Hybridization ddRAD‐sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA
Open Access
- 19 April 2020
- journal article
- research article
- Published by Wiley in Molecular Ecology Resources
- Vol. 20 (5), 1228-1247
- https://doi.org/10.1111/1755-0998.13168
Abstract
Species’ responses at the genetic level are key to understanding the long‐term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high‐resolution time‐series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For non‐model species – with small or large genomes – diversity is traditionally assessed using restriction‐enzyme based sequencing. However, age‐related DNA damage and fragmentation preclude the use of this approach for ancient herbarium DNA. Here, we combine reduced representation sequencing and hybridization‐capture to overcome this challenge and efficiently compare contemporary and historical specimens. Specifically, we describe how homemade DNA baits can be produced from reduced representation libraries of fresh samples, and used to efficiently enrich historical libraries for the same fraction of the genome to produce compatible sets of sequence data from both types of material. Applying this approach to both Arabidopsis thaliana and the non‐model plant Cardamine bulbifera, we discovered polymorphisms de novo in an unbiased, reference‐free manner. We show that the recovered genetic variation recapitulates known genetic diversity in A. thaliana, and recovers geographic origin in both species and over time, independent of bait diversity. Hence, our method enables fast, cost‐efficient, large‐scale integration of contemporary and historical specimens for assessment of genome‐wide genetic trends over time, independent of genome size and presence of a reference genome.Keywords
This publication has 78 references indexed in Scilit:
- DNA analysis of an early modern human from Tianyuan Cave, ChinaProceedings of the National Academy of Sciences of the United States of America, 2013
- The Drosophila melanogaster Genetic Reference PanelNature, 2012
- Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNAScientific Reports, 2011
- Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencingNature Biotechnology, 2009
- Accurate whole human genome sequencing using reversible terminator chemistryNature, 2008
- Evolution of genes and genomes on the Drosophila phylogenyNature, 2007
- Patterns of damage in genomic DNA sequences from a NeandertalProceedings of the National Academy of Sciences of the United States of America, 2007
- PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage AnalysesAmerican Journal of Human Genetics, 2007
- Letter to the editorCytometry Part A, 2003
- Adaptive protein evolution at the Adh locus in DrosophilaNature, 1991