The Limits of Hyb-Seq for Herbarium Specimens: Impact of Preservation Techniques

Abstract

Over the past 300 years of plant collecting for herbaria, the basic method of preservation has remained remarkably consistent-a plant press with absorbent paper. However, the difficulty of drying plant specimens in the humid tropics has led to a variety of additions to this basic technique, primarily to prevent the specimens succumbing to fungal and bacterial breakdown. These additions include drying gently in tents over low fires, soaking the specimens in alcohol before pressing and, more recently, drying the specimens with forced heat from hair dryers. The process of drying is, however, known to cause breakage and damage to the plant's DNA, as well as providing time for non-plant organisms (bacteria and fungi) to multiply in the tissue, potentially "swamping" the plant specimen's own DNA. Contemporary plant collectors therefore usually collect a separate sample for DNA work, usually rapidly dried in silica gel desiccant; historical collections, however, may have been treated with alcohol and/or heat. We have recently shown that Hyb-Seq provides a reliable method for retrieving robust sequence data from even very old and degraded herbarium specimens. In this study we have used a panel of specimens preserved using a variety of methods to assess whether Hyb-Seq is capable of retrieving informative amounts of sequence data from duplicate specimens preserved using a range of specimen preservation methods. We present data on the amount and quality of DNA and of sequence data retrieved, the variation in error types between preservation techniques and the utility of the data for phylogenetic analysis.

Unraveling the Spiraling Radiation: A Phylogenomic Analysis of Neotropical Costus L

“…Our observed level of minimal capture of off-target reads has been documented in other studies (e.g. Villaverde et al, 2018;Forrest et al, 2019) and is perhaps attributable to highly efficient capture by our baits which were designed specifically for Costus. Studies that have particular interest in the plastid genome could still use similarly designed probes but increase the coverage of chloroplast regions by sequencing a mixture of captured and uncaptured libraries (Weitemier et al, 2014).…”

Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

“…Like Villaverde et al (2018), we also found that specimen age affected capture success (Figure 2), probably due to accumulated DNA damage and its effect on genomic library preparation (Der Sarkissian et al, 2015). The large variance in capture success of post-1940s specimens could be explained in terms of variability in collection, preservation, and storage techniques (Brewer et al, 2019;Forrest et al, 2019).…”

Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants

“…Initial DNA template quality has perhaps the highest impact on final quality of sequence data. A variety of existing extraction protocols account for tissue type (e.g., leaves, petioles, stems, roots), age of the specimen (recent vs. old), preservation strategy (e.g., silica vs. air dried, doused in ethanol, mercuric chloride biocide treatment), and other attributes impacting template quality and output quantity (Brewer et al., ; Forrest et al., ; Shapiro et al., ; Andermann et al., ). Plant cells can have up to three wall layers that need to be crushed prior to DNA purification.…”