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

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 trnL (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 trnL 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 trnL 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.

Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest

“…Amplicons were sequenced on an Illumina HiSeq 2000 (Illumina, San Diego, CA, USA) at the University of Oregon, quality-filtered to remove low-quality bases and putative chimeras, and clustered into operational taxonomic units at 97% sequence similarity using the program UCHIME (Edgar, 2010) in the QIIME platform . Plant community composition was determined by direct PCR (Phire Direct PCR, ThermoScientific, Waltham, MA, USA) and Sanger sequencing of the chloroplast trnL intron region (Taberlet et al, 1991(Taberlet et al, , 2007 of roots from the same soil cores collected for microbial community analysis. Root sequences were grouped by plant genera on the basis of top BLAST matches to the GenBank database (Supplementary Table 1 Table 2).…”

Long livestock farming history and human landscape shaping revealed by lake sediment DNA

“…These primers were designed using the ecoPrimers program 43 (http://www.grenoble.prabi.fr/trac/ecoPrimers). Plant DNA was amplified using universal primers (g, 5 0 -GGGCAATCCTGAG CCAA-3 0 ; and h, 5 0 -CCATTGAGTCTCTGCACCTATC-3 0 ) that targeted the P6 loop region of the chloroplast trnL (UAA) intron 44 . The length of the amplified fragment is highly variable among species and ranges from 10 to 146 bp (mean length of 45 bp).…”

DNA barcodes: Genes, genomics, and bioinformatics

“…The inability of CO1 to work as a barcode in plants (8) set off a race among botanists to find a more appropriate marker (9). A number of candidate gene regions have been suggested as possible barcodes for plants (10)(11)(12)(13)(14), but none have been widely accepted by the taxonomic community. This lack of consensus is in part due to the limitations inherent in a plastid marker relative to plant CO1, and also because a quantitative context for selecting a gene region as a barcode for plants has not been offered.…”