Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding
Pierre Taberlet, Eric Coissac, François Pompanon, Ludovic Gielly, Christian Miquel, Alice Valentini, Thierry Vermat, Gérard Corthier, Christian Brochmann, Eske Willerslev, Pierre Taberlet, Eric Coissac, François Pompanon, Ludovic Gielly, Christian Miquel, Alice Valentini, Thierry Vermat, Gérard Corthier, Christian Brochmann, Eske Willerslev
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.
Figures
References
- Floyd R., Abebe E., Papert A., Blaxter M. Molecular barcodes for soil nematode identification. Mol. Ecol. 2002;11:839–850.
- Hebert P.D.N., Cywinska A., Ball S.L., de Waard J.R. Biological identification through DNA barcodes. Proc. R. Soc. Lond., B. Biol. Sci. 2003;270:313–321.
- Hebert P.D.N., Gregory T.R. The promise of DNA barcoding for taxonomy. Syst. Biol. 2005;54:852–859.
- Chase M.W., Salamin N., Wilkinson M., Dunwell J.M., Kesanakurthi R.P., Haidar N., Savolainen V. Land plants and DNA barcodes: short-term and long-term goals. Philos. Trans. R. Soc. B Biol. Sci. 2005;360:1889–1895.
- Hebert P.D.N., Ratnasingham S., de Waard J.R. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond. B Biol. Sci. 2003;270:S96–S99.
- Kress W.J., Wurdack K.J., Zimmer E.A., Weigt L.A., Janzen D.H. Use of DNA barcodes to identify flowering plants. Proc. Natl Acad. Sci. USA. 2005;102:8369–8374.
- Vences M., Thomas M., van der Meijden A., Chiari Y., Vieites D. Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front. Zool. 2005;2:5.
- Hebert P.D.N., Penton E.H., Burns J.M., Janzen D.H., Hallwachs W. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Natl Acad. Sci. USA. 2004;101:14812–14817.
- Hebert P.D.N., Stoeckle M.Y., Zemlak T.S., Francis C.M. Identification of birds through DNA barcodes. PLoS Biol. 2004;2:e312.
- Tautz D., Arctander P., Minelli A., Thomas R.H., Vogler A.P. A plea for DNA taxonomy. Trends Ecol. Evol. 2003;18:70–74.
- Álvarez I., Wendel J.F. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 2003;29:417–434.
- Poinar H.N., Hofreiter M., Spaulding W.G., Martin P.S., Stankiewicz B.A., Bland H., Evershed R.P., Possnert G., Pääbo S. Molecular coproscopy: Dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science. 1998;281:402–406.
- Scharaschklin T., Doyle J.A. Phylogeny and historical biogeography of Anaxagorea (Annonaceae) using morphology and noncoding chloroplast sequence data. Syst. Bot. 2005;30:712–735.
- McDade L.A., Daniel T.F., Kiel C.A., Vollesen K. Phylogenetic relationships among Acantheae (Acanthaceae): major lineages present contrasting patterns of molecular evolution and morphological differentiation. Syst. Bot. 2005;30:834–862.
- Chen S.Y., Xia T., Wang Y.J., Liu J.Q., Chen S.L. Molecular systematics and biogeography of Crawfurdia, Metagentiana and Tripterospermum (Gentianaceae) based on nuclear ribosomal and plastid DNA sequences. Ann. Bot. 2005;96:413–424.
- Ronning S.B., Rudi K., Berdal K.G., Holst-Jensen A. Differentiation of important and closely related cereal plant species (Poaceae) in food by hybridization to an oligonucleotide array. J. Agric. Food Chem. 2005;53:8874–8880.
- Ward J., Peakall R., Gilmore S.R., Robertson J. A molecular identification system for grasses: a novel technology for forensic botany. Forensic Sci. Int. 2005;152:121–131.
- Shaw J., Lickey E.B., Beck J.T., Farmer S.B., Liu W., Miller J., Siripun K.C., Winder C.T., Schilling E.E., Small R.L. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am. J. Bot. 2005;92:142–166.
- Taberlet P., Gielly L., Pautou G., Bouvet J. Universal primers for amplification of three noncoding regions of chloroplast DNA. Plant Mol. Biol. 1991;17:1105–1109.
- Gielly L., Taberlet P. A phylogeny of the European gentians inferred from chloroplast trnL (UAA) intron sequences. Bot. J. Linn. Soc. 1996;120:57–75.
- Quandt D., Stech M. Molecular evolution of the trnL (UAA) intron in bryophytes. Mol. Phylogenet. Evol. 2005;36:429–443.
- Quandt D., Müller K., Stech M., Frahm J.P., Frey W., Hilu K.W., Borsch T. Molecular evolution of the chloroplast trnL-F region in land plants. Monogr. Syst. Bot. Missouri Botanic Garden. 2004;98:13–37.
- Shinozaki K., Ohme M., Tanaka M., Wakasugi T., Hayashida N., Matsubayashi T., Zaita N., Chunwongse J., Obokata J., Yamaguchi-Shinozaki K., et al. The complete nucleotide sequence of tobacco chloroplast genome: its gene organization and expression. EMBO J. 1986;5:2043–2049.
- Palmer J.D. Plastid chromosomes: structure and evolution. Cell Cult. Som. Cell Genet. Plants. 1991;7A:5–53.
- Michel F., Jacquier A., Dujon B. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie. 1982;64:867–881.
- Davies R.W., Waring R.B., Ray J.A., Brown T.A., Scazzocchio C. Making ends meet—a model for RNA splicing in fungal mitochondria. Nature. 1982;300:719–724.
- Wu S., Manber U. Agrep-a fast approximate pattern-matching tool. Proceedings of the USENIX Winter 1992 Technical Conference; Berkeley, CA: USENIX Association; 1992. pp. 153–162.
- Willerslev E., Cooper A. Ancient DNA. Proc. R. Soc. Lond. B. 2005;272:3–16.
- Godon J.J., Zumstein E., Dabert P., Habouzit F., Moletta R. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl. Environ. Microbiol. 1997;63:2802–2813.
- Willerslev E., Hansen A.J., Binladen J., Brand T.B., Gilbert M.T.P., Shapiro B., Bunce M., Wiuf C., Gilichinsky D.A., Cooper A. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science. 2003;300:791–795.
- Brownstein M.J., Carpten J.D., Smith J.R. Modulation of non-templated nucleotide addition by Taq polymerase: primer modification that facilitate genotyping. BioTechniques. 1996;20:1004–1010.
- Magnuson V.L., Ally D.S., Nylund S.J., Karanjawala Z.E., Rayman J.B., Knapp J.I., Lowe A.L., Ghosh S., Collins F.S. Substrate nucleotide-determinated non-templated addition of adenine by Taq DNA polymerase: implications for PCR-based genotyping and cloning. BioTechniques. 1996;21:700–709.
- Borsch T., Hilu K.W., Quandt D., Wilde V., Neinhuis C., Barthlott W. Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms. J. Evol. Biol. 2003;16:558–576.
Source: PubMed