Major submissions tool developments at the European nucleotide archive

The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena), Europe's primary nucleotide sequence resource, captures and presents globally comprehensive nucleic acid sequence and associated information. Covering the spectrum from raw data to assembled and functionally annotated genomes, the ENA has witnessed a dramatic growth resulting from advances in sequencing technology and ever broadening application of the methodology. During 2011, we have continued to operate and extend the broad range of ENA services. In particular, we have released major new functionality in our interactive web submission system, Webin, through developments in template-based submissions for annotated sequences and support for raw next-generation sequence read submissions

Genomic Diversity in Two Related Plant Species with and without Sex Chromosomes - Silene latifolia and S. vulgaris

Genome size evolution is a complex process influenced by polyploidization, satellite DNA accumulation, and expansion of retroelements. How this process could be affected by different reproductive strategies is still poorly understood.We analyzed differences in the number and distribution of major repetitive DNA elements in two closely related species, Silene latifolia and S. vulgaris. Both species are diploid and possess the same chromosome number (2n = 24), but differ in their genome size and mode of reproduction. The dioecious S. latifolia (1C = 2.70 pg DNA) possesses sex chromosomes and its genome is 2.5× larger than that of the gynodioecious S. vulgaris (1C = 1.13 pg DNA), which does not possess sex chromosomes. We discovered that the genome of S. latifolia is larger mainly due to the expansion of Ogre retrotransposons. Surprisingly, the centromeric STAR-C and TR1 tandem repeats were found to be more abundant in S. vulgaris, the species with the smaller genome. We further examined the distribution of major repetitive sequences in related species in the Caryophyllaceae family. The results of FISH (fluorescence in situ hybridization) on mitotic chromosomes with the Retand element indicate that large rearrangements occurred during the evolution of the Caryophyllaceae family.Our data demonstrate that the evolution of genome size in the genus Silene is accompanied by the expansion of different repetitive elements with specific patterns in the dioecious species possessing the sex chromosomes

Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia, a Plant with Young Sex Chromosomes

Evidence for dosage compensation in Silene latifolia, a plant with 10-million-year-old sex chromosomes, reveals that dosage compensation can evolve rapidly in young XY systems and is not an animal-specific phenomenon

Application of structural equation modeling for assessing relationships between organic carbon and soil properties in semiarid Mediterranean region

Restoration of atmospheric carbon in soils has principal many good effects. Arid lands cover more than 40 % of the global earth area, but only stock 16 % from the global carbon stock. It seems to be a suitable solution for this environmental issue, but still all variables controlling organic carbon in such kinds of soil, was ignored. This study aims to develop two models of organic carbon under clayey and sandy soils in semi-arid Mediterranean zones basing on physical and chemical soil properties. For establishing both models, structural equation modeling was used. For modeling organic carbon, two Tunisian soil databases composed from clayey and sandy soils made respectively, of 450 and 602 soil horizons were used. Using the two databases for all properties, the principal component analysis shows two components for clayey soil; (i) chemical properties and bulk density and (ii) physical properties. For the sandy soil it reveals two components; (i) chemical properties and (ii) physical properties. According to the derived components for each soil category, two models have been built. Structural equation modeling results show that clayey model has proved that organic carbon was controlled by chemical properties and bulk density more than physical properties and sandy model has proved that organic carbon was controlled by chemical properties more than physical properties. The root mean square errors of approximation were 0.079 and 0.050 for the clayey and sandy models, respectively. Then these two models were validated with two other databases from Tunisian dry land soils

Relationship between phosphorus status and nitrogen fixation by common beans ( Phaseolus vulgaris L.) under drip irrigation

The current study aims to examine, the response of contrasted recombinant inbred lines of common bean to the application of phosphorus, to identify the bean recombinant inbred lines which were efficient in phosphorus utilization when dependent on nitrogen fixation as a source of nitrogen. The experiment was conducted at the experimental farm of Agricultural Research Station of the Nubaria district, Behera, Egypt, during the winter seasons of 2008-2009. Three levels of mineral phosphorus fertilizers were applied (0, 45 and 90 kg ha-1 phosphorus pentoxide). Nodulation, plant growth parameters, leaf area, soil Olsen phosphorus, pH, and phosphorus and nitrogen of shoots, nodules and seeds were measured. The results have shown that the recombinant inbred lines responded positively to P application levels. The best values were observed in recombinant inbred lines 75, 83 and 34. Vegetative growth parameters were significantly enhanced by increasing levels of phosphorus. The highest level of phosphorus, i.e., 90 kg ha-1 phosphorus pentoxide gave the optimal values of growth parameters for all common bean recombinant inbred lines while control plants obtained the lowest values. An increase of Olsen-P and a decrease of soil pH were also observed with increases in phosphorus. These results led to the conclusions that phosphorus applied to Nubaria soil: (1) improved the soil fertility; (2) enhanced the ability of root nodules of common bean recombinant inbred lines to fix atmospheric nitrogen; and (3) increased the release of hydrogen by roots, thus decreasing soil pH and reducing the immobilization of phosphorus in the soil solution and transforming it into available form for the plant

Semi-quantitative evaluation of waterlogging duration using two models based on soil colour in a representative upland catchment of northern Lao PDR

Groundwater is a vital resource for rural populations in tropical areas who depend on seasonal rainfall. Groundwater is often the only source of water feeding streams, allowing them to flow throughout the dry season. The aim of this study was to evaluate two models for estimating the average duration that soil is waterlogged by shallow groundwater table. These models, based on variations in soil colour, were developed by Blavet et al (2000) from observations and measurements made in a semi-arid environment in West Africa. Therefore there is a need to evaluate whether these models are also pertinent in a mountainous context of northern Laos. Our approach consisted in comparing data obtained from field measurements (water table level, morpho-pedological features including soil colour) with predictions made by the models. This study was carried out along two transects with contrasting characteristics in terms of the landscape morphology as well as the soil hydrodynamic: the first was in an open swampy valley with convex hillslopes, the second was in a steep-banked and narrow valley with convexo-concave hillslopes. Preliminary results from our study identified relationships between soil colour and the mean rate of soil waterlogging and are a first step for developing an inexpensive and simple method to predict soil saturation in this environment

Proposal of soil indicators for spatial analysis of carbon stocks evolution

International audienceAs erosion, exacerbated by the extension of vine growing on hillslopes in Mediterranean environment, takes part in the spatial reorganization of topsoil and his carbon stock, indicators stemmed from this phenomena could be useful for studying space-time variations of carbon stocks. On the other hand, aggregate stability indexes could be useful also to define such indicators because they can be relevant in this environment inducing runoff and erosion when soils are uncovered or low plant covered. Within this framework, our objective was to test four widely used methods for aggregate stability determination, that includes slaking effects and gives indexes such as macro-aggregates rates (MA 200) or mean weight diameter (MWD). The test was performed in three French Mediterranean study sites characterized by brown calcareous soils, vineyard and the existence of previous erosion data from simulated rainfalls.Our first goal was to select the aggregate stability method which was best correlated with datas from simulated rainfalls. For that, we chose 5 farming situations, corresponding to 14 simulated rainfalls with an intensity of 60 mm/h, located on the stations of Corconne village and Pradel. Significant relationship were found between rainfall simulations data and aggregate stability indexes : the relationships are positive and linear in case of the runoff initiation variable and negative and curvilinear in case of the other runoff and soil losses variables. The 2 indexes resulting from the method of Le Bissonnais (MWD in its logarithmic form and MA 200) are the best adjusted with all these variables. The second goal was to analyze the relationship between aggregate stability and soil properties that were relatively easy to spatialize. We took complementary soil samples on various situations of the 3 selected sites ; thus, 68 soil samples were carried out on the whole. The relationships between the 2 indexes of Le Bissonnais's method and soil properties show that there is a very significant correlation with the organic carbon rate (CSOM), while the adjustments are significantly better with curvilinear regression models. The 2 indexes of Le Bissonnais's method, that give very significant correlations with simulated erosion data and CSOM which is a good indicator for the spatialization of these 2 indexes, appears to be very useful for the forecasting of the spatial evolution of carbon stocks in the studied area