An efficient and effective RNA extraction protocol for ferns

• Published in: Applications in plant sciences Vol. 12; no. 6; pp. e11617 - n/a
• Main Authors: Pelosi, Jessie A., Davenport, Ruth, Barbazuk, W. Brad, Sessa, Emily B., Kuo, Li‐Yaung
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.11.2024; John Wiley and Sons Inc; Wiley
• Subjects: absorbance; Acids; Cell walls; Cetyltrimethylammonium bromide; cetyltrimetylammonium bromide (CTAB); Detergents; Ferns; ferns and fern allies; Gene expression; genes; genomics; Metabolites; Nitrogen; Optical density; Phylogeny; Polyphenols; Protocol; Protocol Note; Ratios; Ribonucleic acid; RNA; RNA extraction; secondary compounds; United States > US; Germany; California; secondary compounds; RNA extraction; cetyltrimetylammonium bromide (CTAB); ferns
• ISSN: 2168-0450; 2168-0450
• DOI: 10.1002/aps3.11617

Premise The extraction of high‐quality RNA is the critical first step for the analysis of gene expression and gene space. This remains particularly challenging in plants, and especially in ferns, where the disruption of the cell wall and separation of organic compounds from nucleic acids is not trivial. Methods We developed a cetyltrimethylammonium bromide (CTAB)‐based RNA extraction protocol that consistently performs well across a large phylogenetic breadth of ferns—a lineage of plants high in secondary compounds—and in an array of tissue types. Two alternative options (precipitation vs. clean‐up without intermediate precipitation) are presented, both of which yield high‐quality RNA extracts with optical density (OD) ratios of OD 260/280 = 1.9–2.1 and OD 260/230 > 1.6, and RNA integrity numbers >7. Conclusions This study presents an efficient protocol for the extraction of high‐quality RNA from multiple tissues and across the fern phylogeny, a clade of plants that still lags behind other major lineages in the development of genomic resources. We hope that this method can be used to help facilitate the closing of this gap.