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'.

Keywords: genome skimming; hybrid baits; next-generation sequencing; plant DNA barcoding; species discrimination.

Figure 1.

Example uses of DNA barcoding. (a) Species discovery in the bryophyte Herbertus (Herbertaceae). Image: David Genney, (b) first complete national DNA barcode database, for the flora of Wales. Image: Alex Twyford, (c) floristic barcoding of the Cape Flora. Image: Olivier Maurin, (d) DNA barcoding the flora of China. Image: De-Zhu Li, (e) pollen identification and the study of pollen movement. Image: USGS Bee Inventory and Monitoring Lab, (f) species identification of historical mixed pollen samples. Image: Dartmouth Electron Microscope Facility, (g) a stand selling plant products in Johannesburg. Image: Zandisile Shongwe, (h) confiscated illegal Encephalartos (Zamiaceae), Image: Eastern Cape Department of Economic Development, Environmental Affairs and Tourism, (i) identification of plant compounds (here extract from Ginkgo biloba) in herbal supplements. Image: Juan Carlos Lopez Almansa.

Figure 2.

Comparison between promising genomic barcodes. (a) Target enrichment focuses sequencing reads (blue arrows) on homologous regions of the genome surrounding bait sites (red dots), with many regions with high coverage (dark-grey shading). Samples missing a suitable bait site (yellow cross) are not represented in the data. Off-bait reads (pink open arrows) may be informative, particularly if they map to high-copy ribosomal DNA or organelles. (b) Genome skimming can be used to generate a fragmented nuclear assembly with low sequence coverage. Homologous sequences are a random collection of regions where assemblies overlap (grey boxes).