Herbarium genomics: skimming and plastomics from archival specimens

Abstract

Using massive parallel sequencing, which has become known as second-generation sequencing, some of the classic roadblocks to using herbarium DNA have been overcome. For instance, no longer is the degraded nature of most herbarium DNA preventing sequencing (because of blocking effective amplification). Instead, several kilobases of genomic sequence can be obtained on a routine basis, especially from high-copy number compartments such as plastomes (chloroplast genomes). With approaches such as genomic skimming a fair coverage of repetitive genome compartments (such as plastomes) can be obtained, enabling fast assembly of associated sequences. Although assembly of complete 150+ kilobase herbarium plastomes based on skimming still needs more investment, the generation of large contigs spanning several kilo bases is straightforward. It presents an important and cost-effective boost to using herbarium DNA-sequences in phylogenetic studies at species-level and beyond. At the same time, although herbarium DNA appears to bear the signature of ancient DNA, the accuracy of the herbarium DNA sequences obtained appears to be surprisingly high, as post-mortem miscoding lesion damage in most herbarium DNA is found to be negligible.