Genome skimming herbarium specimens for DNA barcoding and phylogenomics

• DOI: 10.1186/s13007-018-0300-0
• Publication Date: 2018-06-05T01:26:41Z
• Authors: Chun-Xia Zeng; Peter M. Hollings...; Jing Yang; Zheng-Shan He; Zhi-Rong Zhang; De-Zhu Li; Jun-Bo Yang
• Keywords: Herbarium; Sanger sequencing; Phylogenomics; DNA Barcoding

The world's herbaria contain millions of specimens, collected and named by thousands researchers, over hundreds years. However, this treasure has remained largely inaccessible to genetic studies, because both generally limited success DNA extraction the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing world, opportunities prospects for historical have changed dramatically, as most NGS methods are actually designed taking short fragmented molecules templates. As a practical test routine recovery rDNA plastid genome sequences from herbarium we sequenced 25 specimens up 80 years old 16 different Angiosperm families. Paired-end reads were generated, yielding successful assemblies 23 species nuclear rDNAs 24 species, respectively. These data showed that skimming can be used generate genomic information using little 500 pg starting plastome is feasible cost-effective (compare Sanger or plastome-enrichment approaches), performed sample destruction.