Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning
Microbial communities are extremely abundant and diverse on earth surface and play key role in the ecosystem functioning. Thus, although next-generation sequencing (NGS) technologies have greatly improved knowledge on microbial diversity, it is necessary to reduce the biological complexity to better understand the microorganism functions. To achieve this goal, we describe a promising approach, based on the solution hybrid selection (SHS) method for the selective enrichment in a target-specific biomarker from metagenomic and metatranscriptomic samples. The success of this method strongly depends on the determination of sensitive, specific, and explorative probes to assess the complete targeted gene repertoire. Indeed, in this method, RNA probes were used to capture large DNA or RNA fragments harboring biomarkers of interest that potentially allow to link structure and function of communities of interest.
Key wordsSolution hybrid selection Metagenomics Metatranscriptomics Microbial diversity RNA probes Next-generation sequencing
- 11.Jaziri F, Peyretaillade E, Missaoui M et al (2014) Large scale explorative oligonucleotide probe selection for thousands of genetic groups on a computing grid: application to phylogenetic probe design using a curated small subunit ribosomal RNA gene database. Sci World J. doi: 10.1155/2014/350487 Google Scholar
- 14.Parisot N, Denonfoux J, Dugat-Bony E et al (2014) Software tools for the selection of oligonucleotide probes for microarrays. In: He Z (ed) Current technology, innovations and applications. Academic, New YorkGoogle Scholar