The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.     

Incidental captures of sea turtles by swordfish and albacore longlines in the Ionian sea

ABSTRACT:   Incidental catches in pelagic longline fishing pose a serious threat to sea turtle populations throughout the world's seas and oceans. In this work, carried out in the framework of the EC-DG-Fisheries 98/008 project, information on sea turtle catch rates from swordfish and albacore longline fishing activities observed in Italian waters off the Ionian Sea during 1999 and 2000, are reported. In addition, biometric data, health status, and tagging return rate of sea turtles captured are provided. A total of 200 sea turtles were caught (198 loggerhead turtles and 2 green turtles), comprising 0.5–15.7% of the total catch in number of individuals. The estimates of the sea turtles caught by the total fishing effort of both longlines in the whole study area were 1084 specimens in 1999 (95% CI = 667–1502) and 4447 specimens in 2000 (95% CI = 3189–5705). Although all sea turtles were released alive, nearly half of them had hooks that could not be removed and remained deeply embedded in the digestive tract.     

Assessing the impact of population decline on mating system in the overexploited Mediterranean red coral

1. Understanding the interactions among demographic parameters, mating system and population dynamics is key to predict the response of populations to global change. The Mediterranean red coral is a precious octocoral suffering from population decline due to overfishing and warming‐driven mass mortality events.
2. While the demographic consequences of these two pressures are well characterized, little is known regarding their impact on population dynamics and evolution of red coral populations. The main objective of this study was to fill this gap focusing more particularly on mating pattern and genetic drift.
3. Combining sibship and progeny arrays analyses, a genetic characterization of the red coral mating system was conducted. In addition, a synchronic approach was developed comparing mating patterns in two populations with contrasting demographic patterns: a pristine‐like population and a declining population.
4. The results show that polyandry is likely to be the norm in red coral. The similar patterns of genetic diversity between adults and larvae combined with the lack of differential reproductive success among putative fathers did not support significant sweepstakes effects during larval production. While instantaneous biparental inbreeding was detected, no long‐term inbreeding was observed even in the declining population. Mating patterns and effective population sizes in the two populations were not statistically different. Nevertheless, a trend towards a slightly higher inbreeding and a lower number of breeders was observed in the declining population.
5. Accordingly, we hypothesized that an increase in male gamete dispersal may buffer the increase of genetic drift expected in the declining population. This feedback between demographic decline and reproductive pattern may potentially take part in the long‐term persistence of red coral populations. However, the negative trend reported in the declining population unambiguously supports the need to maintain high densities of reproductive colonies to the functioning of red coral populations.

     

Complementary physical and chemical treatments as an alternative to fungicide use to control postharvest decay incidence and fruit quality of Montenegrina tangerines

Heat treatments affect the germination and development of pathogens and enhance the ability of fruits to resist infection after harvest. In the present work, the effects of heat, in combination with other alternative decay control methods, were studied on ‘Montenegrina’ tangerines along with the effects on the cuticular surface of the fruit. Different treatment combinations using hot water (60 °C), brushing, and immersion in chloride dioxide, imazalil, sodium bicarbonate, and hand-applied carnauba wax were used. The tangerines were then put in cold storage for 20 days at 5 °C and retrieved to ambient conditions for 7 more days. Fruit samples were analyzed for total soluble solids, titratable acidity, epidermal color, weight loss, and decay incidence; an analysis of fruit surface was done through scanning electron microscopy. Heat treatments significantly reduced the number of tangerines with decay symptoms and enhanced the efficacy of the tested products. Carnauba wax significantly increased the number of rotten fruits, exerting a protective effect on the fungi by covering their structure. Sodium bicarbonate in combination with heat exerted a good control on decay incidence. The heat treatments partially removed the hyphae and spores of pathogens on the surface and also melted the cuticular waxes that cover stomata and cracks, reducing possible entry points for pathogens.     

Characterizing the Saltol Quantitative Trait Locus for Salinity Tolerance in Rice

This study characterized Pokkali-derived quantitative trait loci (QTLs) for seedling stage salinity tolerance in preparation for use in marker-assisted breeding. An analysis of 100 SSR markers on 140 IR29/Pokkali recombinant inbred lines (RILs) confirmed the location of the Saltol QTL on chromosome 1 and identified additional QTLs associated with tolerance. Analysis of a series of backcross lines and near-isogenic lines (NILs) developed to better characterize the effect of the Saltol locus revealed that Saltol mainly acted to control shoot Na⁺/K⁺ homeostasis. Multiple QTLs were required to acquire a high level of tolerance. Unexpectedly, multiple Pokkali alleles at Saltol were detected within the RIL population and between backcross lines, and representative lines were compared with seven Pokkali accessions to better characterize this allelic variation. Thus, while the Saltol locus presents a complex scenario, it provides an opportunity for marker-assisted backcrossing to improve salt tolerance of popular varieties followed by targeting multiple loci through QTL pyramiding for areas with higher salt stress.     

Combined effects of dietary mannan oligosaccharides and total fish oil substitution by soybean oil on European sea bass (Dicentrarchus labrax) juvenile diets

This study evaluates the effects of dietary mannan oligosaccharides (MOS) on growth, tissue composition, fatty acid profiles and liver morphology of European sea bass (Dicentrarchus labrax) fed diets containing either soybean oil (SBO; SBOMOS) or fish oil (FO; FOMOS) as unique oil source for 8 weeks. Results showed that MOS supplementation enhanced specific growth rate, regardless of the oil source used, and that dietary oil source reduced fish length, regardless of dietary MOS supplementation. Dietary MOS favoured lipid accumulation in muscle and anterior intestine when supplemented in FO‐based diets compared to fish fed SBO diet and reduces it in liver in relation to lower hepatocyte area, particularly in fish fed SBOMOS diet. Dietary MOS favoured liver and not muscular ∑n‐3 PUFA, DHA, EPA and ARA deposition, when combined with FO but not when included in SBO‐based diets. Thus, MOS dietary supplementation favours fish performance and helps to minimize the side effects derived from high dietary SBO supplementation on liver lipid accumulation and hepatocyte vacuolization, which could be of especial interest on long‐term feeding trials; however, the effects on favoured deposition ∑n‐3 PUFA are limited to FO‐based diets.     

Effects on mortality and stress response in European sea bass, Dicentrarchus labrax (L.), fed mannan oligosaccharides (MOS) after Vibrio anguillarum exposure

The effects of dietary mannan oligosaccharides (MOS; 4 g kg^?1; Bio‐Mos, Alltech Inc, USA) in diets for European sea bass, Dicentrarchus labrax (L.), juveniles in relation to disease and stress resistance, combining intestinal infection with Vibrio anguillarum and stress challenge by confinement, were assessed in this study. After 8 weeks of MOS supplementation, fish were exposed to a pathogen challenge test against V. anguillarum by direct gut inoculation combined with a confinement stressor panel. Cumulative mortality of fish fed MOS caused by anally inoculated V. anguillarum decreased from 66% to 12.5% and from 54.1% to 25% in infected and infected + stressed fish, respectively, compared to fish fed control diet. Results for European sea bass revealed a positive effect of MOS dietary inclusion on disease resistance, in terms of cumulative mortality, against gut inoculated V. anguillarum, as well as reduced effects of stress on microbiota diversity. Both of these findings, together with the enhanced innate immune response and the higher gut mucus production and density of eosinophil granulocytes in gut mucosa obtained in previous studies after MOS supplementation ( Torrecillas et al. 2007, 2011a,b ) suggest that general reinforcement of the innate immune system, and particularly of the intestinal barrier efficiency, is the main defence mechanism of European sea bass fed MOS against pathogenic microorganisms.     

Genetic analysis of salt tolerance at seedling and reproductive stages in rice (Oryza sativa)

Salinity is a major abiotic stress that limits rice production across rice areas as high‐yielding modern rice varieties are generally sensitive to salt stress. The study was conducted to deduce heritability and combining ability estimates of rice for various morphological and physiological traits using a 7 × 7 full‐diallel‐cross analysis at seedling and reproductive stages. The salinity stress treatment was 12 dS m^?1 at the seedling stage and 8 dS m^?1 at the reproductive stage. Diallel analysis revealed high for salinity tolerance scores and shoot height, moderate for shoot dry weight and root dry weight and low for Na⁺ and K⁺ concentrations and K⁺/Na⁺ ratio. The low‐to‐moderate narrow‐sense heritability for number of panicles, number of fertile spikelets, grain weight, spikelet fertility and K⁺/Na⁺ ratio suggests a large breeding population and delayed selection for tolerance until later generations. Significant maternal effects indicate that selection of the female parent is very important for desired trait development. The results of this study confirmed that salinity tolerance at the seedling and reproductive stages is regulated by a different set of genes that could be pyramided using different donors to enhance the level of tolerance.     

Effects of water stress on irradiance acclimation of leaf traits in almond trees

Photosynthetic acclimation to highly variable local irradiance within the tree crown plays a primary role in determining tree carbon uptake. This study explores the plasticity of leaf structural and physiological traits in response to the interactive effects of ontogeny, water stress and irradiance in adult almond trees that have been subjected to three water regimes (full irrigation, deficit irrigation and rain-fed) for a 3-year period (2006-08) in a semiarid climate. Leaf structural (dry mass per unit area, N and chlorophyll content) and photosynthetic (maximum net CO(2) assimilation, A(max), maximum stomatal conductance, g(s,max), and mesophyll conductance, g(m)) traits and stem-to-leaf hydraulic conductance (K(s-l)) were determined throughout the 2008 growing season in leaves of outer south-facing (S-leaves) and inner northwest-facing (NW-leaves) shoots. Leaf plasticity was quantified by means of an exposure adjustment coefficient (ε=1-X(NW)/X(S)) for each trait (X) of S- and NW-leaves. Photosynthetic traits and K(s-l) exhibited higher irradiance-elicited plasticity (higher ε) than structural traits in all treatments, with the highest and lowest plasticity being observed in the fully irrigated and rain-fed trees, respectively. Our results suggest that water stress modulates the irradiance-elicited plasticity of almond leaves through changes in crown architecture. Such changes lead to a more even distribution of within-crown irradiance, and hence of the photosynthetic capacity, as water stress intensifies. Ontogeny drove seasonal changes only in the ε of area- and mass-based N content and mass-based chlorophyll content, while no leaf age-dependent effect was observed on ε as regards the physiological traits. Our results also indicate that the irradiance-elicited plasticity of A(max) is mainly driven by changes in leaf dry mass per unit area, in g(m) and, most likely, in the partitioning of the leaf N content.