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

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract 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.

Authors 8

1. Yannick Woudstra corresponding

   Netherlands Institute of Ecology

   Affiliation as printed

   Netherlands Institute of Ecology, Department for Terrestrial Ecology;

2. Anne‐Sophie Quatela

   Stockholm University · Science for Life Laboratory

   Affiliation as printed

   Stockholm University, Department for Ecology, Environment and Plant Sciences, Science for Life Laboratory, Sweden;

3. Cornelis A. M. Wagemaker

   Radboud University Nijmegen

   Affiliation as printed

   Radboud University, Radboud Institute for Biological and Environmental Sciences (RIBES);

4. Slavica Ivanovic

   Netherlands Institute of Ecology

   Affiliation as printed

   Netherlands Institute of Ecology, Department for Terrestrial Ecology;

5. Tanja Slotte

   Stockholm University · Science for Life Laboratory

   Affiliation as printed

   Stockholm University, Department for Ecology, Environment and Plant Sciences, Science for Life Laboratory, Sweden;

6. Patrick G. Meirmans

   University of Amsterdam

   Affiliation as printed

   University of Amsterdam (UvA), Institute for Biodiversity and Ecosystem Dynamics (IBED);

7. Barbara Gravendeel Aachen Hortus Botanicus Leiden

   Leiden University

   Affiliation as printed

   Hortus Botanicus Leiden, Leiden University

8. Koen J. F. Verhoeven

   Netherlands Institute of Ecology

   Affiliation as printed

   Netherlands Institute of Ecology, Department for Terrestrial Ecology;