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Updated: Aug 14, 2026

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
Published on: March 8, 2018
Protocol for optimized methylation context-sensitive enzyme ddRAD library preparation from partially degraded genomic
César Herrero-González1, Sylvia Sagen Johnsen2, Rómulo Sacramento Sobral2
1Department of Plant Sciences, Norwegian University of Life Sciences (NMBU), Ås 1433, Norway; Natural History Museum, University of Oslo, Research Group Evolution, eDNA, Genomics and Ethnobotany, 0562 Oslo, Norway.
None:
Here, we present an optimized methylation context-sensitive enzyme ddRAD (MCSeEd) library-preparation protocol for methylation analysis in CG, CHG, and CHH sequence contexts from plant samples that yield low-quality or partially degraded genomic DNA. We describe steps for quadruple restriction-enzyme digestion and adapter ligation, double size selection, freeze-and-squeeze gel purification, and bead-based cleanup. We then detail a two-step PCR enrichment procedure to generate Illumina-compatible epigenomic libraries.

