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<p>Species of the dinoflagellate genus&#xa0;<i>Tripos&#xa0;</i>have attracted extensive attention not only because they play a crucial role in marine ecosystems as primary producers, but also because many <i>Tripos</i> species can cause harmful algal blooms (HABs) with significant negative impact on marine ecosystems. The common molecular marker 18S rDNA V4-based metabarcoding analysis has been demonstrated to be effective for identifying species of the dinoflagellate genus <i>Tripos</i> that could not be unambiguously identified according to morphological features. However, the number of <i>Tripos</i> species whose reference 18S rDNA V4 sequences have been resolved is currently very limited, severely hindering the accurate annotation of <i>Tripos</i> species in metabarcoding analysis. In this project, we attempted to expand the 18S rDNA V4 reference sequences by retrieving and analyzing sequences for 81 <i>Tripos</i> species described in AlgaeBase from the NCBI NT database, successfully identifying reference sequences for 59 <i>Tripos</i> species, including 41 known and 18 yet undescribed <i>Tripos</i> species. In addition, phylogenetic analysis of the reference sequences revealed many groups of <i>Tripos</i> species shared identical sequences, indicating that the resolution of the common molecular marker 18S rDNA V4 for <i>Tripos</i> species is limited. Our findings reaffirm that the common molecular marker 18S rDNA V4 does not have adequate resolution for distinguishing many <i>Tripos</i> species, underscore the necessity and importance of selecting molecular markers with higher resolution to improve species identification capacity and the necessity to enhance reference databases to include more <i>Tripos</i> species for better identification of <i>Tripos</i> species in metabarcoding analysis.</p>

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Optimization and evaluation of 18S rDNA V4-based metabarcoding analysis of Tripos species

  • 期刊论文

  • 发表日期：

    2025年2月4日

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  • Yingchao Li,
  • Nansheng Chen

摘要

Species of the dinoflagellate genus Tripos have attracted extensive attention not only because they play a crucial role in marine ecosystems as primary producers, but also because many Tripos species can cause harmful algal blooms (HABs) with significant negative impact on marine ecosystems. The common molecular marker 18S rDNA V4-based metabarcoding analysis has been demonstrated to be effective for identifying species of the dinoflagellate genus Tripos that could not be unambiguously identified according to morphological features. However, the number of Tripos species whose reference 18S rDNA V4 sequences have been resolved is currently very limited, severely hindering the accurate annotation of Tripos species in metabarcoding analysis. In this project, we attempted to expand the 18S rDNA V4 reference sequences by retrieving and analyzing sequences for 81 Tripos species described in AlgaeBase from the NCBI NT database, successfully identifying reference sequences for 59 Tripos species, including 41 known and 18 yet undescribed Tripos species. In addition, phylogenetic analysis of the reference sequences revealed many groups of Tripos species shared identical sequences, indicating that the resolution of the common molecular marker 18S rDNA V4 for Tripos species is limited. Our findings reaffirm that the common molecular marker 18S rDNA V4 does not have adequate resolution for distinguishing many Tripos species, underscore the necessity and importance of selecting molecular markers with higher resolution to improve species identification capacity and the necessity to enhance reference databases to include more Tripos species for better identification of Tripos species in metabarcoding analysis.