Identifying fishes through DNA barcodes and microarrays

PLoS ONE

Volumn 5, Issue 9, 2010, Pages 1-15

  Kochzius, Marc ^a,b   Seidel, Christian ^a,k   Antoniou, Aglaia ^c   Botla, Sandeep Kumar ^a,l   Campo, Daniel ^d,m   Cariani, Alessia ^e   Vazquez, Eva Garcia ^d   Hauschild, Janet ^a,n   Hervet, Caroline ^f,o   Hjörleifsdottir, Sigridur ^g   Hreggvidsson, Gudmundur ^g,h   Kappel, Kristina ^a   Landi, Monica ^e,p   Magoulas, Antonios ^c   Marteinsson, Viggo ^g   Nölte, Manfred ^a   Planes, Serge ^f,q   Tinti, Fausto ^e   Turan, Cemal ⁱ   Venugopal, Moleyur N ^j   Weber, Hannes ^a   Blohm, Dietmar ^a   more..

^a UNIVERSITY OF BREMEN   (Germany)

^b VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^c INSTITUTE OF OCEANOGRAPHY   (Greece)

^d UNIVERSITY OF OVIEDO   (Spain)

^e UNIVERSITY OF BOLOGNA   (Italy)

^f UNIVERSITÉ DE PERPIGNAN   (France)

^g Matis ohf Iceland   (Iceland)

^h UNIVERSITY OF ICELAND   (Iceland)

ⁱ MUSTAFA KEMAL UNIVERSITY   (Turkey)

^j University   (India)

^k UNIVERSITY OF LEIPZIG   (Germany)

^l GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^m UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

ⁿ FEDERAL RESEARCH INSTITUTE FOR ANIMAL HEALTH   (Germany)

^o CEMAGREF   (France)

^p UNIVERSITY OF MINHO   (Portugal)

^q Centre de Biologie et d Ecologie Tropicale et Méditerranéenne   (French Polynesia)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B; CYTOCHROME C OXIDASE; DNA; RNA 16S; FISH PROTEIN; RIBOSOME DNA;

ANIMAL CELL; ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; DNA BARCODING; DNA HYBRIDIZATION; DNA MICROARRAY; EUROPE; FISH GENETICS; FLATFISH; HIGH THROUGHPUT SCREENING; MARINE SPECIES; NEIGHBOR JOINING METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; PHYLOGENETIC TREE; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; SPECIES IDENTIFICATION; UNINDEXED SEQUENCE; ANIMAL; CLASSIFICATION; FISH; GENETICS; MOLECULAR GENETICS; PHYLOGENY;

PISCES; PLEURONECTIFORMES;

ANIMALS; CYTOCHROMES B; DNA; DNA BARCODING, TAXONOMIC; DNA, RIBOSOMAL; ELECTRON TRANSPORT COMPLEX IV; FISH PROTEINS; FISHES; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY;

EID: 77958588566     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012620     Document Type: Article

References (75)

1. FAO (2009) The state of world fisheries and aquaculture. Food and Agriculture Organization of the United Nations, Rome.
2. Ogden R (2008) Fisheries forensics: the use of DNA tools for improving compliance, traceability and enforcement in the fishing industry. Fish Fish 9: 462-472.
3. Kochzius M (2009) Trends in fishery genetics. In: Beamish RJ, Rothschild BJ, eds. The future of fisheries science in North America. Dordrecht, The Netherlands: Fish & Fisheries Series 31, Springer. pp 453-493.
4. Teletchea F (2009) Molecular identification methods of fish species: reassessment and possible applications. Rev Fish Biol Fish 19: 265-293.
5. Marko PB, Lee SC, Rice AM, Gramling JM, Fitzhenry TM, et al. (2004) Misslabelling of a depleted reef fish. Nature 430: 309-310.
6. Cohen NJ, Deeds JR, Wong ES, Hanner RJ, Yancy HF, et al. (2009) Public health response to puffer fish (Tetrodotoxin) poisoning from mislabelled product. J Food Prot 72: 810-817.
7. Fox CJ, Taylor MI, Pereyra R, Villasana MI, Rico C (2005) TaqMan DNA technology confirms likely overestimation of cod (Gadus morhua L.) egg abundance in the Irish Sea: implications for the assessment of the cod stock and mapping of spawning areas using egg-based methods. Mol Ecol 14: 879-884.
8. Quinteiro J, Sotelo CG, Rehbein H, Pryde SE, Medina I, et al. (1998) Use of mtDNA direct polymerase chain reaction (PCR) sequencing and PCRrestriction fragment length polymorphism methodologies in species identification of canned tuna. J Agric Food Chem 46: 1662-1669.
9. Sotelo CG, Calo-Mata P, Chapela MJ, Pe ́rez-Marti ́n RI, Rehbein H, et al. (2001) Identification of flatfish (Pleuronectiforme) species using DNA-based techniques. J Agric Food Chem 49: 4562-4569.
10. Santaclara FJ, Cabado AG, Vieites JM (2006) Development of a method for genetic identification of four species of anchovies: E. encrasicolus, E. anchoita, E. ringens and E. japonicus. Eur Food Res Technol 223: 609-614.
11. Jérome M, Martinsohn JT, Ortega D, Carreau P, Verrez-Bagnis V, et al. (2008) Towards fish and seafood traceability: anchovy species determination in fish products by molecular markers and support through a public domain database. J Agric Food Chem 56: 3460-3469.
12. Aoyama J, Mochioka N, Otake T, Ishikawa S, Kawakami Y, et al. (1999) Distribution and dispersal of anguillid leptocephali in the western Pacific revealed by molecular analysis. Mar Ecol Prog Ser 188: 193-200.
13. Rocha-Olivares A, Moser GH, Stannard J (2000) Molecular identification and description of pelagic young of the rockfishes Sebastes constellatus and Sebastes ensifer. Fish Bull 98: 353-363.
14. Akimoto S, Kinoshita S, Sezaki K, Mitani I, Watabe S (2002) Identification of alfonsino and related fish species belonging to the genus Beryx with mitochondrial 16S rRNA gene and its application on their pelagic eggs. Fishe Sci 68: 1242-1249.
15. Richardson DE, Vanwye JD, Exum AM, Cowen RK, Crawford DL (2006) High-throughput species identification: from DNA isolation to bioinformatics. Mol Ecol Notes 7: 199-207.
16. Greig TW, Moore MK, Woodley CM, Quattro JM (2005) Mitochondrial gene sequences useful for species identification of western North Atlantic Ocean sharks. Fish Bull 103: 516-523.
17. Hoelzel AR (2001) Shark fishing in fin soup. Conserv Genet 2: 69-72.
18. Kochzius M, Söller R, Khalaf MA, Blohm D (2003) Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae, Pteroinae) based on mitochondrial DNA sequences. Mol Phyl Evol 28: 396-403.
19. Lemer S, Aurelle D, Vigliola L, Durand J-D, Borsa P (2007) Cytochrome b barcoding, molecular systematic and geographic differentiation in rabbitfishes (Siganidae). Comptes Rendus Biologies 330: 86-94.
20. Timm J, Figiel M, Kochzius M (2008) Contrasting patterns in species boundaries and evolution of anemonefishes (Amphiprioninae, Pomacentridae) in the centre of marine biodiversity. Mol Phyl Evol 49: 268-276.
21. Sevilla RG, Diez A, Norén M, Mouchel O, Jérome M, et al. (2007) Primers and polymerase chain reaction conditions for DNA barcoding teleost fish based on the mitochondrial cytochrome b and nuclear rhodopsin genes. Mol Ecol Notes 7: 730-734.
22. Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Biol Sci Ser B 270: 313-321.
23. Hebert PDN, Ratnasingham S, deWaard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Biol Sci Ser B 270 Suppl 1: S96-99.
24. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3: 294-299.
25. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN (2005) DNA barcoding Australia's fish species. Philos Trans Royal Soc B 360: 1847-1857.
26. Ward RD, Hanner R, Hebert PDN (2009) The campain to DNA barcode all fishes, FISH-BOL. J Fish Biol 74: 329-356.
27. Espiñeira M, Gonzáles-Lavín N, Vieites JM, Santaclara F (2008) Development of a method for the genetic identification of flatfish species on the basis of mitochondrial DNA sequences. J Agric Food Chem 56: 8954-8961.
28. Smith PJ, McVeagh SM, Steinke D (2008) DNA barcoding for the identification of smoked fish products. J Fish Biol 72: 464-471.
29. Wong EH-K, Hanner RH (2008) DNA barcoding detects market substitution in North American seafood. Food Res Int 41: 828-837.
30. Yancy HF, Zemlak TS, Mason JA, Washington JD, Tenge BJ, et al. (2008) Potential use of DNA barcodes in regulatory science: applications of the Regulatory Fish Encyclopedia. J Food Prot 71: 210-217.
31. Ward RD, Holmes BH, White WT, Last PR (2008) DNA barcoding Australasian chondrichthyans: results and potential uses in conservation. Mar Freshw Res 59: 57-71.
32. Moura T, Silva MC, Figueiredo I, Neves A, Mun ̃oz PD, et al. (2008) Molecular barcoding of north-east Atlantic deep-water sharks: species identification and application to fisheries management and conservation. Mar Freshw Res 59: 214-223.
33. Holmes BH, Steinke D, Ward RD (2009) Identification of shark and ray fins using DNA barcoding. Fish Res 95: 280-288.
34. Smith PJ, Steinke D, McVeagh SM, Stewards AL, Struthers CD, et al. (2008b) Molecular analysis of Shuthern Ocean skates (Bathyraja) reveals a new species of Antarctic skate. J Fish Biol 73: 1170-1182.
35. Ward RD, Holmes BH, Yearsley GK (2008a) DNA barcoding reveals a likely second species of Asian sea bass (barramundi) (Lates calcarifer). J Fish Biol 72: 458-463.
36. Steinke D, Zemlak TS, Hebert PDN (2009) Barcoding Nemo: DNA-based identification for the marine ornamental fish trade. PLoS One 4: e6300.
37. Zemlak TS, Ward RD, Connell AD, Holmes BH, Hebert PDN (2009) DNA barcoding reveals overlooked marine fishes. Mol Ecol Resources 9: 237-242.
38. Astarloa de JMD, Mabragan ̃a E, Hanner R, Figueroa DE (2008) Morphological and molecular evidence for a new species of longnose skate (Rajiformes: Rajidae: Dipturus) from Argentinean waters based on DNA barcoding. Zootaxa 1921: 35-46.
39. Smith LM, Sanders JZ, Kaiser RJ, Hughes P, Dodd C, et al. (1986) Fluorescence detection in automated DNA sequence analysis. Nature 321: 674-679.
40. Prober JM, Trainor GL, Dam RJ, Hobbs FW, Robertson CW, et al. (1987) A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 238: 336-341.
41. Hutchison CA, III (2007) DNA sequencing: bench to bedside and beyond. Nucleic Acids Res 35: 6227-6237.
42. Kochzius M, Nö lte N, Weber H, Silkenbeumer N, Hjörleifsdottir S, et al. (2008) DNA microarrays for identifying fishes. Mar Biotechnol 10: 207-217.
43. Teletchea F, Bernillon J, Duffraisse M, Laudet V, Hänni C (2008) Molecular identification of vertebrate species by oligonucleotide microarray in food and forensic samples. J Appl Ecol 45: 967-975.
44. Yoon HK, Kim G-E, Jeong D, Jung JW, Chung IH, et al. (2008) Development of salmon identification DNA chip based on mitochondrial COIII-ND3-ND4L variations. Biochip Journal 2: 287-295.
45. Yoon HK, Jeong D, Chung IH, Jung JW, Oh MJ, et al. (2009) Rapid species identification of elasmobranch fish (skates and rays) using oligonucleotide microarray. Biochip Journal 3: 87-96.
46. Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 3: e422.
47. Thompson JG, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
48. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
49. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary analysis and sequence alignment. Briefings in Bioinformatics 5: 150-163.
50. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
51. Nölte M (2002) Optimization of oligonucleotide sets for DNA microarrays. Ph.D. thesis, University of Bremen, Germany.
52. SantaLucia J (1998) A unified view of polymer, dumbbell, and oligonucleotie DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95: 1460-1465.
53. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, et al. (1994) Fast folding and comparison of RNA secondary structures (The Vienna RNA package). Monatshefte fü r Chemie (Chemical Monthly) 125: 167-188.
54. Ducrée J, Gruhler H, Hey N, Müller M, Békési S, et al. (2000) TOPSPOT - a new method for the fabrication of microarrays. Proceedings of the 13th Annual International Conference on Micro Electro Mechanical Systems (MEMS 2000), 23-27 January 2000;. pp 317-322.
55. Bensasson D, Zhang D-X, Hartl DL, Hewitt GM (2001) Mitochondrial pseudogenes: evolution's misplaced witness. Trends Ecol Evol 16: 314-321.
56. Peytavi R, Tang L-Y, Raymond FR, Boissinot K, Bissonnette L, et al. (2005) Correlation between microarray DNA hybridization efficiency and the position of short capture probe on the target nucleic acid. Biotechniques 39: 89-96.
57. Zhang L, Hurek T, Reinhold-Hurek B (2005) Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridisations. Nucleic Acids Res 33: e166.
58. Meier R, Zhang G, Ali F (2008) The use of mean instead of smallest interspecific distances exaggerates the size of the "barcoding gap" and leads to misidentification. Syst Biol 57: 809-813.
59. Ward RD (2009) DNA barcode divergence among species and genera of birds and fishes. Mol Ecol Resources 9: 1077-1085.
60. Ratnasingham S, Hebert PDN (2007) BOLD: the barcode of life data system (www.barcodinglife.org). Mol Ecol Notes 7: 355-364.
61. McClure MR, McEachran JD (1992) Hybridization between Prionotus alatus and P. paralatus in the Northern Gulf of Mexico (Pisces: Triglidae). Copeia 1992: 1039-1046.
62. Kijewska A, Burzyń ski A, Wenne R (2009) Molecular identification of European flounder (Platichthys flesus) and its hybrids with European plaice (Pleuronectes platessa). ICES J Mar Sci 66: 902-906.
63. Hubert N, Hanner R, Holm E, Mandrak NE, Taylor E, et al. (2008) Identifying Canadian freshwater fishes through DNA barcodes. PLoS One 3: e2490.
64. Richly E, Leister D (2006) NUMTs in sequenced eukaryotic genomes. Mol Biol Evol 21: 1081-1084.
65. Chen W, Seifert KA, Lévesque CA (2009) A high density COX1 barcode oligonucleotide array for identification and detection of species of Penicillium subgenus Penicillium. Mole Ecol Resources 9: 114-129.
66. Pozhitkov A, Noble PA, Domazet-Lošo T, Nolte AW, Sonnenberg R, et al. (2006) Test of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Res 34: e66.
67. Hajibabaei M, Singer GAC, Clare EL, Hebert PDN (2007) Design and application of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biol 5: 24.
68. Peplies J, Glöckner FO, Amann R (2003) Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA targeting oligonucleotide probes. Appl Environ Microbiol 69: 1397-1407.
69. Warsen AE, Krug MK, LaFrentz S, Stanek DR, Loge F, et al. (2004) Simultaneous discrimination between 15 fish pathogens by using 16S ribosomal DNA PCR and DNA microarrays. Appl Environ Microbiol 70: 4216-4221.
70. Korimbocus J, Scaramozzino N, Lacroix B, Crance JM, Garin D, et al. (2005) DNA probe array for the simultaneous identification of herpesviruses, enteroviruses, and flaviviruses. J Clin Microbiol 43: 3779-3787.
71. Rønning SB, Rudi K, Berdal KG, Holst-Jensen A (2005) Differentiation of important and closely related cereal plant species (Poaceae) in food by hybridisation to an oligonucleotide array. J Agric Food Chem 53: 8874-8880.
72. Tobler NE, Pfunder M, Herzog K, Frey JE, Altwegg M (2006) Rapid detection and species identification of Mycobacterium spp. using real-time PCR and DNAmicroarray. J Microbiol Methods 66: 116-124.
73. Fare TL, Coffey EM, Dai H, He YD, Kessler DA, et al. (2003) Effects of atmospheric ozone on microarray data quality. Anal Chem 75: 4672-4675.
74. Branham WS, Melvin CD, Han T, Desai VG, Moland CL, et al. (2007) Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements. BMC Biotechnol 7: 8.
75. Todt S (2005) Untersuchungen zur Hybridisierungseffizienz von Oligonukleotiden in DNA-Mikroarray-Experimenten. PhD thesis, University of Bremen. 148 p.