Ferraresso, Serena; Romualdi, Chiara; Cancela, Leonor
Abstract Background Fish has been deemed suitable to study the complex mechanisms of vertebrate skeletogenesis and gilthead seabream (Sparus aurata), a marine teleost with acellular bone, has been successfully used in recent years to study the function and regulation of bone and cartilage related genes during development and in adult animals. Tools recently developed for gilthead seabream, e.g. mineralogenic cell lines and a 4 × 44K Agilent oligo-array, were used to identify molecular determinants of in vitro mineralization and genes involved in anti-mineralogenic action of vanadate. Results Global analysis of gene expression identified 4,223 and 4,147 genes differentially expressed (fold...