Search results for "sequencing"
showing 10 items of 1087 documents
Isolation and characterization of microsatellite markers in the portunid crab Liocarcinus depurator using FIASCO and 454 next-generation sequencing
2012
The portunid crab Liocarcinus depurator is the dominant decapod crustacean present on mud bottoms of the continental shelf of the Mediterranean Sea. In order to better describe its genetic structure, a total of 11 microsatellites were isolated and tested in 28 L. depurator individuals from the Mediterranean locality of Tarragona. Initially, microsatellite isolation was carried out using the FIASCO methodology, but only 2 useful primer pairs could be designed. Given the low yield obtained, an alternative method based on 454 next-generation sequencing was assayed, which provided excellent results and from which another 9 primer pairs gave positive genotyping. All loci tested were polymorphic,…
Data from: Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika
2016
How variation in the genome translates into biological diversity and new species originate has endured as the mystery of mysteries in evolutionary biology. African cichlid fishes are prime model systems to address speciation-related questions for their remarkable taxonomic and phenotypic diversity, and the possible role of gene flow in this process. Here, we capitalize on genome sequencing and phylogenomic analyses to address the relative impacts of incomplete lineage sorting, introgression and hybrid speciation in the Neolamprologus savoryi-complex (the ‘Princess cichlids’) from Lake Tanganyika. We present a time-calibrated species tree based on whole-genome sequences and provide strong ev…
The Car Resequencing Problem with Pull-Off Tables
2011
AbstractThe car sequencing problem determines sequences of different car models launched down a mixed- model assembly line. To avoid work overloads of workforce, car sequencing restricts the maximum occurrence of labor-intensive options, e.g., a sunroof, by applying sequencing rules. We consider this problem in a resequencing context, where a given number of buffers (denoted as pull-off tables) is available for rearranging a stirred sequence. The problem is formalized and suited solution procedures are developed. A lower bound and a dominance rule are introduced which both reduce the running time of our graph approach. Finally, a real-world resequencing setting is investigated.
Next-Generation Sequencing (NGS) application to the detection of mutations endowing herbicide resistance
2014
The Next Generation Sequencing (NGS) technologies offer tremendous possibilities for accurate detection of mutations endowing resistance. Yet, their use for this purpose has not emerged in crop protection. We aim at promoting NGS use for herbicide resistance diagnosis. In an exemplary study, we describe a simple procedure for this purpose, useable by virtually any scientist and implementing freely accessible programs for the analysis of NGS data. Three PCR amplicons encompassing seven codons of the ALS gene that are crucial for herbicide resistance were sequenced using non-quantified pools of crude DNA extracts from 40 plants in each of 28 field populations of two species of barnyard-grass:…
Des chercheurs INRAE traquent les mutations de résistance aux herbicides à l’aide du séquençage à très haut débit. Newsletter SPE (Département INRAE …
2021
Les inhibiteurs de l’ALS en échec face à l’ambroisie à feuilles d’armoiseEn France, la résistance aux herbicides inhibiteurs de l’acétolactate-synthase (ALS) émerge chez l’ambroisie. Très utilisés car applicables sur la majorité des grandes cultures, ces produits phytosanitaires généralistes inhibent l’ALS, une enzyme clé des végétaux dans la synthèse d’acides aminés essentiels. Ils constituent la deuxième famille de désherbants la plus employée, et en paient le tribut : la résistance à cette classe d’herbicides a été identifiée dans plus de 160 espèces d’adventices, ou « mauvaises herbes ». Récemment rajoutée à cette liste, l’ambroisie à feuilles d’armoise (Ambrosia artemisiifolia) est une…
Deep sequencing of the human retinae reveals the expression of odorant receptors
2017
Several studies have demonstrated that the expression of odorant receptors (ORs) occurs in various tissues. These findings have served as a basis for functional studies that demonstrate the potential of ORs as drug targets for a clinical application. To the best of our knowledge, this report describes the first evaluation of the mRNA expression of ORs and the localization of OR proteins in the human retina that set a stage for subsequent functional analyses. RNA-Sequencing datasets of three individual neural retinae were generated using Next-generation sequencing and were compared to previously published but reanalyzed datasets of the peripheral and the macular human retina and to reference…
Does Intraspecific Variation in rDNA Copy Number Affect Analysis of Microbial Communities?
2021
Amplicon sequencing of partial regions of the ribosomal RNA loci (rDNA) is widely used to profile microbial communities. However, the rDNA is dynamic and can exhibit substantial interspecific and intraspecific variation in copy number in prokaryotes and, especially, in microbial eukaryotes. As change in rDNA copy number is a common response to environmental change, rDNA copy number is not necessarily a property of a species. Variation in rDNA copy number, especially the capacity for large intraspecific changes driven by external cues, complicates analyses of rDNA amplicon sequence data. We highlight the need to (i) interpret amplicon sequence data in light of possible interspecific and intr…
Cómo crear una actividad H5P de secuencia de imágenes en el Aula Virtual
2022
En este videotutorial se muestra cómo crear una actividad H5P de secuencia de imágenes (image sequencing) en el Aula Virtual (Moodle 3.11). Este trabajo forma parte del Proyecto de Innovación Docente Multimedia learning objects in moodle: Sustainable Development Goals (Ref: UV-SFPIE_PID-1640789) financiado por el Vicerrectorado de Ocupación y Programas Formativos de la Universitat de València en el curso académico 2021/2022.
Complete genome sequence of the methanogenic neotype strain Methanobacterium formicicum MF(T.).
2014
The neotype strain Methanobacterium formicicum MFT (DSM1535), a hydrogenotrophic methanogenic Archaeon, was isolated from a domestic sewage sludge digestor in Urbana (IL, USA). Here, the complete genome sequence of the methanogen is reported. The genome is 2,478,074 bp in size, featuring a GC content of 41.23%. M. formicicum MFT encodes several genes predicted to be involved in adaptation to abiotic stress such as high osmolarity. The strain MFT is of biotechnological importance since M. formicicum strains are often found in production-scale biogas plants and it is suggested as a starter culture for the anaerobic biomethanation process. (C) 2014 Elsevier B.V. All rights reserved.
Grazing intensity in subarctic tundra affects the temperature adaptation of soil microbial communities
2015
Abstract Grazing by large ungulates, such as reindeer (Rangifer tarandus L.), in subarctic tundra exerts a considerable effect on the soil microclimate. Because of higher insulation by the aboveground vegetation in light versus heavily grazed areas, soil temperatures during the growing season are considerably higher under heavy grazing. Here, we hypothesized that these grazer-induced changes in soil microclimate affect the temperature sensitivity of soil microbial activity. To test this hypothesis, we conducted soil incubations at different temperatures (4 °C, 9 °C and 14 °C) for six weeks using soils from sites with contrasting long-term grazing intensities. Microbial respiration at low te…