Power and limitations of the chloroplast trnL(UAA) intron for plant DNA barcoding. Nucleic Acid Res 35:e14

Tuscia University, Viterbo, Latium, Italy
Nucleic Acids Research (Impact Factor: 9.11). 02/2007; 35(3):e14. DOI: 10.1093/nar/gkl938
Source: PubMed


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.

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    • "The quantity and quality of DNA was checked on nanodrop spectrophotometer (Thermo Scientific ® , USA) and on 0.8% w/v agarose gel electrophoresis, respectively. The trnL-F intergenic spacer of chloroplast genome was amplified using the primer set (forward: 5 -ggttcaagtccctctatccc-3 ; reverse: 5 -atttgaactggtgacacgag-3 ) as earlier described (Taberlet et al., 2007). The ITS1-5.8S-ITS2 region of the rDNA was amplified using the primer set (forward: 5 -tccgtaggtgaacctgcgg-3 ; reverse: 5 - tcctccgcttattgatatgc-3 ) with PCR conditions as earlier described (Korabecna et al., 2003). "
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    • "trnL loci have also been proposed for species identification. Although trnL loci provide a relatively low resolution, its primer is highly conserved and the amplification system is very robust (Taberlet et al., 2007). Furthermore, the combined use of rbcL and trnL as a two-locus cpDNA barcode has shown a high potential for identifying NW-European fern species (de Groot et al., 2011). "
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    • "For example, the P6 loop sequence in three analyzed Solanum species , differed by only one SNP, the length of the loop being the same. In the similar way, the length of the corresponding loop sequences in eight cereal species differed by not more than 5 nucleotides, with the nucleotide sequences of the loop in the Tritii cum genus and the Secale accessions being absolutely identical and a single nucleotide deletion being detected in the Zea mays accession compared to the Panicum accessions (Taberlet et al., 2007). "
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