Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens

Abstract

Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22–82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4–97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2–71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well.

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

“…Most paleogenomic studies to date have focused on large vertebrates that inhabit cold or temperate areas or the close relatives of crop plants that have abundant genomic information available (Allaby et al, 2015;JaenickeDespres et al, 2003), although genome-scale sequencing approaches of herbarium material are increasingly being applied (Bakker et al, 2015;Beck and Semple, 2015;Besnard et al, 2014;Staats et al, 2013;Zedane et al, 2015). The ability to sequence herbarium specimens, which may represent the only samples available for rare, endangered, or extinct taxa, provides great promise towards understanding important issues from biogeographic history to domestication, taxonomy, and conservation.…”

“…DNA obtained from herbarium samples is highly degraded (Staats et al, 2011;Weiss et al, 2015). While its fragmented nature is well suited for the relatively short read lengths produced by second generation sequencing technologies (Knapp and Hofreiter, 2010;Staats et al, 2013), it can be difficult to work with. For example, it has been demonstrated that the decay rate in herbarium samples is about ten times faster than the rate in bones (Weiss et al, 2015), and that 96 -99% of endogenous DNA may be lost during long term tissue storage (Staats et al, 2011).…”

“…In addition, ancient material often contains DNA from environmental contaminants with genomic sequencing typically limited to low fractions of endogenous DNA. For example, in 70 year-old herbarium material, less than 5% of reads were from the target species (Staats et al, 2013). This can complicate high quality assembly of complete genomes, unless extensive sequencing is conducted to recover as much of the endogenous genome as possible.…”

“…Furthermore, mapping reads to a reference genome can be complicated by divergence between the reference and species of interest (Ruffalo et al, 2011). De novo assembly, on the other hand, can be time consuming and computationally intensive (Miller et al, 2010a), and may provide only limited success for herbarium samples (Staats et al, 2013). Comparative, reference-guided assemblers (Ratan, 2009) take an intermediate strategy, and can provide a powerful approach for taxa like the Hawaiian mints, for which no close reference sequence is available.…”

The time has come for Natural History Collections to claim co‐authorship of research articles

“…Technical barriers imposed by low-quality, degraded DNAs found in poorly dried or very old specimens have in many instances been overcome by next-generation sequencing (NGS) technologies. Consequently, an additional wealth of genetic and phylogenetic data derived from NHC became available beginning in the 2000s (Wandeler & al., 2007;Millar & al., 2008;Staats & al., 2013;Andreasen & al., 2014;Buerki & Baker, 2015;Parks & al., 2015;Suchan & al., 2016;Zedane & al., 2016;Silva & al., 2017). Other novel applications applied to NHC include, but are not limited to, isotopic and other chemical element analyses (Gritcan & al., 2016;Körner & al., 2016).…”