title: Telling plant species apart with DNA: from barcodes to genomes.
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 two main 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.This article is part of the themed issue 'From DNA barcodes to biomes'.
authors.affiliation: Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK p.hollingsworth@rbge.org.uk.
authors.forename: Peter M
authors.identifier: 0000-0003-0602-0654
authors.initials: PM
authors.lastname: Hollingsworth
authors.affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming, Yunnan 650201, People's Republic of China.
authors.forename: De-Zhu
authors.initials: DZ
authors.lastname: Li
authors.affiliation: Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland park, Johannesburg PO Box 524, South Africa.
authors.forename: Michelle
authors.initials: M
authors.lastname: van der Bank
authors.affiliation: Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK.
authors.forename: Alex D
authors.identifier: 0000-0002-8746-6617
authors.initials: AD
authors.lastname: Twyford
mesh_terms: D044822:Biodiversity; D058893:DNA Barcoding, Taxonomic; D018745:Genome, Plant; D010944:Plants / Q000145:classification* / Q000235:genetics
keywords: genome skimming; hybrid baits; next-generation sequencing; plant DNA barcoding; species discrimination