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Genome skimming herbarium specimens for DNA barcoding and phylogenomics
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Genome skimming herbarium specimens for DNA barcoding and phylogenomics
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Journal Article
Genome skimming herbarium specimens for DNA barcoding and phylogenomics
2018
Overview
Background
The 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.
Results
As 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.
Conclusions
The 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.
Publisher
BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
Subject
/ Biomedical and Life Sciences
/ DNA
/ Endangered & extinct species
/ Genes
/ Genomes
/ Genomics
/ Herbaria
/ high-throughput nucleotide sequencing
/ Methods
/ Museums
/ Oleaceae
/ rDNA
/ Skimming
/ Studies
/ Success
