University of Perpignan

About: University of Perpignan is a education organization based out in Perpignan, Languedoc-Roussillon, France. It is known for research contribution in the topics: Population & Gene. The organization has 2286 authors who have published 4795 publications receiving 139589 citations.

A unified classification system for eukaryotic transposable elements

Abstract: Our knowledge of the structure and composition of genomes is rapidly progressing in pace with their sequencing. The emerging data show that a significant portion of eukaryotic genomes is composed of transposable elements (TEs). Given the abundance and diversity of TEs and the speed at which large quantities of sequence data are emerging, identification and annotation of TEs presents a significant challenge. Here we propose the first unified hierarchical classification system, designed on the basis of the transposition mechanism, sequence similarities and structural relationships, that can be easily applied by non-experts. The system and nomenclature is kept up to date at the WikiPoson web site.

A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

Abstract: The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile (“universal”) COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups. We first design a new PCR primer within the highly variable mitochondrial COI region, the “mlCOIintF” primer. We then show that this newly designed forward primer combined with the “jgHCO2198” reverse primer to target a 313 bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment. The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies.

Critical science gaps impede use of no-take fishery reserves

Abstract: As well as serving valuable biodiversity conservation roles, functioning no-take fishery reserves protect a portion of the fishery stock as insurance against future overfishing. So long as there is adequate compliance by the fishing community, it is likely that they will also sustain and even enhance fishery yields in the surrounding area. However, there are significant gaps in scientific knowledge that must be filled if no-take reserves are to be used effectively as fishery management tools. Unfortunately, these gaps are being glossed over by some uncritical advocacy. Here, we review the science, identify the most crucial gaps, and suggest ways to fill them, so that a promising management tool can help meet the growing challenges faced by coastal marine fisheries.

Reference genome sequence of the model plant Setaria

Abstract: We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

Forced regressions in a sequence stratigraphic framework; concepts, examples, and exploration significance

Abstract: Sequence stratigraphic concepts suggest that stratal geometries develop and are largely controlled by changes in relative sea level. On the shelf, lowstand deposits, which form during falls and subsequent stillstands of relative sea level, can be recognized by the presence of an unconformity at the base, the isolated and basinward position relative to the previous shoreline, and the abrupt seaward translation of shallow-water and shoreline facies into the basin across an unconformity surface. This seaward translation of facies and shoreline regression in response to relative sea level lowering is termed a "forced regression." A forced regression is independent of variations of sediment flux and is in contrast with "normal" regressions that occur in response to excess sediment flux relative to space available on the shelf (i.e., accommodation). Forced regressions commonly are associated with a zone of sedimentary bypass, subaerial exposure, and possible fluvial erosion between the newly formed and preceding shorelines. Certain shelf sands, previously interpreted as offshore or mid-shelf sand bodies, thus can be reinterpreted as stranded lowstand shorelines associated with forced regressions. This alternative interpretation has economic significance insofar as it suggests different subsurface correlations and reservoir geometries with the potential for development of new play types and enhanced recovery in o der fields. Examples of forced regression can be observed at a variety of scales and ages. Several such examples include the modern East Coulee fan delta and the Lower Cretaceous Viking Formation in Alberta, Canada, the Quaternary Rhone Delta, and the Quaternary Hudson Valley system.