Metatranscriptomics of Soil Eukaryotic Communities
Functions expressed by eukaryotic organisms in soil can be specifically studied by analyzing the pool of eukaryotic-specific polyadenylated mRNA directly extracted from environmental samples. In this chapter, we describe two alternative protocols for the extraction of high-quality RNA from soil samples. Total soil RNA or mRNA can be converted to cDNA for direct high-throughput sequencing. Polyadenylated mRNA-derived full-length cDNAs can also be cloned in expression plasmid vectors to constitute soil cDNA libraries, which can be subsequently screened for functional gene categories. Alternatively, the diversity of specific gene families can also be explored following cDNA sequence capture using exploratory oligonucleotide probes.
Key wordsMetatranscriptomics Environmental RNA cDNA synthesis cDNA size fractionation cDNA libraries Sequence capture
Work on metatranscriptomics of soil eukaryotic microbial communities was supported by the CNRS (program INSU ECCO Microbien), the Agence Nationale de la Recherche (projects 06-BLAN-0088, 06-443-BDIV-006 and 09-GENM-033-001), INRA métaprogramme M2E and the Indo-French Centre for the Promotion of Advanced Research, grant 4709-1.
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