Herbarium Genomics: Plant Archival DNA Explored

Abstract

Herbarium genomics, allowing testing of historic biological hypotheses in plant science, is a promising field mainly driven by recent advances in next-generation sequencing (NGS) technology. Herbarium collections represent an enormous botanical repository of both specimens and of phenotypic observations and locality data, of sometimes long-extinct taxa. Herbarium specimens, a large part of which stem from the nineteenth and eighteenth century, are mostly pressed and mounted and were usually heat-treated and poisoned for preservation. Whereas the presence of post-mortem damage in herbarium DNA has been found to consist of mainly genome fragmentation (single- and double-stranded breaks), damage-derived miscoding lesions appear to be highly limited or even negligible. For organelle genomes and other repetitive genomic compartments, genome skimming appears effective in retrieving sequence data from plant herbarium specimens, whereas studies addressing herbarium nuclear-encoded genes and particularly whole genomes are still in minority. High levels of herbarium genomic fragmentation possibly lead to insert sizes being smaller than Illumina read lengths applied. Using a series of 93 herbarium DNA samples, representing 10 angiosperm families, near-complete plastomes were assembled for 80% of the specimens, some of which are 146 years old. Overlapping read pairs were found to occur in roughly 80% of all read pairs obtained. After merging such overlapping pairs, the resulting fragments and their distribution can be considered to reflect the ongoing process of genome fragmentation up to the moment of DNA extraction. Fragment length distributions appear to fit gamma distributions with either many small fragments present or an increasing number of longer fragments having accumulated. These distributions appear to differ from usually observed first-order genomic degradation kinetics, possibly due to the nonrepresentative nature of genome skimming samples.