title: Metatranscriptomics of Soil Eukaryotic Communities.
abstract: 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.
authors.affiliation: Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université Lyon 1, Université de Lyon, 43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France.
authors.forename: Rajiv K
authors.initials: RK
authors.lastname: Yadav
authors.affiliation: Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université Lyon 1, Université de Lyon, 43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France.|Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli 25, 10125, Turin, Italy.
authors.forename: Claudia
authors.initials: C
authors.lastname: Bragalini
authors.affiliation: Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université Lyon 1, Université de Lyon, 43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France.
authors.forename: Laurence
authors.initials: L
authors.lastname: Fraissinet-Tachet
authors.affiliation: Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université Lyon 1, Université de Lyon, 43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France.
authors.forename: Roland
authors.initials: R
authors.lastname: Marmeisse
authors.affiliation: Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université Lyon 1, Université de Lyon, 43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France. patricia.luis@univ-lyon1.fr.
authors.forename: Patricia
authors.initials: P
authors.lastname: Luis
mesh_terms: D003001:Cloning, Molecular; D056890:Eukaryota / Q000235:genetics* / Q000302:isolation & purification; D020869:Gene Expression Profiling; D015723:Gene Library; D014644:Genetic Variation; D056186:Metagenomics / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012987:Soil
chemical_list: D012333:RNA, Messenger; D012987:Soil
keywords: Environmental RNA; Metatranscriptomics; Sequence capture; cDNA libraries; cDNA size fractionation; cDNA synthesis