Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens.
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.
Biosystematics Group, Wageningen University, Wageningen, The Netherlands.
Martijn
M
Staats
Roy H J
RH
Erkens
Bart
B
van de Vossenberg
Jan J
JJ
Wieringa
Ken
K
Kraaijeveld
Benjamin
B
Stielow
József
J
Geml
James E
JE
Richardson
Freek T
FT
Bakker
D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D018070:Biological Specimen Banks; D002467:Cell Nucleus / Q000235:genetics; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D004249:DNA Damage / Q000235:genetics; D005658:Fungi / Q000235:genetics; D049750:Genome, Insect / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D005838:Genotype; D007313:Insecta / Q000235:genetics*; D009144:Museums; D010944:Plants / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D004247:DNA