Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

International audienceGenomic analyses of microbial populations in their natural environment remain limited by the difficulty to assemble full genomes of individual species. Consequently, the chromosome organization of microorganisms has been investigated in a few model species, but the extent to which the features described can be generalized to other taxa remains unknown. Using controlled mixes of bacterial and yeast species, we developed meta3C, a metagenomic chromosome conformation capture approach that allows characterizing individual genomes and their average organization within a mix of organisms. Not only can meta3C be applied to species already sequenced, but a single meta3C library can be used for assembling, scaffolding and characterizing the tridimensional organization of unknown genomes. By applying meta3C to a semi-complex environmental sample, we confirmed its promising potential. Overall, this first meta3C study highlights the remarkable diversity of microorganisms chromosome organization, while providing an elegant and integrated approach to metagenomic analysis

Applications of high-throughput sequencing

Although different instruments for massively parallel sequencing exist, each with their own chemistry, resolution, error types, error frequencies, throughput and costs; the principle behind them is similar: to deduce an original sequence of bases by sampling many templates. The wide array of applications derives from the biological sources and methods used to manufacture the sequencing libraries and the analytic routines employed. By using DNA as source material, a whole genome can be sequenced or, through amplification methods, a more detailed reconstruction of a specific locus can be obtained. Transcriptomes can also be studied by capturing and sequencing different types of RNA. Other capture methods such as cross-linking followed by immunoprecipitation can be used to study DNA-protein interactions. We will explore these applications and others in the following sections and explain the different analysis strategies that are used to analyze each data type