4.1 Article

Assessing SSU rDNA Barcodes in Foraminifera: A Case Study using Bolivina quadrata

Journal

JOURNAL OF EUKARYOTIC MICROBIOLOGY
Volume 65, Issue 2, Pages 220-235

Publisher

WILEY
DOI: 10.1111/jeu.12471

Keywords

Foraminiferal morphology; foraminiferal phylogeny; foraminiferal polymorphism; protists; Rotaliida; species identification; SSU rDNA hypervariable regions

Categories

Funding

  1. NSF [PLR1341612]
  2. Swiss National Science Foundation [31003A_140766, 31003A_159709]
  3. GSA
  4. International Association of Geochemistry
  5. Elsevier
  6. NAMS
  7. SEPM
  8. Cushman Foundation for Foraminiferal Research
  9. Swiss National Science Foundation (SNF) [31003A_159709, 31003A_140766] Funding Source: Swiss National Science Foundation (SNF)

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The Small Subunit Ribosomal RNA gene (SSU rDNA) is a widely used tool to reconstruct phylogenetic relationships among foraminiferal species. Recently, the highly variable regions of this gene have been proposed as DNA barcodes to identify foraminiferal species. However, the resolution of these barcodes has not been well established, yet. In this study, we evaluate four SSU rDNA hypervariable regions (37/f, 41/f, 43/e, and 45/e) as DNA barcodes to distinguish among species of the genus Bolivina, with particular emphasis on Bolivina quadrata for which ten new sequences (-) were obtained during this study. Our analyses show that a single SSU rDNA hypervariable sequence is insufficient to resolve all Bolivina species and that some regions (37/f and 41/f) are more useful than others (43/e and 45/e) to distinguish among closely related species. In addition, polymorphism analyses reveal a high degree of variability. In the context of barcoding studies, these results emphasize the need to assess the range of intraspecific variability of DNA barcodes prior to their application to identify foraminiferal species in environmental samples; our results also highlight the possibility that a longer SSU rDNA region might be required to distinguish among species belonging to the same taxonomic group (i.e. genus).

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