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

Area of Science:

• Microbiology
• Evolutionary Biology
• Molecular Biology

Background:

• The Small Subunit Ribosomal RNA (SSU rDNA) gene is crucial for phylogenetic studies in foraminifera.
• Highly variable regions of SSU rDNA are proposed as DNA barcodes for species identification.
• The discriminatory power of these SSU rDNA barcodes for foraminifera remains underexplored.

Purpose of the Study:

• To evaluate the efficacy of four SSU rDNA hypervariable regions (37/f, 41/f, 43/e, and 45/e) as DNA barcodes for distinguishing species within the genus Bolivina.
• To assess the intraspecific variability within these proposed DNA barcode regions.
• To determine the suitability of SSU rDNA hypervariable regions for identifying foraminiferal species in environmental samples.

Main Methods:

• Sequencing of ten new SSU rDNA sequences for Bolivina quadrata (GenBank accession numbers KY468817-KY468826).
• Comparative analysis of four SSU rDNA hypervariable regions (37/f, 41/f, 43/e, 45/e) for species resolution within the genus Bolivina.
• Polymorphism analysis to quantify genetic variability within the selected regions.

Main Results:

• A single SSU rDNA hypervariable region is insufficient for resolving all Bolivina species.
• Regions 37/f and 41/f demonstrate greater utility in differentiating closely related species compared to regions 43/e and 45/e.
• High levels of intraspecific variability were observed across the analyzed SSU rDNA hypervariable regions.

Conclusions:

• The effectiveness of SSU rDNA DNA barcodes for foraminiferal species identification varies depending on the chosen hypervariable region.
• Thorough assessment of intraspecific variability is essential before applying SSU rDNA barcodes to environmental samples.
• Longer SSU rDNA regions may be necessary to achieve robust species discrimination within the same taxonomic group, such as a genus.