An updated DNA barcoding tool for Aloe vera and CITES-regulated relatives

AbstractDNA barcoding has revolutionised the identification of illegally traded material of endangered species as it overcomes the lack of resolution encountered with morphological identification. Nonetheless, in recently evolved and highly diverse clades, such as the relatives of Aloe vera, the lack of interspecific sequence variation in standardised markers compromises the barcoding efficacy. We present a new DNA barcoding tool using 189 nuclear markers, optimised for aloes (Asphodelaceae, Alooideae). We built a comprehensive sequence reference dataset from taxonomically verified sources for >300 species and validated its reliability for identification using phylogenomic inference. Seven anonymised samples from verified botanical collections and ten plants seized at London Heathrow Airport were correctly identified to species level, including a critically endangered species from Madagascar. Commercially purchased samples were confirmed to be the species as advertised. An accurate, reliable DNA barcoding method for aloe identification introduces new assurance to regulatory processes for endangered plants in trade.This dataset is associated with the manuscript by Yannick Woudstra et al. (2024) entitled 'An updated DNA barcoding tool for Aloe vera and CITES-restricted relatives'It contains the following files:Alooideae target capture tool reference sequences (“Aloeref.fasta”)Accession information fileSequencing information fileExtinction risk & geographical distribution information fileR script for producing Figure 1 (of main manuscript)Data file to produce plots for Figure 1 (“IUCN_renumbered.csv”)R script for calculating genetic distances and barcoding gaps ("Barcoding-gap_calculation_Aloe-DNA-barcoding.R")Alignments used for calculating genetic distances ("Aloe_DNA-Barcoding_Alignments.tar.gz")Sample metadata file for calculating genetic distances and barcoding gaps ("Sample-Metadata.csv")Raw results of the barcoding gap analysis: top 3 closest samples for every sample ("closest_matches_with_species.csv")Raw results of the barcoding gap analysis: intraspecific distances for all 20 species that were part of the DNA barcoding exercise ("intraspecific-distances.zip"; contains 20 named .csv files, one per species).Detailed annotated results of the barcoding gap analysis ("Barcoding-gap-results.xlsx")R script for producing Figure 4 (of main manuscript; "Figure-barcoding-gaps-per-gene.R")Data file to produce Figure 4 ("gap-data-for-barplot.csv")Co-phylogeny of reference database topologies from concatenation vs. coalescent-based methodologiesPhylogeny with distribution of CITES-appendix listingsRaw sequencing data are deposited in the NCBI short read archive (SRA) consists of the following bioprojects:PRJNA1120785: Alooideae target capture design – pilot studyPRJNA1120847: Alooideae reference database (aloes) & identifications of unknown aloe materialPRJNA1122593: Alooideae reference database (non-aloes)