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<p>Haptophytes, known as golden algae, represent a diverse group of photosynthetic protists that play crucial roles in marine ecosystems and global biogeochemical cycles. Despite their ecological significance, elucidating their phylogenetic relationships using traditional taxonomic approaches has encountered challenges, primarily due to the constraints associated with morphological identification. DNA barcoding, particularly using the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) large subunit (<i>rbc</i>L) gene, has emerged as a reliable tool for species identification and molecular phylogenetics of photosynthetic organisms. However, the existing primer sets for the <i>rbc</i>L gene in haptophytes have limitations, such as low amplification efficiency and taxonomic bias, which hinder comprehensive biodiversity assessments. Herein, we report the development of a novel primer set designed to target the <i>rbc</i>L gene and a part of the <i>rbc</i>S gene. The primer set was optimised to amplify a fragment measuring 1,614–1,654&#xa0;bp with high efficiency and specificity across diverse haptophyte taxa. When evaluated using 11 haptophyte isolates, the new primer set gave consistent amplification and enhanced phylogenetic resolution could be achieved compared with that possible using conventional primers. The generated sequences revealed well-supported phylogenetic relationships, effectively addressing the gaps in taxonomic representation and demonstrating the robustness of the newly developed primer set. These findings contribute to the advancement of molecular tools for DNA barcoding and biodiversity research, thereby enabling broader applications in ecological monitoring, biogeochemical studies, and conservation biology.</p>

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Optimised primer set for accelerated amplification of RuBisCO large subunit (rbcL) gene and identification of haptophytes

  • 期刊论文

  • 发表日期：

    2025年7月4日

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  • Jae Yeong Park,
  • Jeehyo Song,
  • Keun-Yong Kim,
  • Kichul Cho,
  • Sung Min An,
  • Hyun-Ju Hwang

摘要

Haptophytes, known as golden algae, represent a diverse group of photosynthetic protists that play crucial roles in marine ecosystems and global biogeochemical cycles. Despite their ecological significance, elucidating their phylogenetic relationships using traditional taxonomic approaches has encountered challenges, primarily due to the constraints associated with morphological identification. DNA barcoding, particularly using the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) large subunit (rbcL) gene, has emerged as a reliable tool for species identification and molecular phylogenetics of photosynthetic organisms. However, the existing primer sets for the rbcL gene in haptophytes have limitations, such as low amplification efficiency and taxonomic bias, which hinder comprehensive biodiversity assessments. Herein, we report the development of a novel primer set designed to target the rbcL gene and a part of the rbcS gene. The primer set was optimised to amplify a fragment measuring 1,614–1,654 bp with high efficiency and specificity across diverse haptophyte taxa. When evaluated using 11 haptophyte isolates, the new primer set gave consistent amplification and enhanced phylogenetic resolution could be achieved compared with that possible using conventional primers. The generated sequences revealed well-supported phylogenetic relationships, effectively addressing the gaps in taxonomic representation and demonstrating the robustness of the newly developed primer set. These findings contribute to the advancement of molecular tools for DNA barcoding and biodiversity research, thereby enabling broader applications in ecological monitoring, biogeochemical studies, and conservation biology.