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

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

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

Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia

Background: Silene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes. Results: Here we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of similar to 70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30 % of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome. Conclusions: Our BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30 %, higher than previous estimates of 10-20 %

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

Erodibility of Mediterranean calcareous soils: relevant aggregate stability methods and significant soil variables

Correspondence: Y. Le Bissonnais. E-mail: [email protected] extension of viticulture on hill slopes in the Mediterranean basin might be responsible for a loss of organic carbon from the soil, as a result of increasing runoff and erosion. The loss of C makes soil aggregates less stable, which in turn increases erosion risk. We should use indicators of these risks and so be able to identify the most threatened areas. We first tested four widely used methods for determining aggregate stability for their ability to predict runoff and erosion; all include slaking and give indices such as rates of stable (>200 micro m) macro-aggregates (MA200) or mean weight diameter (MWD). We selected three Mediterranean vineyards characterized by brown calcareous soils and on which we had previously studied the effects of simulated rainfall. The tests were made on the soils from five farming situations, corresponding to 14 simulated rainfalls with an intensity of 60 mm hour-1. The two indices that best predict erosion are those resulting from the method of Le Bissonnais (MWD in its logarithmic form and MA200). Then, we analysed the relations between aggregate stability and soil properties on 68 soil samples from various locations within the three selected sites. A very significant correlation between the two indices of Le Bissonnais's method and soil organic carbon content was found and we propose a pedotransfer function linking these indices to soil characteristics. The results stress the need for farming practices that preserve the organic C in Mediterranean vineyard soils in order to reduce erosion risks. We believe that our findings might well apply to similar soils elsewhere in the world

Effet de la gestion des feuilles d'élagage du palmier à huile sur le stock de carbone et les propriétés physico-chimiques du sol dans les palmeraies villageoises du Bénin

Effect of management of pruned fronds of oil palm on soil carbon stock and soil physico-chemical properties in Beninese smallholder plantations. Description of the subject. In Benin, oil palm plantations are widely managed by smallholder farmers. The study addresses the impact on soil properties of the recycling of pruned fronds from these trees. Objectives. The study aims to assess the effect of two modes of management of pruned fronds on the carbon stock and physico-chemical properties of soil. Method. Six oil palm plantations were selected to represent two age classes (7-12 years and 13-24 years) in southeastern Benin. They were used to compare the soil properties of two areas: the areas of total recycling of pruned fronds (TR) and the areas of no recycling of the fronds (NR), which represented the control. In each plantation, soil samples were collected under the two treatments, from holes of up to 50 cm depth, near six oil palm trees. The soil properties were determined using conventional laboratory methods and near-infrared spectroscopy method. Results. Carbon and nitrogen stocks under TR of adult plantations were 58 Mg·ha-1 and 4.3 Mg·ha-1, respectively, and were significantly higher than the stocks in all other treatments (34.6 Mg C·ha-1 and 2.9 Mg N·ha-1). Recycling of pruned fronds improved soil fertility at a depth of up to 20 cm in the adult plantations. The porosity and bulk density of the soil were also improved. Conclusions. The management of the pruned fronds in the smallholders' oil palm plantations modified the soil properties, which were significantly improved in the top soil after 10 years of frond recycling

Cropping systems, carbon sequestration and erosion in Brazil, a review

Soils represent a large carbon pool, approximately 1500 Gt, which is equivalent to almost three times the quantity stored in terrestrial biomass and twice the amount stored in the atmosphere. Any modification of land use or land management can induce variations in soil carbon stocks, even in agricultural systems that are perceived to be in a steady state. Tillage practices often induce soil aerobic conditions that are favourable to microbial activity and may lead to a degradation of soil structure. As a result, mineralisation of soil organic matter increases in the long term. The adoption of no-tillage systems and the maintenance of a permanent vegetation cover using Direct seeding Mulch-based Cropping system or DMC, may increase carbon levels in the topsoil. In Brazil, no-tillage practices (mainly DMC), were introduced approximately 30 years ago in the south in the Parana state, primarily as a means of reducing erosion. Subsequently, research has begun to study the management of the crop waste products and their effects on soil fertility, either in terms of phosphorus management, as a means of controlling soil acidity, or determining how manures can be applied in a more localised manner. The spread of no-till in Brazil has involved a large amount of extension work. The area under no-tillage is still increasing in the centre and north of the country and currently occupies ca. 20 million hectares, covering a diversity of environmental conditions, cropping systems and management practices. Most studies of Brazilian soils give rates of carbon storage in the top 40 cm of the soil of 0.4 to 1.7 t C ha(-1) per year, with the highest rates in the Cerrado region. However, caution must be taken when analysing DMC systems in terms of carbon sequestration. Comparisons should include changes in trace gas fluxes and should not be limited to a consideration of carbon storage in the soil alone if the full implications for global warming are to be assessed