Comparison of potential diatom ‘barcode’ genes (the 18S rRNA gene and ITS, COI, ) and their effectiveness in discriminating and determining species taxonomy in the Bacillariophyta Free

Abstract

Diatoms form an enormous group of photoautotrophic micro-eukaryotes and play a crucial role in marine ecology. In this study, we evaluated typical genes to determine whether they were effective at different levels of diatom clustering analysis to assess the potential of these regions for barcoding taxa. Our test genes included nuclear rRNA genes (the nuclear small-subunit rRNA gene and the 5.8S rRNA gene+ITS-2), a mitochondrial gene (cytochrome -oxidase subunit 1, COI), a chloroplast gene [ribulose-1,5-biphosphate carboxylase/oxygenase large subunit ()] and the universal plastid amplicon (UPA). Calculated genetic divergence was highest for the internal transcribed spacer (ITS; 5.8S+ITS-2) (-distance of 1.569, 85.84 % parsimony-informative sites) and COI (6.084, 82.14 %), followed by the 18S rRNA gene (0.139, 57.69 %), (0.120, 42.01 %) and UPA (0.050, 14.97 %), which indicated that ITS and COI were highly divergent compared with the other tested genes, and that their nucleotide compositions were variable within the whole group of diatoms. Bayesian inference (BI) analysis showed that the phylogenetic trees generated from each gene clustered diatoms at different phylogenetic levels. The 18S rRNA gene was better than the other genes in clustering higher diatom taxa, and both the 18S rRNA gene and performed well in clustering some lower taxa. The COI region was able to barcode species of some genera within the Bacillariophyceae. ITS was a potential marker for DNA based-taxonomy and DNA barcoding of Thalassiosirales, while species of , and gathered in separate clades, and were paraphyletic with those of . Finally, UPA was too conserved to serve as a diatom barcode.

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 41176098)
  • Shandong Provincial Natural Science Foundation, China (Award ZR2011DZ002)
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2015-04-01
2024-03-28
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References

  1. Adl S. M., Simpson A. G. B., Farmer M. A., Andersen R. A., Anderson O. R., Barta J. R., Bowser S. S., Brugerolle G. U. Y., Fensome R. A. et al. ( 2005 ). The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. . J Eukaryot Microbiol 52, 399451. [View Article] [PubMed]
    [Google Scholar]
  2. Alverson A. J. ( 2008 ). Molecular systematics and the diatom species. . Protist 159, 339353. [View Article] [PubMed]
    [Google Scholar]
  3. Alverson A. J., Cannone J. J., Gutell R. R., Theriot E. C. ( 2006 ). The evolution of elongate shape in diatoms. . J Phycol 42, 655668. [View Article]
    [Google Scholar]
  4. Behnke A., Friedl T., Chepurnov V. A., Mann D. G. ( 2004 ). Reproductive compatibility and rDNA sequence analyses in the Sellaphora pupula species complex (Bacillariophyta). . J Phycol 40, 193208. [View Article]
    [Google Scholar]
  5. Beszteri B., Ács É., Medlin L. K. ( 2005 ). Ribosomal DNA sequence variation among sympatric strains of the Cyclotella meneghiniana complex (Bacillariophyceae) reveals cryptic diversity. . Protist 156, 317333. [View Article] [PubMed]
    [Google Scholar]
  6. Bruder K., Medlin L. K. ( 2007 ). Molecular assessment of phylogenetic relationships in selected species/genera in the naviculoid diatoms (Bacillariophyta). I. The genus Placoneis . . Nova Hedwigia 85, 331352. [View Article]
    [Google Scholar]
  7. de Vere N., Rich T. C. G., Ford C. R., Trinder S. A., Long C., Moore C. W., Satterthwaite D., Davies H., Allainguillaume J. et al. ( 2012 ). DNA barcoding the native flowering plants and conifers of Wales. . PLoS ONE 7, e37945. [View Article] [PubMed]
    [Google Scholar]
  8. Evans K. M., Wortley A. H., Mann D. G. ( 2007 ). An assessment of potential diatom “barcode” genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta). . Protist 158, 349364. [View Article] [PubMed]
    [Google Scholar]
  9. Godhe A., McQuoid M. R., Karunasagar I., Karunasagar I., Rehnstam-Holm A. S. ( 2006 ). Comparison of three common molecular tools for distinguishing among geographically separated clones of the diatom Skeletonema marinoi Sarno et Zingone (Bacillariophyceae). . J Phycol 42, 280291. [View Article]
    [Google Scholar]
  10. Guillard R. R. L. ( 1975 ). Culture of phytoplankton for feeding marine invertebrates. . In Culture of Marine Invertebrate Animals, pp. 2960. Edited by Smith W. L., Chanley M. H. . New York:: Springer;. [View Article]
    [Google Scholar]
  11. Hamsher S. E., Evans K. M., Mann D. G., Poulíčková A., Saunders G. W. ( 2011 ). Barcoding diatoms: exploring alternatives to COI-5P. . Protist 162, 405422. [View Article] [PubMed]
    [Google Scholar]
  12. Hebert P. D., Cywinska A., Ball S. L., deWaard J. R. ( 2003 ). Biological identifications through DNA barcodes. . Proc Biol Sci 270, 313321. [View Article] [PubMed]
    [Google Scholar]
  13. Jung S. W., Han M.-S., Ki J.-S. ( 2010 ). Molecular genetic divergence of the centric diatom Cyclotella and Discostella (Bacillariophyceae) revealed by nuclear ribosomal DNA comparisons. . J Appl Phycol 22, 319329. [View Article]
    [Google Scholar]
  14. Kooistra W. H., Medlin L. K. ( 1996 ). Evolution of the diatoms (Bacillariophyta). IV. A reconstruction of their age from small subunit rRNA coding regions and the fossil record. . Mol Phylogenet Evol 6, 391407. [View Article] [PubMed]
    [Google Scholar]
  15. Kooistra W. H., Sarno D., Hernández-Becerril D. U., Assmy P., Di Prisco C., Montresor M. ( 2010 ). Comparative molecular and morphological phylogenetic analyses of taxa in the Chaetocerotaceae (Bacillariophyta). . Phycologia 49, 471500. [View Article]
    [Google Scholar]
  16. Kress W. J., Erickson D. L. ( 2008 ). DNA barcodes: genes, genomics, and bioinformatics. . Proc Natl Acad Sci U S A 105, 27612762. [View Article] [PubMed]
    [Google Scholar]
  17. Kucera H., Saunders G. W. ( 2008 ). Assigning morphological variants of Fucus (Fucales, Phaeophyceae) in Canadian waters to recognized species using DNA barcoding. . Botany 86, 10651079. [View Article]
    [Google Scholar]
  18. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A. et al. ( 2007 ). Clustal W and Clustal X version 2.0. . Bioinformatics 23, 29472948. [View Article] [PubMed]
    [Google Scholar]
  19. Lee M. A., Faria D. G., Han M. S., Lee J., Ki J. S. ( 2013 ). Evaluation of nuclear ribosomal RNA and chloroplast gene markers for the DNA taxonomy of centric diatoms. . Biochem Syst Ecol 50, 163174. [View Article]
    [Google Scholar]
  20. Lundholm N., Moestrup Ø., Kotaki Y., Hoef-Emden K., Scholin C., Miller P. ( 2006 ). Inter- and intraspecific variation of the Pseudo-nitzschia delicatissima complex (Bacillariophyceae) illustrated by RNA probes, morphological data and phylogenetic analyses. . J Phycol 42, 464481. [View Article]
    [Google Scholar]
  21. Luo A., Qiao H., Zhang Y., Shi W., Ho S. Y., Xu W., Zhang A., Zhu C. ( 2010 ). Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. . BMC Evol Biol 10, 242. [View Article] [PubMed]
    [Google Scholar]
  22. MacGillivary M. L., Kaczmarska I. ( 2011 ). Survey of the efficacy of a short fragment of the rbcL gene as a supplemental DNA barcode for diatoms. . J Eukaryot Microbiol 58, 529536. [View Article] [PubMed]
    [Google Scholar]
  23. MacGillivary M. L., Kaczmarska I. ( 2012 ). Genetic differentiation within the Paralia longispina (Bacillariophyta) species complex. . Botany 90, 205222. [View Article]
    [Google Scholar]
  24. Mann D., Droop S. ( 1996 ). Biodiversity, biogeography and conservation of diatoms. . Hydrobiologia 336, 1932. [View Article]
    [Google Scholar]
  25. Medlin L. K., Kaczmarska I. ( 2004 ). Evolution of the diatoms: V. Morphological and cytological support for the major clades and a taxonomic revision. . Phycologia 43, 245270. [View Article]
    [Google Scholar]
  26. Medlin L. K., Williams D., Sims P. ( 1993 ). The evolution of the diatoms (Bacillariophyta). I. Origin of the group and assessment of the monophyly of its major divisions. . Eur J Phycol 28, 261275. [View Article]
    [Google Scholar]
  27. Medlin L. K., Kooistra W. H., Gersonde R., Wellbrock U. ( 1996 ). Evolution of the diatoms (Bacillariophyta). II. Nuclear-encoded small-subunit rRNA sequence comparisons confirm a paraphyletic origin for the centric diatoms. . Mol Biol Evol 13, 6775. [View Article] [PubMed]
    [Google Scholar]
  28. Medlin L. K., Kooistra W., Gersonde R., Sims P., Wellbrock U. ( 1997 ). Is the origin of diatoms related to the end-Permian mass extinction?. Nova Hedwigia 65, 111.
    [Google Scholar]
  29. Medlin L. K., Kooistra W. H. C. F., Schmid A. M.-M. ( 2000 ). A review of the evolution of the diatoms – a total approach using molecules, morphology and geology. . In The Origin and Early Evolution of the Diatoms: Fossil, Molecular and Biogeographical Approaches, pp. 1335. Edited by Witkowski A., Siemińska J. . Kraków:: Władysław Szafer Institute of Botany, Polish Academy of Sciences;.
    [Google Scholar]
  30. Moniz M. B., Kaczmarska I. ( 2009 ). Barcoding diatoms: is there a good marker?. Mol Ecol Resour 9 (Suppl. s1), 6574. [View Article] [PubMed]
    [Google Scholar]
  31. Moniz M. B., Kaczmarska I. ( 2010 ). Barcoding of diatoms: nuclear encoded ITS revisited. . Protist 161, 734. [View Article] [PubMed]
    [Google Scholar]
  32. Moritz G., Paulsen M., Delker C., Picl S., Kumm S. ( 2001 ). Identification of thrips using ITS-RFLP analysis. In Thrips and Tospoviruses: Proceedings of the 7th International Symposium on Thysanoptera, pp. 365–367. Edited by R. Marullo & L. Mound. Calabria, Italy, 2–7 July 2001.
  33. Posada D., Crandall K. A. ( 1998 ). modeltest: testing the model of DNA substitution. . Bioinformatics 14, 817818. [View Article] [PubMed]
    [Google Scholar]
  34. Rambaut A. ( 2013 ). FigTree. Available from http://tree.bio.ed.ac.uk/software/figtree/
  35. Ratnasingham S., Hebert P. D. N. ( 2007 ). bold: the Barcode of Life Data System (http://www.barcodinglife.org). . Mol Ecol Notes 7, 355364. [View Article] [PubMed]
    [Google Scholar]
  36. Rogers S. O., Bendich A. J. ( 1985 ). Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. . Plant Mol Biol 5, 6976. [View Article] [PubMed]
    [Google Scholar]
  37. Ronquist F., Huelsenbeck J. P. ( 2003 ). MrBayes 3: Bayesian phylogenetic inference under mixed models. . Bioinformatics 19, 15721574. [View Article] [PubMed]
    [Google Scholar]
  38. Round F. E., Crawford R. M., Mann D. G. ( 1990 ). The Diatoms. Biology and Morphology of the Genera. Cambridge:: Cambridge University Press;.
    [Google Scholar]
  39. Saunders G. W. ( 2005 ). Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. . Philos Trans R Soc Lond B Biol Sci 360, 18791888. [View Article] [PubMed]
    [Google Scholar]
  40. Savolainen V., Cowan R. S., Vogler A. P., Roderick G. K., Lane R. ( 2005 ). Towards writing the encyclopedia of life: an introduction to DNA barcoding. . Philos Trans R Soc Lond B Biol Sci 360, 18051811. [View Article] [PubMed]
    [Google Scholar]
  41. Schoch C. L., Seifert K. A., Huhndorf S., Robert V., Spouge J. L., Levesque C. A., Chen W., Bolchacova E., Voigt K. et al. ( 2012 ). Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi . . Proc Natl Acad Sci U S A 109, 62416246. [View Article] [PubMed]
    [Google Scholar]
  42. Seifert K. A. ( 2009 ). Progress towards DNA barcoding of fungi. . Mol Ecol Resour 9 (Suppl. s1), 8389. [View Article] [PubMed]
    [Google Scholar]
  43. Sherwood A. R., Presting G. G. ( 2007 ). Universal primers amplify a 23S rDNA plastid marker in eukaryotic algae and cyanobacteria. . J Phycol 43, 605608. [View Article]
    [Google Scholar]
  44. Simonsen R. ( 1972 ). Ideas for a more natural system of the centric diatoms. . Nova Hedwigia Beih 39, 3754.
    [Google Scholar]
  45. Simonsen R. ( 1979 ). The diatom system: ideas on phylogeny. . Bacillaria 2, 971.
    [Google Scholar]
  46. Sörhannus U. ( 2004 ). Diatom phylogenetics inferred based on direct optimization of nuclear-encoded SSU rRNA sequences. . Cladistics 20, 487497. [View Article]
    [Google Scholar]
  47. Sörhannus U. ( 2007 ). A nuclear-encoded small-subunit ribosomal RNA timescale for diatom evolution. . Mar Micropaleontol 65, 112. [View Article]
    [Google Scholar]
  48. Stern R. F., Andersen R. A., Jameson I., Küpper F. C., Coffroth M.-A., Vaulot D., Le Gall F., Véron B., Brand J. J. et al. ( 2012 ). Evaluating the ribosomal internal transcribed spacer (ITS) as a candidate dinoflagellate barcode marker. . PLoS ONE 7, e42780. [View Article] [PubMed]
    [Google Scholar]
  49. Stevenson R. J., Pan Y., Van Dam H. ( 2010 ). Assessing environmental conditions in rivers and streams with diatoms. . In The Diatoms: Applications for the Environmental and Earth Sciences, , 2nd edn., pp. 5785. Edited by Smol J. P., Stoermer E. F. . Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  50. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013 ). mega6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol 30, 27252729. [View Article] [PubMed]
    [Google Scholar]
  51. Theriot E. C., Ashworth M., Ruck E., Nakov T., Jansen R. K. ( 2010 ). A preliminary multigene phylogeny of the diatoms (Bacillariophyta): challenges for future research. . Plant Ecol Evol 143, 278296. [View Article]
    [Google Scholar]
  52. Trobajo R., Mann D. G., Clavero E., Evans K. M., Vanormelingen P., McGregor R. C. ( 2010 ). The use of partial cox1, rbcL and LSU rDNA sequences for phylogenetics and species identification within the Nitzschia palea species complex (Bacillariophyceae). . Eur J Phycol 45, 413425. [View Article]
    [Google Scholar]
  53. Urbánková P., Veselá J. ( 2013 ). DNA-barcoding: a case study in the diatom genus Frustulia (Bacillariophyceae). . Nova Hedwigia Beih 142, 147162.
    [Google Scholar]
  54. Vanormelingen P., Hegewald E., Braband A., Kitschke M., Friedl T., Sabbe K., Vyverman W. ( 2007 ). The systematics of a small spineless Desmodesmus species, D. costato-granulatus (Sphaeropleales, Chlorophyceae), based on ITS2 rDNA sequence analyses and cell wall morphology. . J Phycol 43, 378396. [View Article]
    [Google Scholar]
  55. Vanormelingen P., Cottenie K., Michels E., Muylaert K., Vyverman W. et al. ( 2008 ). The relative importance of dispersal and local processes in structuring phytoplankton communities in a set of highly interconnected ponds. . Freshw Biol 53, 21702183.
    [Google Scholar]
  56. Von Dassow P., Petersen T. W., Chepurnov V. A., Armbrust E. V. ( 2008 ). Inter- and intraspecific relationships between nuclear DNA content and cell size in selected members of the centric diatom genus Thalassiosira (Bacillariophyceae). . J Phycol 44, 335349. [View Article]
    [Google Scholar]
  57. Xia X., Xie Z. ( 2001 ). dambe: software package for data analysis in molecular biology and evolution. . J Hered 92, 371373. [View Article] [PubMed]
    [Google Scholar]
  58. Yool A., Tyrrell T. ( 2003 ). Role of diatoms in regulating the ocean’s silicon cycle. . Global Biogeochem Cycles 17, 1103. [View Article]
    [Google Scholar]
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