A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

PLoS ONE

Volumn 2, Issue 6, 2007, Pages

  Kress, W John ^a   Erickson, David L ^a  

^a DEPARTMENT OF PALEOBIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROPLAST DNA; PHOTOSYSTEM II, PSBA SUBUNIT; PLANT DNA; RBCL PROTEIN, PLASTID; RIBOSOMAL SPACER DNA; RIBULOSEBISPHOSPHATE CARBOXYLASE;

ARTICLE; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; INFORMATION PROCESSING; PHOTOSYSTEM II; PHYLOGENY; PLANT; POLYMERASE CHAIN REACTION; SPECIES DIFFERENCE;

AUTOMATIC DATA PROCESSING; DNA, CHLOROPLAST; DNA, PLANT; DNA, RIBOSOMAL SPACER; PHOTOSYSTEM II PROTEIN COMPLEX; PHYLOGENY; PLANTS; POLYMERASE CHAIN REACTION; RIBULOSE-BISPHOSPHATE CARBOXYLASE; SPECIES SPECIFICITY;

EID: 77951631088     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000508     Document Type: Article

References (35)

1. Hebert PDN, Cywinska NA, Ball SL, deWaard JR, (2003a) Biological identifications through DNA barcodes. Proc Roy Soc B-Biol Sci 270: 313-321.
2. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM, (2004a) Identification of birds through DNA barcodes. PLoS Biol 2 (10): e312.
3. Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R, (2005) Towards writing the encyclopedia of life: an introduction to DNA barcoding. Phil Trans Roy Soc Lond Ser B Biol Sci 360: 1850-1811.
4. Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA, (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet doi:10.1016/j.tig.2007.02.001.
5. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W, (2004b) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci U S A 101: 14812-14817.
6. Will K, Rubinoff D, (2004) Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20: 47-55.
7. Rubinoff D, Cameron S, Will K, (2006) Are plant DNA barcodes a search for the Holy Grail? Trends Ecol Evol 21: 1-2.
8. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH, (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci U S A 102: 8369-8374.
9. Hebert PDN, Ratnasingham S, deWaard JR, (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Roy Soc B-Biol Sci 270 (suppl.): S96-S99.
10. Cho Y, Qiu Y-L, Kuhlman P, Palmer JD, (1998) Explosive invasion of plant mitochondria by a group I intron. Proc Natl Acad Sci U S A 95: 14244-14249.
11. Adams KL, Palmer JD, (2003) Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 29: 380-395.
12. Cho Y, Mower JP, Qiu Y-L, Palmer JD, (2004) Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proc Natl Acad Sci U S A 101: 17741-17746.
13. Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, et al.(2006) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Rese 1-8 doi:10.1093/nar/gkl938.
14. Renner SS, (1999) Circumscription and phylogeny of the Laurales: evidence from molecular and morphological data. Amer J Bot 86: 1301-1315.
15. Salazar GA, Chase MW, Arenas MAS, Ingrouille M, (2003) Phylogenetics of Cranichideae with emphasis on Spiranthinae (Orchidaceae, Orchidoideae): evidence from plastid and nuclear DNA sequences. Amer J Bot 90: 777-795.
16. Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, et al.(2005) Land plants and DNA barcodes: short-term and long-term goals. Philos Trans, Ser B 360: 1889-1895.
17. Newmaster SG, Fazekas, Ragupathy S, (2006) DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Can J Bot 84: 335-441.
18. Nilsson RH, Ryberg M, Kristiansson E, Abarenkov K, Larrson K-H, et al.(2006) Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective. PLoS ONE 1 (1): e59 doi:10.1371/journal.pone.0000059.
19. Goremykin VV, Holland B, Hirsch-Ernst KI, Hellwig FH, (2005) Analysis of Acorus calamus chloroplast genome and its phylogenetic implications. Mol Phylogenet Evol 22: 1813-1822.
20. Shaw J, Lickey EB, Beck JT, Farmer JB, Liu W, et al.(2005) The tortoise and the hare II: Comparison of the relative utility of 21 non-coding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92: 142-166.
21. Ratnasingham S, Hebert PDN, (2007) Mol Ecol Notes BOLD: The Barcode of Life Data System (www.barcodinglife.org). doi: 10.1111/j.1471-8286.2006.01678.x.
22. Little D, Stevenson DW, (2006) A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms. Cladistics 22: 1-21.
23. Soltis DE, Kuzoff RK, Mort ME, Zanis M, Fishbein, et al.(2001) Elucidating deep-level phylogenetic relationships in Saxifragaceae using sequences for six chloroplastic and nuclear DNA regions. Ann Missouri Bot Gard 88: 669-693.
24. Yamaguchi A, Kawamura H, Horiguchi T, (2006) A further phylogenetic study of the heterotrophic dinoflagellate genus Protoperidinium (Dinophyceae) based on small and large subunit ribosomal RNA gene sequences. Phycol Res 54: 317-329.
25. Rogers MB, Gilson PR, Su V, McFadden GI, Keeling PJ, (2006) The Complete Chloroplast Genome of the Chlorarachniophyte Bigelowiella natans: Evidence for Independent Origins of Chlorarachniophyte and Euglenid Secondary Endosymbionts. Mol Biol Evol 24: 54-62.
26. Asmussen CB, Chase MW, (2001) Coding and noncoding plastid DNA in palm systematics. Amer J Bot 88: 1103-1117.
27. Treutlein J, Vorster P, Wink M, (2005) Molecular relationships in Encephatartos (Zamiaceae, Cycadales) based on nucleotide sequences of nuclear ITS 1 & 2, Rbcl, and genomic ISSR fingerprinting. Plant Biol 7: 79-90.
28. Cowan RS, Chase MW, Kress WJ, Savolainen V, (2006) 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon 55: 611-616.
29. Meyer CP, Paulay G, (2005) DNA Barcoding: Error Rates Based on Comprehensive Sampling. PLoS Biol 3 (12): e422.
30. Kellogg E, Juliano ND, (1997) The structure and function of RuBisCo and their implications for systematic studies. Amer J Bot 84: 413-428.
31. Wiersema JH, León B, (2007) World Economic Plants. USDA, ARS, National Genetic Resources Program. Germplasm Resources Information Network- (GRIN) Beltsville, Maryland National Germplasm Resources Laboratory http://www.ars-grin.gov/cgi-bin/npgs/html/wep.pl.
32. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al.(1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Res 25: 3389-3402.
33. Zar JH, (1999) Biostatistical Analysis Englewood Cliffs, NJ Prentice-Hall.
34. ANGIOSPERM PHYLOGENY GROUP II(2003) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot J Linn Soc 141: 399-436.
35. Givnish TJ, Pires JC, Graham SW, McPherson MA, Prince LM, et al.(2006) Phylogenetic relationships of monocots based on the highly informative plastid gene ndhf: evidence for widespread concerted convergence. In: Columbus JT, Friar EA, Porter JM, Prince LM, Simpson MG, editors. Monocots: comparative biology and evolution Claremont Rancho Santa Ana Botanic Garden pp. 28-51.