Alexandra Leitão

An Efficient Method for Genomic DNA Extraction from Different Molluscs Species

The selection of a DNA extraction method is a critical step when subsequent analysis depends on the DNA quality and quantity. Unlike mammals, for which several capable DNA extraction methods have been developed, for molluscs the availability of optimized genomic DNA extraction protocols is clearly insufficient. Several aspects such as animal physiology, the type (e.g., adductor muscle or gills) or quantity of tissue, can explain the lack of efficiency (quality and yield) in molluscs genomic DNA extraction procedure. In an attempt to overcome these aspects, this work describes an efficient method for molluscs genomic DNA extraction that was tested in several species from different orders: Veneridae, Ostreidae, Anomiidae, Cardiidae (Bivalvia) and Muricidae (Gastropoda), with different weight sample tissues. The isolated DNA was of high molecular weight with high yield and purity, even with reduced quantities of tissue. Moreover, the genomic DNA isolated, demonstrated to be suitable for several downstream molecular techniques, such as PCR sequencing among others.

Genetic differences between wild and hatchery populations of Diplodus sargus and D. vulgaris inferred from RAPD markers: implications for production and restocking programs design

Restocking and stock enhancement programs are now recognized as an important tool for the management of fishery resources. It is important, however, to have an adequate knowledge on the genetic population structure of both the released stock and the wild population before carrying out such programs. In this study, random amplified polymorphic DNA (RAPD) markers were applied to assess genetic diversity and population structure of wild and hatchery populations of the white seabreamDiplodus sargus and the common two-banded seabreamD. vulgaris (Sparidae). The estimated values for intrapopulation genetic variation, measured using the percentage of polymorphic loci (%P), Shannon indexH’, and Nei’s gene diversity (h), showed high values for all populations. The percentage of genetic variation withinD. sargus andD. vulgaris populations, based on coefficient of gene differentiation, reached 82.5% and 90% of the total genetic variation, respectively. An undeniable decrease in genetic variation was found in both hatchery populations, particularly inD. sargus, compared to the wild ones. However, the high values of variation within all populations and the low levels of genetic variation among populations did not indicate inbreeding or depression effects, thus indicating a fairly proper hatchery management. Nevertheless, the results of this study highlight the importance of monitoring the genetic variation of hatchery populations, particularly those to be used in restocking programs. The creation of a genetic baseline database will contribute to a more efficient conservation management and to the design of genetically sustainable restocking programs.

A Microarray-Based Analysis of Gametogenesis in Two Portuguese Populations of the European Clam Ruditapes decussatus

The European clam, Ruditapes decussatus is a species with a high commercial importance in Portugal and other Southern European countries. Its production is almost exclusively based on natural recruitment, which is subject to high annual fluctuations. Increased knowledge of the natural reproductive cycle of R. decussatus and its molecular mechanisms would be particularly important in providing new highly valuable genomic information for better understanding the regulation of reproduction in this economically important aquaculture species. In this study, the transcriptomic bases of R. decussatus reproduction have been analysed using a custom oligonucleotide microarray representing 51,678 assembled contigs. Microarray analyses were performed in four gonadal maturation stages from two different Portuguese wild populations, characterized by different responses to spawning induction when used as progenitors in hatchery. A comparison between the two populations elucidated a specific pathway involved in the recognition signals and binding between the oocyte and components of the sperm plasma membrane. We suggest that this pathway can explain part of the differences in terms of spawning induction success between the two populations. In addition, sexes and reproductive stages were compared and a correlation between mRNA levels and gonadal area was investigated. The lists of differentially expressed genes revealed that sex explains most of the variance in gonadal gene expression. Additionally, genes like Foxl2, vitellogenin, condensing 2, mitotic apparatus protein p62, Cep57, sperm associated antigens 6, 16 and 17, motile sperm domain containing protein 2, sperm surface protein Sp17, sperm flagellar proteins 1 and 2 and dpy-30, were identified as being correlated with the gonad area and therefore supposedly with the number and/or the size of the gametes produced.

Insights into Molecular Features of Venerupis decussata Oocytes: A Microarray-Based Study

The production of Venerupis decussata relies on wild seed collection, which has been recently compromised due to recruitment failure and severe mortalities. To address this issue and provide an alternative source of seed, artificial spawning and larval rearing programs were developed. However, hatchery-based seed production is a relatively new industry and it is still underdeveloped. A major hurdle in the European clam seed production is the control of spawning and reproduction, which is further hindered by the impossibility of obtaining fertile gametes by gonadal “stripping”, as meiosis re-initiation is constrained to a maturation process along the genital ducts. In the present study, oocytes were collected from 15 females and microarray analyses was performed to investigate gene expression profiles characterizing released and stripped ovarian oocytes. A total of 198 differentially expressed transcripts between stripped and spawned oocytes were detected. Functional analysis carried out on these transcripts highlighted the importance of a few biological processes, which are most probably implicated in the control of oocyte competence. Significant differences were observed for transcripts encoding proteins involved in meiosis progression (e.g. dual specificity phosphatase CDC25), WNT signalling (e.g. frizzled class receptor 8, wingless-type MMTV integration site family member 4), steroid synthesis (e.g. progestin and adipoQ receptor family member 3, cytochrome P450-C17), mRNA processing (e.g. zinc finger protein XlCOF28), calcium regulation (e.g. regucalcin, calmodulin) and ceramide metabolism (ceramidase B, sphingomyelinase). This study provides new information on transcriptional profiles putatively associated with ovarian egg infertility, and suggests potential mechanisms regulating early oocyte development in clams. Genes which were differentially expressed between stripped and spawned oocytes might have a pivotal role during maturation process in the gonadal duct and could be interesting targets for further functional studies aiming to make ovarian oocytes fertilizable.

Genetic diversity of two Portuguese populations of the pullet carpet shell Venerupis senegalensis, based on RAPD markers: contribution to a sustainable restocking program

The pullet carpet shell Venerupis senegalensis (=V. pullastra) is a commercially important species in Portugal, Spain, France, and Italy. In Portugal, this species was once abundant in the Ria Formosa (southern Portugal). However, in the early 1980s, its abundance declined dramatically due to overfishing. In order to reverse this negative trend, the genetic sustainable management of the wild stocks of V. senegalensis should be performed by promoting successful restocking actions and the development of an aquaculture commercial production program of this species. In order to find the best broodstock for aquaculture purposes and therefore minimize the deleterious effects of hatchery practices, we analyzed the genetic diversity of the natural population to be restocked (Ria Formosa) but also of another potential genetically close population (Ria de Aveiro) by RAPD. Similar and substantive percentage of polymorphic loci, effective number of alleles, Nei’s gene diversity, and Shannon’s diversity index was found within both populations. This high genetic variability within populations suggests that they might have a gene pool with sufficient genetic plasticity to support changes in the environmental conditions. Analyses of population genetic structure also revealed a small genetic differentiation between the two populations. The high genetic variability of the natural population to be restocked makes it the preferential broodstock for aquaculture purposes. However, the Ria de Aveiro population could also be a viable alternative, due to its genetic plasticity and the genetic similarity of both populations. The results of this study can be useful to the sustainable management of wild stocks as well as in promoting successful restocking actions based on aquaculture production.

RESTRICTION ENZYME DIGESTION CHROMOSOME BANDING ON TWO COMMERCIALLY IMPORTANT VENERID BIVALVE SPECIES: RUDITAPES DECUSSATUS AND CERASTODERMA EDULE

Abstract Reliable banding techniques are a major necessity for the genetic research in marine bivalves. Restriction enzyme banding (HaeIII) was performed, in this study, on chromosomes of two commercially important species of veneroid bivalves: the clam Ruditapes decussatus (Adams and Reeve) and the cockle Cerastoderma edule. Identification of the nineteen individual chromosome pairs was obtained for both species. The cytogenetic studies made in marine molluscs have recently experienced a very fast development caused by the introduction of new molecular techniques mainly fluorescence in situ hybridization (FISH). Recently it has been shown in mammalian chromosomes that restriction enzyme banding is compatible with FISH, allowing simultaneous banding, and consequent accurate identification of the localization of the probes and unambiguously identification of the chromosome(s) carrier(s). As far as we know this is the first RE-banding obtained in karyotypes of veneroid species. The application of restriction enzyme chromosome banding in veneroids are diverse and this study can constitute a fundamental step for future gene mapping on this commercially important group of bivalves and could offer a new approach to specific problems in veneroid taxonomy and genetics.

Is metal contamination responsible for increasing aneuploidy levels in the Manila clam Ruditapes philippinarum

The present study assessed the metal genotoxicity potential at chromosome-level in the bivalve Ruditapes philippinarum collected along different areas of the Tagus estuary. Higher levels of aneuploidy on gill cells were detected at the most sediment contaminated area both in May (31.7%) and October (36.0%) when compared to a less contaminated area over the same periods (20.3% and 29.0% respectively). Interestingly, metal bioaccumulation in gills was higher in the specimens collected at the least contaminated area with the exception of Pb. Indeed, the multivariate analysis revealed a stronger relation between aneuploidy and sediment contamination than between aneuploidy and the bioaccumulation of the metals. The temporal and spatial inconsistency found for the bioaccumulation of metals in R. philippinarum and the positive correlation between sediment contamination and aneuploidy at the most contaminated area suggest that these chromosome-level effects might be due to chronic metal contamination occurring in the Tagus estuary, rather than a direct result of the temporal variation of bioavailable contaminants. The vertical transmission phenomenon of bivalve aneuploidy levels may then be perpetuating those levels on clams from the most contaminated area. The present results shed light about the effect of metal toxicity at the chromosome-level in species inhabiting chronic contaminated areas and highlight the use of aneuploidy as an effective tool to identify persistent contamination in worldwide transitional waters.

Sarcoma in the thymus of juvenile meagre Argyrosomus regius reared in an intensive system.

Juvenile meagre Argyrosomus regius (Asso, 1809) maintained in experimental conditions developed lateral and/or bilateral circular-shaped sarcoma within the opercular cavity. The sarcoma was dense, reddish and its growth from the branchial arch exerted pressure on the operculum forcing it to open. Histologically, the neoplasm exhibited marked proliferation of mesenchymal connective tissue composed largely of fusiform cells, which developed in a solid pattern accompanied by abundant mononuclear cell types. Multifocal areas of discrete necrosis were also observed, compatible with a sarcomatous proliferation. The immunological parameters analysed suggested an inflammatory response. No bacteria were isolated from the hematopoietic organs. However, Vibrio species, components of the normal seawater flora, were isolated from the tumour, which may have had a role in eliciting the immune response. No evidence of viral pathogens was found by electron microscopy. In order to look for cytogenetic alterations often linked to sarcomas, the diploid number and karyotype of this species were determined for the first time. An increase in the aneuploidy level was observed in sarcoma cell metaphase stages compared to other tissues. The aetiology of this tumour remains unknown.

Reproductive effort of the European clam Ruditapes decussatus (Linnaeus, 1758): influence of different diets and temperatures

Abstract Ruditapes decussatus is a species of importance to aquaculture. For hatcheries to consistently produce spat it is essential to develop broodstock conditioning techniques. Food and temperature are the main factors that regulate the timing and rate of energy storage and reproduction in bivalves. This study was designed to evaluate the effects of different diets and temperatures on reproductive output of R. decussatus and express the evolution of the different lipid classes during sexual maturation. Broodstock clams were conditioned at 20 ± 1 °C under four nutritional regimes: unfed, two mono-specific diets, Isochrysis galbana clone T-ISO and Chaetoceros calcitrans and, a mixture of these microalgae. Another group of clams was conditioned at 22 ± 1 °C and was fed the same mixture of microalgae. Gametogenesis, energy storage and spawning success were all influenced by the nutritional value of the diet received, as evidenced by the differences in reproductive effort among the single and combined supplemental diets. Temperature must be carefully managed to improve the reproductive conditioning of bivalves: high temperature throughout gametogenesis shortens the time to full ripeness but does not produce better reproductive output. The combination diet at 20 ± 1 °C is best for R. decussatus broodstock conditioning.

Geomalacus and letourneuxia (mollusca, pulmonata) : a cytogenetic assessment

The terrestrial malacofauna of the Iberian Peninsula is extremely rich and shows the highest diversity of arionid slug species in Europe (and probably worldwide), with 30 to 50 species, including several endemic ones (Castillejo, 1998). However, the taxonomic status of several of these species remains unclear due to the extreme variability in body size and color and the lack of reliable diagnostic morphological traits (Backeljau & De Bruyn, 1990). The taxonomy of terrestrial slugs is based almost entirely on the morphology of their reproductive apparatus, which varies according to developmental stage and sexual maturation, often