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<p>Reduced representation sequencing is a powerful population genomics method but is often limited in anthozoans due to the challenges in interpreting mixed host-dinoflagellate data when not using reference genomes. To circumvent endosymbiont contamination, we menthol bleached <i>Condylactis gigantea</i> sea anemones and assembled an aposymbiotic reference sample. Quantitative PCR detected only trace amounts of endosymbiont presence, supporting the efficacy of our bleaching approach. With this, we then reexamined a previously published holobiont ddRADseq dataset to test the hypothesis that reference sample information would eliminate endosymbiont loci and significantly change prior results. Incorporating the aposymbiotic reference sample did not substantively change the results of the prior study. We demonstrate that bleaching a reference sample for reduced representation sequencing may not be justified because of the marginal difference in results. This work supports a recent hypothesis that ddRADseq data assembly pipelines act as de facto endosymbiont filtering steps for symbiotic anthozoans.</p>

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Further evidence that reduced representation approaches are effective for symbiotic anthozoans without reference samples

  • 期刊论文

  • 发表日期：

    2026年6月1日

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  • Nancy E. Sheridan,
  • Kristine C. Fisher,
  • Seifu Seyoum,
  • Elizabeth M. Wallace,
  • Benjamin M. Titus,
  • Christina L. Richards,
  • Aaron W. Schrey

摘要

Reduced representation sequencing is a powerful population genomics method but is often limited in anthozoans due to the challenges in interpreting mixed host-dinoflagellate data when not using reference genomes. To circumvent endosymbiont contamination, we menthol bleached Condylactis gigantea sea anemones and assembled an aposymbiotic reference sample. Quantitative PCR detected only trace amounts of endosymbiont presence, supporting the efficacy of our bleaching approach. With this, we then reexamined a previously published holobiont ddRADseq dataset to test the hypothesis that reference sample information would eliminate endosymbiont loci and significantly change prior results. Incorporating the aposymbiotic reference sample did not substantively change the results of the prior study. We demonstrate that bleaching a reference sample for reduced representation sequencing may not be justified because of the marginal difference in results. This work supports a recent hypothesis that ddRADseq data assembly pipelines act as de facto endosymbiont filtering steps for symbiotic anthozoans.