Barcoding bamboozled by bacteria: Convergence to metazoan mitochondrial primer targets by marine microbes

Systematic Biology

Volumn 58, Issue 4, 2009, Pages 445-451

  Siddall, Mark E ^a   Fontanella, Frank M ^b   Watson, Sara C ^a   Kvist, Sebastian ^a   Erséus, Christer ^c  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

^c UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C OXIDASE; SEA WATER;

ANIMAL; CLASSIFICATION; GAMMAPROTEOBACTERIA; GENETIC PROCEDURES; GENETICS; METHODOLOGY; MICROBIOLOGY; NOTE;

ANIMALS; CLASSIFICATION; ELECTRON TRANSPORT COMPLEX IV; GAMMAPROTEOBACTERIA; GENETIC TECHNIQUES; SEAWATER;

BACTERIA (MICROORGANISMS); METAZOA;

EID: 70349422298     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syp033     Document Type: Note

References (35)

1. Baumann L., Baumann P., Mandel M., Allen R.D. 1972. Taxonomy of aerobic marine eubacteria. J. Bacteriol. 110:402-429.
2. Bely A. E., Wray G.A. 2004. Molecular phytogeny of naidid worms (Annelida: Clitellata) based on cytochrome oxidase I. Mol. Phylogenet. Evol. 30:50-63.
3. Blankenship L.E., Yayanos A.A. 2005. Universal primers and PCR of gut contents to study marine invertebrate diets. MoI. Ecol. 14: 891-899.
4. Cho E.S., Jung C.G., Sohn S.G., Kim C. W., and Han S. J. 2007. Population genetic structure of the ark shell Scapharca broughtonii Schrenck from Korea, China, and Russia based on COI gene sequences. J. Mar. Biotechnol. 9:203-216.
5. Crick F.H. 1966. Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19:548-555.
6. Deppe U., Richnow, H.H., Michaelis W., Antranikian G. 2005. Degradation of crude oil by an arctic microbial consortium. Extremophiles 9:461-470. (Pubitemid 41831054)
7. De Waard J.R., Ivanova, N.V., Hajibabaei M., Hebert P.D.N. 2008. Assembling DNA barcodes. Analytical protocols. Methods Mol. Biol. 410:275-294.
8. Edgar R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797. (Pubitemid 38832724)
9. Folmer O., Black M., Hoen W., Lutz R., Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metozoan invertebrates. Mol. Mar. Biol. Biotechnol. 3:294-299.
10. Gerdes B., Brinkmeyer R., Dieckmann G., Helmke E. 2005. Influence of crude oil on changes of bacterial communities in Arctic sea-ice. FEMS Microbiol. Ecol. 53:129-139.
11. Halanych K.M., Janosik A.M. 2006. A review of molecular markers used for annelid phylogenetics. Integr. Comp. Biol. 46:533-543.
12. Hebert P.D.N., Stoeckle M.Y., Zemlak S.T., Francis CM. 2004. Identification of birds through DNA barcodes. PLoS Biol. 2:1657-1663.
13. Holmström C., James S., Neilan B. A., White D.C., Kjelleberg S. 1998. Pseudoalteromonas tunicata sp. nov., a bacterium that produces antifouling agents. Int. J. Syst. Bacteriol. 48:1205-1212.
14. Ivanova E.P., Chun J., Romanenko L.A., Matte M.H., Mikhailov V.V., Huq A., Colwell R.R. 2000. Reclassification of Alteromonas distincta Romanenko et al., 1995 as Pseudoalteromonas distincta comb, nov. Int. J. Syst. Evol. Microbiol. 50:141-144.
15. Ivanova E.P., Kiprianova E.A., Mikhailov V.V., Levanova G.F., Garagulya A.D., Gorshkova N.M., Yumoto N., Yoshikawa S. 1996. Characterization and identification of marine Alteromonas nigrifaciens strains and emendation of the description. Int. J. Syst. Bacteriol. 46:223-228.
16. Ivanova E.P., Shevchenko L.S., Sawabe T., Lysenko A.M., Svetashev V.I., Gorshkova N.M., Satomi M., Christen R., Mikhailov V.V. 2002. Pseudoalteromonas maricaloris sp. nov., isolated from an Australian sponge, and reclassification of [Pseudoalteromonas aurantia] NCIMB 2033 as Pseudoalteromonas flavipulchra sp. nov. Int. J. Syst. Evol. Microbiol. 52:263-271.
17. Ivanova N.V., Zemlak T. S., Hanner R. H., Hebert P.D.N. 2007. Universal primer cocktails for fish DNA barcoding. Mol. Ecol. Notes 7:544-548.
18. Khachane A.N., Timmis K.N., dos Santos M., Vitor A.P. 2005. Uracil content of 16S rRNA of thermophilic and psychrophilic prokaryotes correlates inversely with their optimal growth temperatures. Nucleic Acids Res. 33:4016-4022.
19. Martin A.P. 1995. Metabolic rate and directional nucleotide substitution in animal mitochondrial DNA. Mol. Biol. Evol. 12:1124-1131.
20. McGarey D.J., Milanesi L., Foley D.P., Reyes B. Jr., Frye L.C., Lim D.V 1991. The role of motile aeromonads in the fish disease, ulcerative disease syndrome (UDS). Experientia 47:441-444.
21. Mikhailov V.V., Romanenko L.A., Ivanova E.P. 2006. The genus Alteromonas and related proteobacteria. Prokaryotes 6:597-645.
22. Nakano T, Ozawa T. 2007. Worldwide phylogeography of limpets of the order Patellogastropoda: molecular, morphological and palaeontological evidence. J. Mollusc. Stud. 73:79-99.
23. Nilsson R.H., Ryberg M., Kristiansson E., Abarenkov K., Larsson K.H., Kõljalg U. 2006. Taxonomie reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS ONE 1:e59.
24. Perna N.T., Kocher T.D. 1995. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41:353-358.
25. Saitou N., Nei M. 1987. The Neighbor-Joining method-a new method for reconstructing phylogenetic trees. Mol Biol. Evol. 4:406-425.
26. Simidu U., Kita-Tsukamoto K., Yasumoto T., Yotsu M. 1990. Taxonomy of four bacterial strains that produce tetrodotoxin. Int. J. Syst. Bacteriol. 40:331-336.
27. Smith M.A., Rodriguez J.J., Whitfield J.B., Deans A.R., Janzen D.H., Hallwachs W, Hebert P.D. 2008. Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections. PNAS 105: 12359-12364.
28. Song H., Buhay J.E., Whiting M.F., Crandall K.A. 2008. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. PNAS 105:13486-13491.
29. Stamatakis A., Ott M., Ludwig T. 2005. RAxML-OMP: an efficient program for phylogenetic inference on SMPs. Lect. Notes Comput. Sci. 3606:288-302.
30. Swofford D. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4.0b. Computer software and manual. Sunderland (MA): Sinauer Associates.
31. Tao N., Richardson R., Bruno W., Kuiken C. 2008. Find Model. Available from: http://www.hiv.lanl.gov/content/sequence/ findmodel/findmodel.html (date last accessed June 22,2009).
32. Traub R.J., Hobbs R.P., Adams P.J., Behnke J.M., Harris P.D., Thompson R.C.A. 2007. A case of mistaken identity-reappraisal of the species of canid and felid hookworms (Ancybstoma) present in Australia and India. Parasitology 134:113-119.
33. Vilgalys R. 2003. Taxonomie misidentification in public DNA databases. New Phytol. 160:4-5. (Pubitemid 37155966)
34. Webb K.E., Barnes D.K.A., Clark M.S., Bowden D.A. 2006. DNA barcoding: a molecular tool to identify Antarctic marine larvae. Deep Sea Res. Part II 53:1053-1060.
35. Zhang W., Wendel J.F., Clark L.G. 1997. Bamboozled again! Inadvertent isolation of fungal rDNA sequences from bamboos (Poaceae: Bambusoideae). MoI. Phylogenet. Evol. 8:205-217.