Telling plant species apart with DNA: From barcodes to genomes

Peter M. Hollingsworth, De Zhu Li, Michelle Van Der Bank, Alex D. Twyford

Research output: Contribution to journalArticlepeer-review

210 Citations (Scopus)

Abstract

Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity—yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article,we tackle twomain topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets.

Original languageEnglish
Article number20150338
JournalPhilosophical Transactions of the Royal Society B: Biological Sciences
Volume371
Issue number1702
DOIs
Publication statusPublished - 5 Sept 2016

Keywords

  • Genome skimming
  • Hybrid baits
  • Next-generation sequencing
  • Plant DNA barcoding
  • Species discrimination

ASJC Scopus subject areas

  • General Biochemistry,Genetics and Molecular Biology
  • General Agricultural and Biological Sciences

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