Metagenomics
8 views | +0 today
Follow
Your new post is loading...
Your new post is loading...
Rescooped by Martin Chilvers from Fungal|Oomycete Biology
Scoop.it!

Sequence diversity in the large subunit of RNA polymerase I contributes to Mefenoxam insensitivity in Phytophthora infestans

Sequence diversity in the large subunit of RNA polymerase I contributes to Mefenoxam insensitivity in Phytophthora infestans | Metagenomics | Scoop.it

Phenylamide fungicides have been widely used for the control of oomycete-incited plant diseases for over 30 years. Insensitivity to this chemical class of fungicides was recorded early in its usage history, but the precise protein(s) conditioning insensitivity has proven difficult to determine. To determine the genetic basis of insensitivity and inform strategies for cloning the gene(s) responsible, genetic crosses were established between Mefenoxam sensitive and intermediate insensitive isolates ofPhytophthora infestans, the potato late blight pathogen. F1 progeny showed the expected semi-dominant phenotypes for Mefenoxam insensitivity and suggested the involvement of multiple loci, complicating positional cloning of the gene(s) conditioning insensitivity to Mefenoxam. Instead, a candidate gene strategy was used, based on previous observations that the primary effect of phenylamide compounds was to inhibit ribosomal RNA synthesis. The subunits of RNA polymerase I (RNApolI) were sequenced from sensitive and insensitive isolates and F1 progeny. Single nucleotide polymorphisms (SNPs) specific to insensitive field isolates were identified in the gene encoding the large subunit of RNApolI. In a survey of field isolates, SNP T1145A (Y382F), showed an 86 % association with Mefenoxam insensitivity. Isolates not showing this association belonged predominantly to one P. infestans genotype. Transfer of the ‘insensitive’ allele of RPA190 to a sensitive isolate yielded transgenic lines that were insensitive to Mefenoxam. These results demonstrate that sequence variation in RPA190 contributes to insensitivity to Mefenoxam in P. infestans.


Via Alejandro Rojas
more...
No comment yet.
Rescooped by Martin Chilvers from The Plant Microbiome
Scoop.it!

PLoS One: Bioinformatic Approaches Reveal Metagenomic Characterization of Soil Microbial Community

PLoS One: Bioinformatic Approaches Reveal Metagenomic Characterization of Soil Microbial Community | Metagenomics | Scoop.it

As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment) and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.


Via Stéphane Hacquard
more...
No comment yet.
Rescooped by Martin Chilvers from Fungal|Oomycete Biology
Scoop.it!

Front. Plant Sci.: Analysis of plant microbe interactions in the era of next generation sequencing technologies (2014)

Front. Plant Sci.: Analysis of plant microbe interactions in the era of next generation sequencing technologies (2014) | Metagenomics | Scoop.it

Next generation sequencing (NGS) technologies have impressively accelerated research in biological science during the last years by enabling the production of large volumes of sequence data to a drastically lower price per base, compared to traditional sequencing methods. The recent and ongoing developments in the field allow addressing research questions in plant-microbe biology that were not conceivable just a few years ago. The present review provides an overview of NGS technologies and their usefulness for the analysis of microorganisms that live in association with plants. Possible limitations of the different sequencing systems, in particular sources of errors and bias, are critically discussed and methods are disclosed that help to overcome these shortcomings. A focus will be on the application of NGS methods in metagenomic studies, including the analysis of microbial communities by amplicon sequencing, which can be considered as a targeted metagenomic approach. Different applications of NGS technologies are exemplified by selected research articles that address the biology of the plant associated microbiota to demonstrate the worth of the new methods.

 

Claudia Knief

 


Via Nicolas Denancé, Alejandro Rojas
more...
No comment yet.