Biological and growth parameters of Plotosus lineatus in the Mediterranean Sea.

This study examined the age distribution and growth characteristics of the striped eel catfish (Plotosus lineatus), which is an invasive alien species in the eastern Mediterranean. A total of 1,011 samples were collected from Iskenderun Bay (Turkey), with lengths ranging from 5.1 to 16.8 cm, predominantly comprising females (1:1.92). Age 3 represented the majority in the population (52.03%). The value of the scaling exponent "b" of the length-weight relationship was less than "3" for both sexes (females: 2.28; males: 2.26; combined: 2.27). The results for the von Bertalanffy growth parameters were observed for the combined sexes as, L∞ = 24.9934 cm, k = 0.1718 year-1, and t0 = -1.7707 years. The striped eel catfish populations in Iskenderun Bay exhibited negative allometric growth patterns and were predominantly composed of adult individuals. This study presents the dataset on the length-weight correlations, age-growth characteristics, and von Bertalanffy growth parameters of Plotosus lineatus in the Mediterranean Sea, thereby significantly contributing to comprehending the stock dynamics. It is anticipated that this study will make a significant contribution to the management of P. lineatus stocks, given its invasive nature.

First record of a Lessepsian migrant: the sea cucumber Holothuria (Theelothuria) hamata Pearson, 1913.

First record of a Lessepsian migrant: the sea cucumber Holothuria (Theelothuria) hamata Pearson, 1913. A single specimen of the Indo-West Pacific sea cucumber Holothuria (Theelothuria) hamata Pearson, 1913 has been captured in 2017 in the Mediterranean Sea, Turkey, Iskenderun Bay, at 30 m depth. This specimen is here described, and the taxonomy of the species is briefly discussed. Despite the lack of timed biogeographic evidence, we here argue that H. hamata is a Lessepsian migrant; the first in its genus and only the second holothuroid.

Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus).

Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double-digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.

Identifying Fishes through DNA Barcodes and Microarrays.

BACKGROUND: International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. METHODOLOGY/PRINCIPAL FINDINGS: This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. CONCLUSIONS/SIGNIFICANCE: Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

Systematics of Scorpaeniformes species in the Mediterranean Sea inferred from mitochondrial 16S rDNA sequence and morphological data.

Genetic and morphological divergence and phylogenetic relationships of Scorpaeniformes fish including two genera and six species, Helicolenus dactylopterus, Scorpaena maderensis, Scorpaena porcus, Scorpaena elongata, Scorpaena scrofa, Scorpaena notata, living in the Mediterranean Sea, were investigated with morphological and mitochondrial 16S rDNA sequence data. The mean nucleotide diversity was found to be 0.0792. Average sequence divergence between species of Sebastidae and Scorpaenidae was 8.4%, and 6.4%. between species of the genus Scorpaena. For congeneric comparisions, the lowest genetic divergence (0.7%) was observed between S. porcus and S. notata, and the highest divergence (10.8%) was detected between S. maderensis and S. notata. High levels of nucleotide divergence were detected between species of two families, and the maximum value was found to be 14.5% between H. dactylopterus and S. elongata. The two phylogenetic methods (NJ and MP) identified two major lineages. In the NJ tree S. elongata was the sister group to S. scrofa. S. maderensis was more divergent from these groups. Another lineage contained S. porcus and S. notata. The topology of the MP tree is similar to that of the NJ tree. The pattern and degree of morphological differentiation was not congruent with the genetic differentiation. The Euclidiean distances of morphological data revealed very high morphological divergence between the two families. The highest morphological divergence was observed between H. dactylopterus and S. porcus, and the lowest was detected between S. elongata and S. notata. The present genetic and morphological data support the present monophyletic status of the Scorpaena genus.

Levels of heavy metals in some commercial fish species captured from the Black Sea and Mediterranean coast of Turkey.

The distribution of some heavy metals in the muscle tissue of Merlangius merlangus (whiting), Mullus barbatus (red mullet), Engraulis encrasicholus (anchovy) from Black and Mediterranean Seas were studied. The highest Al (95.313 microg/g dw), Mn (1.390 microg/g dw), Zn (25.416 microg/g dw) concentration was detected in E. encrasicholus from Black Sea; the highest Li (3.200 microg/g dw) concentration was detected in E. encrasicholus from Mediterranean Sea; the highest Cd (1.685 microg/g dw) concentration was detected in M. merlangus from Mediterranean Sea; the highest Ni (1.363 microg/g dw) concentration was detected in M. merlangus from Black Sea; the highest Pb (0.727 microg/g dw) concentration was detected in M. barbatus from Black Sea and the highest Cr (1.893 microg/g dw), Fe (21.901 microg/g dw) concentration was detected in M. barbatus from Mediterranean Sea.

Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs.

BACKGROUND: EST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. While much progress has been made in catfish genomics, large-scale EST resources have been lacking. The objectives of this project were to construct primary cDNA libraries, to conduct initial EST sequencing to generate catfish EST resources, and to obtain baseline information about highly expressed genes in various catfish organs to provide a guide for the production of normalized and subtracted cDNA libraries for large-scale transcriptome analysis in catfish. RESULTS: A total of 17 cDNA libraries were constructed including 12 from channel catfish (Ictalurus punctatus) and 5 from blue catfish (I. furcatus). A total of 31,215 ESTs, with average length of 778 bp, were generated including 20,451 from the channel catfish and 10,764 from blue catfish. Cluster analysis indicated that 73% of channel catfish and 67% of blue catfish ESTs were unique within the project. Over 53% and 50% of the channel catfish and blue catfish ESTs, respectively, had significant similarities to known genes. All ESTs have been deposited in GenBank. Evaluation of the catfish EST resources demonstrated their potential for molecular marker development, comparative genome analysis, and evaluation of ancient and recent gene duplications. Subtraction of abundantly expressed genes in a variety of catfish tissues, identified here, will allow the production of low-redundancy libraries for in-depth sequencing. CONCLUSION: The sequencing of 31,215 ESTs from channel catfish and blue catfish has significantly increased the EST resources in catfish. The EST resources should provide the potential for microarray development, polymorphic marker identification, mapping, and comparative genome analysis.

Localization of germin genes and their products in developing wheat coleoptiles.

Germination is a process which characterized with nescient synthesis of genes. Among the genes synthesized during the germination of wheat embryos, germin genes, proteins and their enzymatic activity were defined. Germin is a water soluble homopentameric glycoprotein which is remarkable resistant to degradation by a broad range of proteases including pepsin. Germin proteins found to have strong oxalate oxidase activity which produces hydrogen peroxide by degrading oxalic acid. The current study, aimed to localize the germin genes, proteins and enzymatic activities in developing coleoptiles which is a rapidly growing protective tissue of leaf primordium and shoot apex. Non-radioactively labeled germin riboprobes were employed to localize germin mRNAs in situ. FITC (Fluorescein isothiocyanate) and alkaline phosphatase linked anti-germin antibodies were used to localize germin proteins under the fluorescence and light microscopy and finally germin enzymatic activity was localized by using appropriate enzyme assay. The results revealed that in coleoptiles germin genes, proteins and their enzymatic activity were predominantly associated with the cells of epidermis and vascular bundle sheath cells.