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

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

A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome

Sex chromosomes are particularly interesting regions of the genome for both molecular genetics and evolutionary studies; yet, for most species, we lack basic information, such as the gene order along the chromosome. Because they lack recombination, Y-linked genes cannot be mapped genetically, leaving physical mapping as the only option for establishing the extent of synteny and homology with the X chromosome. Here, we developed a novel and general method for deletion mapping of non-recombining regions by solving "the travelling salesman problem", and evaluate its accuracy using simulated datasets. Unlike the existing radiation hybrid approach, this method allows us to combine deletion mutants from different experiments and sources. We applied our method to a set of newly generated deletion mutants in the dioecious plant Silene latifolia and refined the locations of the sex-determining loci on its Y chromosome map

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 dryland soils

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 %

The intercropping cowpea-maize improves soil phosphorus availability and maize yields in an alkaline soil

Aim: This study assessed whether growing cowpea can increase phosphorus (P) availability in the rhizosphere and improve the yield of legume-cereal systems. In alkaline Mediterranean soils with P deficiency, it is assumed that legumes increase inorganic P availability.Methods: A field experiment was conducted at the Staoueli experimental station, in Algiers province, Algeria, to compare the growth, grain yield, P availability, and P uptake by plants with sole-cropped cowpea (Vigna unguiculata L. cv. Moh Ouali) and maize (Zea mays L. cv. ILT), intercropped cowpea-maize, and fallow. Results: P availability in the rhizosphere was increased in both sole cropping and intercropping systems compared with fallow. It was highest in intercropping. The increase in P availability was associated with (i) significant pH changes of the rhizosphere of cowpea in sole cropping and intercropping systems, with the rhizosphere acidification significantly higher in intercropping (−0.73 units) than in sole cropping (−0.42 units); (ii) significant increase in the rhizosphere pH of intercropped maize (+0.49 units) compared to fallow; (iii) increased soil respiration (C-CO2 from microbial and root activity) in intercropping compared with sole cropping and fallow; and (iv) higher efficiency in utilization of the rhizobial symbiosis in intercropping than in sole-cropped cowpea. Conclusion With cowpea-maize intercropping, cowpea increased the P uptake, by increasing the P availability by rhizosphere pH changes in an alkaline soil. Overall, this study showed that intercropping cowpea improved the plant biomass and grain yield of maize in this soil

Allometric equations for estimating oil palm stem biomass in the ecological context of Benin, West Africa [+ Corrigendum 2019, vol. 33, no 1, p. 315]

Key messageThe models we developed used palm stem diameter at 1.5m, stem density measured by core sampling at 1.5m, and the height of the palm to estimate palm stem biomass.AbstractAllometric equations based on non-destructive methods were developed to estimate palm stem biomass. Twenty mature palms of different ages were subject to destructive and non-destructive measurements: stem height from the collar to the bottom of the frond at the 33rd position in the crown (frond 33), dry weight, the diameter and thickness of cylindrical slices sectioned at different heights along the stem, and the dry weight of samples of stem tissue taken from the core of each slice. The densities of the stem slices obtained using the destructive method (D-true) and the non-destructive method (D-core) were linearly correlated: D-true=1.062xD(core) (R-2=0.99) independently of the height, age and genetic origin of the palm. Stem density varied with height, reaching its maximum at around 1.5m, after which it remained more or less constant to the top of the stem. Stem linear density (SLD) estimated from the product of the density and the section of the stem fell to a threshold value that remained more or less constant above 1.5m. SLD between observed slices was estimated by interpolation based on a hyperbolic model to compute the true biomass of each palm. An equation derived from the integral of the hyperbolic model was fitted to estimate palm stem biomass as a function of wood density observed by non-destructive sampling at 1.5m on the stem and of the diameter at the same height. With this equation, palm stem biomass can be estimated with an error of 5%

Determination of potential denitrification in a range of tropical topsoils using near infrared reflectance spectroscopy (NIRS)

Microbial denitrification plays a central role in nitrous oxide (N2O)-emitting processes, which are involved in ecosystem services such as crop production and climate regulation. Field characterization of N2O-emitting processes being time-consuming due to great variability, laboratory determination of potential denitrification (upon incubation) is often used as a valuable test. Near infrared reflectance spectroscopy (NIRS) is a time- and cost-effective approach that has been reported to allow accurate determination of several soil properties. The objective of the present study was to assess the interest of NIRS for determining potential denitrification over a set of 460 topsoils sampled under crops, tree plantations, savanna or rainforest, originating from Madagascar, Congo-Brazzaville, Brazil, and French Guiana. Prediction of potential denitrification using NIRS was satisfying over the total set, especially with LOCAL calibration, which builds a model for each sample separately using its spectral neighbours in the calibration subset (R-2=0.79 for validation). For the other sets, either textural or geographical, global calibration only was performed, involving for each set a unique prediction model built with all calibration samples. The accuracy of NIRS determination depended on the sample set, decreasing in the following order: Malagasy clayey set > total set approximate to. Brazilian sandy loam set > coarse-textured set (Congo-Brazil) approximate to Guianese sandy clay loam set approximate to Congolese sandy set > non-clayey set (Congo-Brazil-Guiana), with cross-validation R-2 ranging from 0.88 to 0.44 (external validation was not carried out for small-sized sets). Thus NIRS prediction was more accurate over the clayey homogeneous set than over the non-clayey heterogeneous set. As a result of global calibration, potential denitrification was expressed as a linear combination of absorbance at every wavelength. Wavelengths that contributed most to NIRS prediction of soil potential denitrification corresponded to wavelengths that literature has assigned to organic nitrogenous compounds, amide-containing ones especially, and to carbonaceous compounds such as cellulose or including CH3 or CH2 groups. This related to the importance of amides in soil organic nitrogen and microbial biomass, and to the dependence of denitrification on soil organic matter. In short, NIRS is a time- and cost-effective approach that proved relevant for determining soil potential denitrification with acceptable accuracy, especially for clayey samples or when LOCAL calibration was performed