An evaluation of LSU rDNA D1-D2 sequences for their use in species identification

Frontiers in Zoology - 2007
Rainer Sonnenberg1, Arne W. Nolte2, Diethard Tautz3
1Ichthyology, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
2Département de Biologie, Laboratoire du Prof. L. Bernatchez, Pavillon Charles-Eugène-Marchand, Université Laval, Ste-Foy, Québec, G1K 7P4, Canada
3Department of Genetics, University of Cologne, Zülpicherstrasse 47, 50674, Köln, Germany

Tóm tắt

Abstract Background Identification of species via DNA sequences is the basis for DNA taxonomy and DNA barcoding. Currently there is a strong focus on using a mitochondrial marker for this purpose, in particular a fragment from the cytochrome oxidase I gene (COI). While there is ample evidence that this marker is indeed suitable across a broad taxonomic range to delineate species, it has also become clear that a complementation by a nuclear marker system could be advantageous. Ribosomal RNA genes could be suitable for this purpose, because of their global occurrence and the possibility to design universal primers. However, it has so far been assumed that these genes are too highly conserved to allow resolution at, or even beyond the species level. On the other hand, it is known that ribosomal gene regions harbour also highly divergent parts. We explore here the information content of two adjacent divergence regions of the large subunit ribosomal gene, the D1-D2 region. Results Universal primers were designed to amplify the D1-D2 region from all metazoa. We show that amplification products in the size between 800–1300 bp can be obtained across a broad range of animal taxa, provided some optimizations of the PCR procedure are implemented. Although the ribosomal genes occur in multiple copies in the genomes, we find generally very little intra-individual polymorphism (<< 0.1% on average) indicating that concerted evolution is very effective in most cases. Studies in two fish taxa (genus Cottus and genus Aphyosemion) show that the D1-D2 LSU sequence can resolve even very closely related species with the same fidelity as COI sequences. In one case we can even show that a mitochondrial transfer must have occurred, since the nuclear sequence confirms the taxonomic assignment, while the mitochondrial sequence would have led to the wrong classification. We have further explored whether hybrids between species can be detected with the nuclear sequence and we show for a test case of natural hybrids among cyprinid fish species (Alburnus alburnus and Rutilus rutilus) that this is indeed possible. Conclusion The D1-D2 LSU region is a suitable marker region for applications in DNA based species identification and should be considered to be routinely used as a marker complementing broad scale studies based on mitochondrial markers.

Từ khóa


Tài liệu tham khảo

Hebert PDN, Cywinska A, Ball SL, deWaard JR: Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B. 2003, 270: 313-321. 10.1098/rspb.2002.2218.

Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP: A plea for DNA taxonomy. Trends in Ecology & Evolution. 2003, 18: 70-74. 10.1016/S0169-5347(02)00041-1.

Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM: Identification of Birds through DNA Barcodes. PLoS Biology. 2004, 2: 7-10.1371/journal.pbio.0020312.

Blaxter M: The promise of a DNA taxonomy. Philosophical Transactions of the Royal Society, London, Series B, Biological Sciences. 2004, 359: 669-679. 10.1098/rstb.2003.1447.

Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R: Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society, London, Series B, Biological Science. 2005, 360: 1805-1811. 10.1098/rstb.2005.1730.

Vogler AP, Monaghan MT: Recent advances in DNA taxonomy. Journal of Zoological Systematics and Evolutionary Research.

Markmann M, Tautz D: Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences. Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences. 2005, 360: 1917-1924. 10.1098/rstb.2005.1723.

Monaghan MT, Balke M, Gregory TR, Vogler AP: DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers. Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences. 2005, 360: 1925-1933. 10.1098/rstb.2005.1724.

Vences M, Thomas M, van der Meijden A, Chiari Y, Vieites DR: Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front Zool. 2005, 2 (1): 5-10.1186/1742-9994-2-5.

Ballard JWO, Whitlock MC: The incomplete natural history of mitochondria. Molecular Ecology. 2004, 13: 729-744. 10.1046/j.1365-294X.2003.02063.x.

Grant PR, Grant BR: Hybridization of bird species. Science. 1992, 256: 193-197. 10.1126/science.256.5054.193.

Scribner KT, Page KS, Bartron ML: Hybridization in freshwater fishes: a review of case studies and cytonuclear methods of biological inference. Reviews in Fish Biology and Fisheries. 2001, 10: 293-323. 10.1023/A:1016642723238.

Seehausen O: Hybridization and adaptive radiation. Trends in Ecology and Evolution. 2004, 19: 198-207. 10.1016/j.tree.2004.01.003.

Gross BL, Rieseberg LH: The ecological genetics of homoploid hybrid speciation. J Hered. 2005, 96: 241-252. 10.1093/jhered/esi026.

Nolte AW, Freyhof J, Stemshorn K, Tautz D: An invasive lineage of sculpins, Cottus sp. (Pisces, Teleostei) in the Rhine with new habitat adaptations has originated by hybridization between old phylogeographic groups. Proc Biol Sci. 2005, 272 (1579): 2379-87.

Herder F, Nolte AW, Pfaender J, Schwarzer J, Hadiaty RK, Schliewen UK: Adaptive radiation and hybridization in Wallace's Dreamponds: evidence from sailfin silversides in the Malili Lakes of Sulawesi. Proc Biol Sci. 2006, 273 (1598): 2209-17. 10.1098/rspb.2006.3558.

Bachtrog D, Thornton K, Clark A, Andolfatto P: Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group. Evolution. 2006, 60: 292-302. 10.1554/05-337.1.

Avise JC, Wollenberger K: Phylogenetics and the origin of species. Proceedings of the National Academy of Scienes USA. 1997, 94: 7748-7755. 10.1073/pnas.94.15.7748.

Moritz C, Cicero C: DNA Barcoding: Promise and Pitfalls. PLoS Biology. 2004, 2 (10): e354-10.1371/journal.pbio.0020354.

Long EO, Dawid IB: Repeated genes in eukaryotes. Annual Reviews in Biochemistry. 1980, 49: 727-764. 10.1146/annurev.bi.49.070180.003455.

Hassouna N, Michot B, Bachellerie JP: The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes. Nucleic Acids Research. 1984, 12: 3563-3583. 10.1093/nar/12.8.3563.

Ralser M, Querfurth R, Warnatz H-J, Lehrach H, Yaspo M-L, Krobitsch S: An efficient and economic enhancer mix for PCR. Biochemical and Biophysical Research Communications. 2006, 347: 747-751. 10.1016/j.bbrc.2006.06.151.

Elder JF, Turner BJ: Concerted evolution of repetitive DNA sequences in eukaryotes. Quarterly Review in Biology. 1995, 70: 297-320. 10.1086/419073.

Liao D: Concerted evolution: molecular mechanism and biological implications. American Journal of Human Genetics. 1999, 64: 24-30. 10.1086/302221.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. Journal of Molecular Biology. 1990, 215: 403-410.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank. Nucleic Acids Research. 2006, 34: D16-D20. 10.1093/nar/gkj157.

Kumar S, Tamura K, Nei M: MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics. 2004, 5: 150-163. 10.1093/bib/5.2.150.

Freyhof J, Kottelat M, Nolte AW: Taxonomic diversity of European Cottus with description of eight new species (Teleostei: Cottidae). Ichthyological Exploration of Freshwaters. 2005, 16: 107-172.

Huber JH: Killi – Data 2000. 2000, Paris: Société Française d'Ichthyologie;, german

Busse K, Freyhof J, Zarske A: Serum-electrophoretic patterns of various cyprinid hybrids from the Rivers Elbe and Sieg (Teleostei: Cyprinidae). Faunistische Abhandlungen, Staatliches Museum für Tierkunde Dresden. 1999, 21: 265-272.

Keller I, Chintauan-Marquier IC, Veltsos P, Nichols RA: Ribosomal DNA in the grasshopper Podisma pedestris: escape from concerted evolution. Genetics. 2006, 174: 863-874. 10.1534/genetics.106.061341.

Harpke D, Peterson A: Non-concerted ITS evolution in Mammillaria (Cactaceae). Molecular Phylogenetics and Evolution. 2006,

Krieger J, Fuerst PA: Characterization of nuclear 18S rRNA gene sequence diversity and expression in an individual lake sturgeon (Acipenser fulvescens). Journal of Applied Ichthyology. 2004, 20: 433-439. 10.1111/j.1439-0426.2004.00610.x.

Krieger J, Hett AK, Fuerst PA, Birstein VJ, Ludwig A: Unusual intraindividual variation of the nuclear 18S rRNA gene is widespread within the acipenseridae. Journal of Heredity. 2006, 97: 218-225. 10.1093/jhered/esj035.

Carranza S, Giribet G, Ribera C, Barguna Riutort M: Evidence that two types of 18S rDNA coexist in the genome of Dugesia (Schmidtea) mediterranea (Platyhelminthes, Turbellaria, Tricladida). Molecular Biology and Evolution. 1996, 13: 824-832.

Santos SR, Kinzie RA, Sakai K, Coffroth MA: Molecular characterization of nuclear small subunit (18S)-rDNA pseudogenes in a symbiotic dinoflagellate (Symbiodinium, Dinophyta). Journal of Eukaryotic Microbiology. 2003, 50: 417-421. 10.1111/j.1550-7408.2003.tb00264.x.

Kmiec B, Woloszynska M, Janska H: Heteroplasmy as a common state of mitochondrial genetic information in plants and animals. Current Genetics. 2006, 50: 149-159. 10.1007/s00294-006-0082-1.

Pons J, Vogler AP: Complex pattern of coalescence and fast evolution of a mitochondrial rRNA pseudogene in a recent radiation of tiger beetles. Molecular Biology and Evolution. 2005, 22: 991-1000. 10.1093/molbev/msi085.

Hazkani-Covo E, Graur D: A Comparative Analysis of Numt Evolution in Human and Chimpanzee. Molecular Biology and Evolution. 2007, 24: 13-18. 10.1093/molbev/msl149.

Schlötterer C, Tautz D: Chromosomal homogeneity of Drosophila ribosomal DNA arrays suggests intrachromosomal exchanges drive concerted evolution. Current Biology. 1994, 4: 777-783. 10.1016/S0960-9822(00)00175-5.

Kottelat M: European freshwater fishes. An heuristic checklist of the freshwater fishes of Europe (exclusive of former USSR), with an introduction for non-systematists and comments on nomenclature and conservation. Biologia, Bratislava, Section Zoology. 1997, 52 (Supplement 5): 1-271.

Stemshorn KC, Nolte AW, Tautz D: A Genetic Map of Cottus gobio (Pisces, Teleostei) based on microsatellites can be linked to the Physical Map of Tetraodon nigroviridis . Journal Evolutionary Biology. 2005, 18: 1619-1624.

Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R: DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology. 1994, 3: 294-299.

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research. 1997, 24: 4876-4882. 10.1093/nar/25.24.4876.

Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series. 1999, 41: 95-98.

Thông tin
Thông tin xuất bản

Frontiers in Zoology

Thông tin tác giả