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.
Highlights
As genomic studies are becoming more ‘horizontal’ by comparing genome data from different species, including close relatives of model organisms, the need for well-described and databased tissue collections will increase
Total DNA yields extracted from herbarium specimens ranged between 2400 and 45000 ng (Table 1) and the DNA was typically highly degraded with DNA fragment sizes mostly below 1kb (Figure S1)
We have demonstrated that genome-scale sequences can be generated efficiently and accurately from a wide variety of dry-preserved plant (Arabidopsis thaliana, Laburnum anagyroides, Liriodendron tulipifera), fungal (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) and insect (Anoplophora glabripennis, Aedes albopictus, Ceratitis capitata) specimens from historical collections using a standard multiplex and paired-end Illumina HiSeq 2000 sequencing procedure
Summary
As genomic studies are becoming more ‘horizontal’ by comparing genome data from different species, including close relatives of model organisms, the need for well-described and databased tissue collections will increase. Natural history collections around the world contain an immense number of expert-verified specimens that can contribute invaluable insights to the geographical distribution, phenotypic variation and taxonomy of virtually all known plant, fungal and insect species. The use of such collections is relevant for species that are becoming extinct or increasingly rare (or rather invasive). Lowcopy nuclear genomic sequences have always remained significantly more difficult to obtain from historical DNA Their acquisition is highly desirable, as they will allow historical specimens to be included in genome-scale evolutionary, domestication and population genomic analyses [12,13,14]. Considerable effort has been spent on optimizing DNA extraction protocols and, in general, fragments shorter than 300 bp can be extracted from a broad range of historical specimens [15,17,18]
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