A basic ddRADseq two-enzyme protocol performs well with herbarium and silica-dried tissues across four genera.

Area of Science:

• Genomics
• Molecular Biology
• Botany

Background:

• Herbarium specimens offer extensive taxonomic and geographic data.
• Genome-scale sequencing from historical samples is challenging but valuable.
• Double-digest restriction site-associated DNA sequencing (ddRADseq) is a method for genome-wide data generation.

Purpose of the Study:

• To evaluate the utility of a basic ddRADseq protocol for DNA extracted from herbarium specimens.
• To assess the impact of DNA degradation, taxon, and specimen age on ddRADseq data recovery.
• To determine if herbarium samples can be effectively used for large-scale phylogenetic studies.

Main Methods:

• DNA was extracted from four genera (Draba, Boechera, Solidago, Ilex) preserved as silica-dried and herbarium tissues.
• A basic double-digest restriction site-associated DNA sequencing (ddRADseq) protocol was applied to the extracted DNAs.
• Data recovery was analyzed in relation to DNA degradation, taxon, and specimen age.

Main Results:

• Phylogenetically informative data sets were successfully obtained from most herbarium samples.
• Taxon, preservation method, and specimen age influenced the amount of data recovered.
• Despite variations, the ddRADseq protocol proved effective for herbarium-derived DNA.

Conclusions:

• Herbarium specimens are a viable source for ddRADseq-based genomic studies.
• Specimen age can serve as a preliminary indicator for sample suitability in ddRADseq projects.
• The provided protocol facilitates cost-effective, fieldwork-independent ddRADseq studies using herbarium collections.