Universal Hyb-Seq kits capture considerable intraspecific variation: Less is more in herbarium-inclusive molecular ecology

Target capture sequencing has enhanced the study of plant evolution and molecular ecology, particularly through the access to degraded DNA from herbarium specimens. Universal "off-the-shelf" kits, such as Angiosperms-353, are cheap and readily available but are considered to expose insufficient variation below the species level, because they are designed to target highly conserved regions. However, this remains to be tested in a direct comparison with customised approaches below the species level. In this study, near-identical genotypes from both herbarium and fresh material of the common dandelion (apomictic lineages in Taraxacum officinale F.H.Wigg.) are characterised with customised and universal approaches of target capture sequencing. An RNA-bait panel was designed to capture (i) highly variable loci normally obtained with a Genotyping-by-Sequencing (GBS) approach customised for dandelions; (ii) custom selected genes with potential for environmental adaptation, likely to harbour intraspecific genetic variation; (iii) conserved exons from universal kits (Angiosperms-353; Compositae-COS). Although exons from universal kits yield considerably less intraspecific genetic variation than both customised approaches, they still provided sufficient genetic variation to discriminate between near-identical genotypes of the same apomictic lineage. Given that universal kits save time, money, and the need for genomic reference data, this approach is recommended to increase the number of samples under budgetary constraints while still capturing considerable levels of intraspecific genetic variation.