CoChat
Sign Up
Cited by 1,079

The DOI matches its Crossref record.

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

Taberlet, P., Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T., Corthier, G., Brochmann, C., Willerslev, E.·2007·Nucleic Acids Research
DOI 10.1093/nar/gkl938PMC PMC1807943
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/nar/gkl938

Cites

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Authentication of metabarcoding results relies on reproducibility across multiple PCR replicates and demonstrating that negative controls are blank or contain different sequence signatures.

    “As with PCR-based aDNA approaches used in the 1990s, the authentication of metabarcoding [G] results relies instead on reproducibility across multiple PCR replicates 128 and demonstrating that negative controls are either blank or contain different sequence signatures than that seen within the samples.”

    From Ancient DNA analysis (2021) · cites this paper as [128]

    The citation follows the claim about reproducibility across multiple PCR replicates. The Materials and Methods section (‘Robustness of the system for biotechnological applications’; page unavailable) describes multiple extraction and PCR blank controls, but does not say that authentication relies on reproducibility across PCR replicates. Searches for replicate amplification and reproducibility found no passage establishing that point. (LLM, conf=0.72)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

No references could be resolved yet.

Research works printed but not linked: 27

  1. [1]Floyd R. Abebe E. Papert A. Blaxter M. Molecular barcodes for soil nematode identification Mol. Ecol. 2002 11 839 850 11972769
  2. [2]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 PMC1691236 12614582
  3. [3]Hebert P.D.N. Gregory T.R. The promise of DNA barcoding for taxonomy Syst. Biol. 2005 54 852 859 16243770
  4. [4]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 PMC1609218 16214746
  5. [5]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 PMC1698023 12952648
  6. [6]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 15928076 PMC1142120
  7. [7]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 15771783 PMC555853
  8. [8]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 15465915 PMC522015
  9. [9]Hebert P.D.N. Stoeckle M.Y. Zemlak T.S. Francis C.M. Identification of birds through DNA barcodes PLoS Biol. 2004 2 e312 15455034 PMC518999
  10. [11]Álvarez I. Wendel J.F. Ribosomal ITS sequences and plant phylogenetic inference Mol. Phylogenet. Evol. 2003 29 417 434 14615184
  11. [12]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 9665881
  12. [15]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 15994844 PMC4246770
  13. [16]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 16277378
  14. [17]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 15978338
  15. [18]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 21652394
  16. [19]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 1932684
  17. [21]Quandt D. Stech M. Molecular evolution of the trnL (UAA) intron in bryophytes Mol. Phylogenet. Evol. 2005 36 429 443 16005648
  18. [23]Shinozaki K. Ohme M. Tanaka M. Wakasugi T. Hayashida N. Matsubayashi T. Zaita N. Chunwongse J. Obokata J. Yamaguchi-Shinozaki K. The complete nucleotide sequence of tobacco chloroplast genome: its gene organization and expression EMBO J. 1986 5 2043 2049 16453699 PMC1167080
  19. [25]Michel F. Jacquier A. Dujon B. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure Biochimie 1982 64 867 881 6817818
  20. [26]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 6757759
  21. [27]Wu S. Manber U. Agrep-a fast approximate pattern-matching tool 1992 Proceedings of the USENIX Winter 1992 Technical Conference Berkeley, CA USENIX Association 153 162
  22. [28]Willerslev E. Cooper A. Ancient DNA Proc. R. Soc. Lond. B 2005 272 3 16 PMC1634942 15875564
  23. [29]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 9212428 PMC168577
  24. [30]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 12702808
  25. [31]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 8780871
  26. [32]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 8891224
  27. [33]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 14632220

Cited by

Sorted by citations

Metadata

Authors
Taberlet, P., Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T., Corthier, G., Brochmann, C., & Willerslev, E.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2007-01-26
Volume
35
Issue
3
Pages
e14-e14
ISSN
  • 0305-1048
  • 1362-4962
DOI
10.1093/nar/gkl938
PMC
PMC1807943
Cited by
1,079
References
0
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review