Abstract
BackgroundThe world’s herbaria contain millions of specimens, collected and named by thousands of researchers, over hundreds of years. However, this treasure has remained largely inaccessible to genetic 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 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.ResultsAs a practical test of routine recovery of rDNA and plastid genome sequences from herbarium specimens, we sequenced 25 herbarium specimens up to 80 years old from 16 different Angiosperm families. Paired-end reads were generated, yielding successful plastid genome assemblies for 23 species and nuclear rDNAs for 24 species, respectively. These data showed that genome skimming can be used to generate genomic information from herbarium specimens as old as 80 years and using as little as 500 pg of degraded starting DNA.ConclusionsThe routine plastome sequencing from herbarium specimens is feasible and cost-effective (compare with Sanger sequencing or plastome-enrichment approaches), and can be performed with limited sample destruction.
Highlights
The world’s herbaria contain millions of specimens, collected and named by thousands of researchers, over hundreds of years
In this paper we provide a further practical test of the genome skimming methodology applied to herbarium specimens
We evaluated the success and failure rates of rDNA and plastid genome sequencing from genome skims of 25 different species from herbarium specimens, and explored the impacts of parameters such as amount of input DNA and PCR cycle numbers
Summary
The world’s herbaria contain millions of specimens, collected and named by thousands of researchers, over hundreds of years. This treasure has remained largely inaccessible to genetic studies, because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. There are approximately 3400 herbaria in the world, containing around 350 million specimens, collected over the past 400 years (http://sciweb.nybg.org/science2/indexHerbariorum.asp). These collections cover most of the world’s plant species, including many rare and endangered local endemics, and species collected from places that are currently expensive or difficult to access [1]. The millions of samples that are required for this endeavor, each needing corresponding voucher specimens and meta-data, create a strong impetus for making best-use of previously collected material
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