A simple and effective method for high quality co-extraction of genomic DNA and total RNA from low biomass Ectocarpus siliculosus, the model brown alga.

PLoS One

Department of Biology, Ecology and Earth Sciences, Laboratory of Plant Cyto-physiology, University of Calabria, Arcavacata di Rende (Cosenza), Italy.

Published: December 2015

AI Article Synopsis

  • The study focuses on Ectocarpus siliculosus, a brown seaweed that's used as a model species in scientific research due to its wide distribution and variety of strains.
  • A novel method is proposed for efficiently extracting high-quality DNA and RNA from various strains of the seaweed while overcoming challenges posed by harmful secondary metabolites.
  • This method allows for small biomass samples to yield sufficient nucleic acids for various applications, confirming its effectiveness through tests that ensure high quality and successful results in PCR-related projects.

Article Abstract

The brown seaweed Ectocarpus siliculosus is an emerging model species distributed worldwide in temperate coastal ecosystems. Over 1500 strains of E. siliculosus are available in culture from a broad range of geographic locations and ecological niches. To elucidate the molecular mechanisms underlying its capacity to cope with different environmental and biotic stressors, genomic and transcriptomic studies are necessary; this requires the co-isolation of genomic DNA and total RNA. In brown algae, extraction of nucleic acids is hindered by high concentrations of secondary metabolites that co-precipitate with nucleic acids. Here, we propose a reliable, rapid and cost-effective procedure for the co-isolation of high-quality nucleic acids using small quantities of biomass (25-, 50- and 100 mg) from strains of E. siliculosus (RHO12; LIA4A; EC524 and REP10-11) isolated from sites with different environmental conditions. The procedure employs a high pH extraction buffer (pH 9.5) which contains 100 mM Tris-HCl and 150 mM NaCl, with the addition of 5 mM DTT and 1% sarkosyl to ensure maximum solubility of nucleic acids, effective inhibition of nuclease activity and removal of interfering contaminants (e.g. polysaccharides, polyphenols). The use of sodium acetate together with isopropanol shortened precipitation time and enhanced the yields of DNA/RNA. A phenol:chlorophorm:isoamyl alcohol step was subsequently used to purify the nucleic acids. The present protocol produces high yields of nucleic acids from only 25 mg of fresh algal biomass (0.195 and 0.284 µg mg(-1) fresh weigh of RNA and DNA, respectively) and the high quality of the extracted nucleic acids was confirmed through spectrophotometric and electrophoretic analyses. The isolated RNA can be used directly in downstream applications such as RT-PCR and the genomic DNA was suitable for PCR, producing reliable restriction enzyme digestion patterns. Co-isolation of DNA/RNA from different strains indicates that this method is likely to have wider applications for intra- and inter-specific studies on other brown algae.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035266PMC
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096470PLOS

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