A comparison of freezer‐stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming

Abstract

Premise: The use of DNA from herbarium specimens is an increasingly important source for evolutionary studies in plant biology, particularly in cases where species are rare or difficult to obtain. Here we compare the utility of DNA from herbarium tissues to their freezer-stored DNA counterparts via the Hawaiian Plant DNA Library. Methods: Plants collected for the Hawaiian Plant DNA Library were simultaneously accessioned as herbarium specimens at the time of collection, from 1994-2019. Paired samples were sequenced using short-read sequencing and assessed for chloroplast assembly and nuclear gene recovery. Results: Herbarium specimen-derived DNA was statistically more fragmented than freezer-stored DNA derived from fresh tissue, leading to poorer chloroplast assembly and overall lower coverage. The number of nuclear targets recovered varied mostly by total sequencing reads per library and age of specimen, but not by storage method (herbarium or long-term freezer). Although there was evidence of DNA damage in the samples, there was no evidence that it was related to the length of time in storage, whether frozen or as herbarium specimens. Discussion: DNA extracted from herbarium tissues will continue to be invaluable, despite being highly fragmented and degraded. Rare floras would benefit from both traditional herbarium storage methods and extracted DNA freezer banks.

Optimizing efficient PCR‐amplifiable DNA extraction from herbarium specimens

“…While DNA can be stable in dried plant specimens for centuries (Palmer et al, 2011), multiple studies have shown that DNA from herbarium samples tends to become fragmented over time (Särkinen et al, 2012; Krinitsina et al, 2015; Weiß et al, 2016; Shepherd, 2017; Jordon‐Thaden et al, 2020; McAssey et al, 2023). We therefore used universal plant primers with different predicted amplicon sizes to assess DNA quality based on PCR amplification success.…”

Emerging methods in botanical DNA/RNA extraction

“…Recently, researchers have moved toward storing frozen DNA samples along with typical herbarium samples. McAssey et al ( 2023 ) creatively use a data set—the Hawaiian Plant DNA Library, collected from 1994–2019—with both frozen DNA accessions and herbarium sheets to compare each storage method for use in downstream sequencing applications. A comparison of paired samples revealed that DNA obtained from herbarium specimens was significantly more fragmented than DNA stored in a freezer, and consequently produced lower‐quality chloroplast assemblies.…”

Geographical–Historical Analysis of the Herbarium Specimens Representing the Economically Important Family Amaranthaceae (Chenopodiaceae-Amaranthaceae Clade) Collected in 1821–2022 and Preserved in the Herbarium of the Jagiellonian University in Krakow

“…An important aspect is also the studies of phylogenetic relationships. Increasingly, phylogenetic analyses are based on samples collected from herbarium materials, e.g., [ 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 ], despite problems related to post-mortem DNA damage [ 23 , 24 ]. Herbaria also play an important role in research related to the distribution of plants.…”