Effective application of next-generation sequencing (NGS) approaches in systematics and population genetics: case studies in Eucalyptus and Acacia
Hugh Cross A B C , Ed Biffin A B , Kor-jent van Dijk B , Andrew Lowe B and Michelle Waycott A B
+ Author Affiliations
- Author Affiliations
A State Herbarium of South Australia, Department of Environment, Water and Natural Resources, PO Box 1047, Adelaide, SA 5001, Australia.
B Environment Institute and School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia.
C Corresponding author. Present address: Norwegian Institute of Bioeconomy Research, Department of Forest Health, Postboks 115, N-1431 Aas, Norway. Email: hugh.cross@nibio.no; hughbcross@gmail.com
Australian Systematic Botany 29(3) 235-246 https://doi.org/10.1071/SB16019
Submitted: 16 April 2016 Accepted: 8 September 2016 Published: 29 November 2016
Abstract
Next-generation sequencing (NGS) provides numerous tools for population and systematic studies. These tools are a boon to researchers working with non-model and poorly characterised organisms where little or no genomic resources exist. Several techniques have been developed to subsample the genomes of multiple individuals from related populations and species, so as to discover variable regions. We describe here the use of a modified AFLPseq method that provides a rapid and cost-effective approach to screening variable gene regions (SNPs) for multiple samples. Our method provides an adaptable toolkit for multiple downstream applications, which can be scaled up or down depending on the needs of the research question and budget. Using minor modifications to the protocol, we successfully recovered variable and useful markers that were applied to three case studies examining different scales of biological organisation, namely, from within populations to phylogenetic questions at the genus level and above. The case studies on Acacia and Eucalyptus generated genomic data across multiple taxonomic hierarchies, including demonstrating the detection of Acacia pinguifolia J.M.Black individuals used in restoration and their population origins, regional phylogeography of Acacia pycnantha Benth., and SNP-marker conservatism across some 70 million years of divergence among the Myrtaceae.
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