Intragenomic variations of the harmful algal bloom species Phaeocystis globosa through single-strain metabarcoding analysis.

Recent studies demonstrated that the existence of high-levels intragenomic variations (IGVs) may lead to overinterpretation of species diversity and genetic diversity in metabarcoding analysis. In this study, IGVs of the V4 region of 18S rRNA gene (18S rDNA V4) in Phaeocystis globosa were ascertained through metabarcoding analysis results of 54 P. globosa strains. Each P. globosa strain harbored over 200 ASVs, in which one ASV was dominant with higher relative abundance than others. According to different dominant ASVs, 54 strains could be divided into two groups, suggesting the high genetic diversity of P. globosa. ASVs were shared in different strains, suggesting that IGVs were genuine existed, rather than sequencing errors. Metabarcoding analysis of field samples identified large numbers of IGVs. High levels of IGVs may be due to incomplete homogenization or existence of nonfunctional pseudogenes. An accurate understanding of IGVs is necessary for the correct interpretation of metabarcoding analysis results.