RNA extraction from decaying wood for (meta)transcriptomic analyses.

@article{Adamo2017RNAEF,
  title={RNA extraction from decaying wood for (meta)transcriptomic analyses.},
  author={Martino Adamo and Samuele Voyron and Mariangela Girlanda and Roland Marmeisse},
  journal={Canadian journal of microbiology},
  year={2017},
  volume={63 10},
  pages={
          841-850
        }
}
Wood decomposition is a key step of the terrestrial carbon cycle and is of economic importance. It is essentially a microbiological process performed by fungi and to an unknown extent by bacteria. To gain access to the genes expressed by the diverse microbial communities participating in wood decay, we developed an RNA extraction protocol from this recalcitrant material rich in polysaccharides and phenolic compounds. This protocol was implemented on 22 wood samples representing as many tree… 
View on PubMed
tspace.library.utoronto.ca
1 Citations

Figures and Tables from this paper

One Citation

Citation Type

Citation Type

Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats.
TLDR
It is concluded that metabarcoding on eRNA provides original functional information on the specific roles of several taxonomic or functional groups that would not have been revealed using eDNA alone.

References

SHOWING 1-10 OF 52 REFERENCES
PCR Primers to Study the Diversity of Expressed Fungal Genes Encoding Lignocellulolytic Enzymes in Soils Using High-Throughput Sequencing
TLDR
This high-throughput sequencing approach using several degenerate primers constitutes a robust method, which allows the simultaneous characterization of the diversity of different fungal transcripts involved in plant organic matter degradation and may lead to the discovery of complex patterns in gene expression of soil fungal communities.
RNA reveals a succession of active fungi during the decay of Norway spruce logs
The Plant Cell Wall–Decomposing Machinery Underlies the Functional Diversity of Forest Fungi
TLDR
Fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota through convergent evolution and divergence among fungal decomposers.
Isolation of Fungal Cellobiohydrolase I Genes from Sporocarps and Forest Soils by PCR
TLDR
New oligonucleotide primers for fungal exocellulase genes (cellobiohydrolase, cbhI) were developed and used to isolate distinct c BhI homologues from four species of litter-decomposing basidiomycete fungi and two species of ascomycete mushrooms.
Tree species select diverse soil fungal communities expressing different sets of lignocellulolytic enzyme-encoding genes
Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils
TLDR
The phylogenetic affiliation of 12 full-length carbohydrate active enzymes showed that most of them were distantly related to sequences from known fungi, suggesting a potentially significant contribution of non-fungal eukaryotes in the actual hydrolysis of soil organic matter.
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
TLDR
Comparative analyses of 31 fungal genomes suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species.
Metatranscriptomics of Soil Eukaryotic Communities.
TLDR
This chapter describes two alternative protocols for the extraction of high-quality RNA from soil samples and explores the diversity of specific gene families explored following cDNA sequence capture using exploratory oligonucleotide probes.
A micromethod for high throughput RNA extraction in forest trees.
TLDR
This protocol was adapted to a micro-scale by modifying the classical cetyltrimethylammonium protocol developed for pine, and is suitable for applications such as real time reverse transcription polymerase chain reaction, cDNA library construction or synthesis of complex targets for microarray analysis.
Soil eukaryotic functional diversity, a metatranscriptomic approach
TLDR
To appreciate the functional diversity of communities of soil eukaryotic micro-organisms, an experimental approach based on the construction and screening of a cDNA library using polyadenylated mRNA extracted from a forest soil found that more than 180 species could be present in the soil samples studied.
...
1
2
3
4
5
...