Search results for "Sequencing"

Recherche d'indicateurs de la résistance des sols aux maladies d'origine tellurique

2014

Characterisation of rye-grass (Lolium sp.) transcriptome-wide response to ALS-inhibiting herbicides

2014

International audience; Non-target-site-resistance (NTSR) to herbicides is a major cause for failure in the chemical control of a number of weeds, and is especially widespread and important in grass weeds. Although several gene families have been shown to be involved in NTSR (cytochromes p450, glutathione-S-transferases, glycosyl-transferases, ABC transporters, esterases…), the genetic determinants of NTSR are still poorly known to date. NTSR is part of the response of weeds to herbicides. To unravel NTSR, it is thus of interest to firstly characterise the processes involved in herbicide stress response in grasses. For this purpose, we implemented a comparative whole-transcriptome sequencin…

Responses of soil bacterial and fungal communities to extreme soil drought and rewetting

2013

Question: The patterns of resource allocation and activity of the soil microbial community over the dry summer in Mediterranean grasslands are still largely unknown. The microbial response to summer desiccation reflects adaptation strategies, setting the stage for a large rainfall-induced soil CO2 pulse upon rewetting, an important component of the ecosystem carbon budget. Methods: In three California annual grasslands, the present (DNA-based) and potentially active (RNA-based) soil bacterial and fungal communities were tracked over a summer season and in response to controlled rewetting of intact soil cores. Phylogenetic marker genes for bacterial (16S) and fungal (28S) RNA and DNA were se…

Genetic diversity of Tuber aestivum / uncinatum

2012

SPE IPM CT2 (vu VM)SPEIPMCT2 (vu VM); Tuber aestivum and Tuber uncinatum share a complicated common history from a taxonomic point of view. Indeed, different previous studies have shown contradictory conclusions. For some authors, Tuber aestivum and Tuber uncinatum are a single species and for others, they are two different species. In another study, we used 9 molecular markers: ITS1, ITS2, nuSSU, nuLSU, mtLSU, mtSSU, EF1α, β-tubulin and RPB2. The results show some genetic differences between samples for some of the analyzed sequences. However, no genetic differentiation that would support the separation of two different species was observed. We have concluded that Tuber aestivum and Tuber …

Exploiting Glomus intraradices sequencing data to dissect molecular mechanisms of plant genome control over fungal gene expression in mycorrhiza

2006

International audience

High-throughput sequencing of amplicons for monitoring yeast biodiversity in must and during alcoholic fermentation

2014

Abstract We compared pyrosequencing technology with the PCR-ITS-RFLP analysis of yeast isolates and denaturing gradient gel electrophoresis (DGGE). These methods gave divergent findings for the yeast population. DGGE was unsuitable for the quantification of biodiversity and its use for species detection was limited by the initial abundance of each species. The isolates identified by PCR-ITS-RFLP were not fully representative of the true population. For population dynamics, high-throughput sequencing technology yielded results differing in some respects from those obtained with other approaches. This study demonstrates that 454 pyrosequencing of amplicons is more relevant than other methods …

The Largest Subunit of RNA Polymerase II as a New Marker Gene to Study Assemblages of Arbuscular Mycorrhizal Fungi in the Field

2014

Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an…

Evolution of herbicide resistance in mugwort (Ambrosia artemisiifolia L.): search for genetic determinisms and application to molecular diagnosis

2022

Common ragweed (Ambrosia artemisiifolia L.), a particularly troublesome and allergenic weed, is mainly controlled in agricultural fields using ALS inhibitor herbicides. Recent cases of herbicide resistance have been reported in France and are jeopardising the efficacy of this mode of action. Both target site resistance (TSR, structural mutation in ALS gene) and non target site resistance (NTSR, regulatory and/or structural mutations in secondary metabolism) are involved. The fundamental aim of this work was to identify the genetic determinisms of resistance to ALS inhibitors that have evolved in common ragweed populations in France. As an applied objective, this work also aimed to prepare t…

Defining gut mycobiota for wild animals: a need for caution in assigning authentic resident fungal taxa

2021

Animal gut mycobiota, the community of fungi that reside within the gastrointestinal tract, make an important contribution to host health. Accordingly, there is an emerging interest to quantify the gut mycobiota of wild animals. However, many studies of wild animal gut mycobiota do not distinguish between the fungi that likely can reside within animal gastrointestinal tracts from the fungal taxa that are non-residents, such as macrofungi, lichens or plant symbionts/pathogens that can be ingested as part of the host’s diet. Confounding the non-resident and resident gut fungi may obscure attempts to identify processes associated with the authentic, resident gut mycobiota per se. To redress th…

Complete Genome Sequence of a New Ruminococcaceae Bacterium Isolated from Anaerobic Biomass Hydrolysis

2018

ABSTRACT A new Ruminococcaceae bacterium, strain HV4-5-B5C, participating in the anaerobic digestion of grass, was isolated from a mesophilic two-stage laboratory-scale leach bed biogas system. The draft annotated genome sequence presented in this study and 16S rRNA gene sequence analysis indicated the affiliation of HV4-5-B5C with the family Ruminococcaceae outside recently described genera.