Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding

TLDR

DNA barcoding aims to rapidly and accurately identify species using a standardized DNA region. The study assessed the resolution of the full chloroplast trnL (UAA) intron and its shorter P6 loop fragment, amplified with conserved primers, using GenBank and newly generated sequences. The full intron resolves only about 67 % of species and the P6 loop about 19 %, yet both outperform alternative markers and perform better in specific ecosystems or common foods; their highly conserved primers and robust amplification—including degraded samples—make them useful for food industry, forensic science, diet analyses, and ancient DNA studies.

Abstract

DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. Based on sequences available in GenBank and sequences produced for this study, we evaluated the resolution power of the whole chloroplast trn L (UAA) intron (254–767 bp) and of a shorter fragment of this intron (the P6 loop, 10–143 bp) amplified with highly conserved primers. The main limitation of the whole trn L intron for DNA barcoding remains its relatively low resolution (67.3% of the species from GenBank unambiguously identified). The resolution of the P6 loop is lower (19.5% identified) but remains higher than those of existing alternative systems. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. Despite the relatively low resolution, the whole trn L intron and its P6 loop have many advantages: the primers are highly conserved, and the amplification system is very robust. The P6 loop can even be amplified when using highly degraded DNA from processed food or from permafrost samples, and has the potential to be extensively used in food industry, in forensic science, in diet analyses based on feces and in ancient DNA studies.