Abstract
Repetitive DNA has an important role in angiosperm genomes and is relevant to our understanding of genome size variation, polyploidisation and genome dynamics more broadly. Much recent work has harnessed the power of high-throughput sequencing (HTS) technologies to advance the study of repetitive DNA in flowering plants. Herbarium collections provide a useful historical perspective on genome diversity through time, but their value for the study of repetitive DNA has not yet been explored. We propose that herbarium DNA may prove as useful for studies of repetitive DNA content as it has for reconstructed organellar genomes and low-copy nuclear sequence data. Here we present a case study in the tobacco genus (Nicotiana; Solanaceae), showing that herbarium specimens can provide accurate estimates of the repetitive content of angiosperm genomes by direct comparison with recently-collected material. We show a strong correlation between the abundance of repeat clusters, e.g. different types of transposable elements and satellite DNA, in herbarium collections versus recent material for four sets of Nicotiana taxa. These results suggest that herbarium specimen genome sequencing (herbariomics) holds promise for both repeat discovery and analyses that aim to investigate the role of repetitive DNAs in genomic evolution, particularly genome size evolution and/or contributions of repeats to the regulation of gene space.
Highlights
Current developments in high-throughput sequencing (HTS) have unlocked herbarium collections that had previously been largely intractable for molecular use in most cases
Most studies that have far utilized HTS for herbarium specimen sequencing have focussed on genome skimming (Dodsworth, 2015a) for organellar genome reconstruction, in particular for assembling the plastid genome (Bakker et al, 2016; Bakker, 2017). This is due to several factors, including ease of assembly and the predominance of plastid regions in angiosperm phylogenetics
Herbarium specimens were prepared in 2005 and sampled for DNA in 2015 from the following duplicate collections housed at BM: N. heterantha (C Marks 230, N. rosulata subsp. ingulba (C Marks 182), N. cavicola (C Marks 158), and N. velutina (C Marks 175)
Summary
Current developments in high-throughput sequencing (HTS) have unlocked herbarium collections that had previously been largely intractable for molecular use in most cases. The main advantage is that these methodologies ligate adapters directly to whatever intact DNA is present in the sample, thereby creating a library of sequencable DNA fragments that does not Herbariomics and Repetitive DNA require prior amplification. These can be universally amplified in order to get an appropriate concentration to sequence, and provided this is not overdone, the distribution of fragments across the genome should represent those that were present in the original sample. High-copy DNA is present in such samples, from both the mitochondrial genome and nuclear genomes, of which the chief component is repetitive elements
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