Microcystis-dominated cyanobacterial harmful algal blooms (cyanoHABs) have a global impact on freshwater environments, affecting both wildlife and human health. Microcystis diversity and function in field samples and laboratory cultures can be determined by sequencing whole genomes of cultured isolates or natural populations, but these methods remain computationally and financially expensive. Amplicon sequencing of marker genes is a lower cost and higher throughput alternative to characterize strain composition and diversity in mixed samples. However, the selection of appropriate marker gene region(s) and primers requires prior understanding of the relationship between single gene genotype, whole genome content, and phenotype. To identify phylogenetic markers of Microcystis strain diversity, we compared phylogenetic trees built from each of 2,351 individual core genes to an established phylogeny and assessed the ability of these core genes to predict whole genome content and bioactive compound genotypes. We identified single-copy core genes better able to resolve Microcystis phylogenies than previously identified marker genes. We developed primers suitable for current Illumina-based amplicon sequencing with near-complete coverage of available Microcystis genomes and demonstrate that they outperform existing options for assessing Microcystis strain composition. Results showed that genetic markers can be used to infer Microcystis gene content and phenotypes such as potential production of bioactive compounds , although marker performance varies by bioactive compound gene and sequence similarity. Finally, we demonstrate that these markers can be used to characterize the Microcystis strain composition of laboratory or field samples like those collected for surveillance and modeling of Microcystis-dominated cyanobacterial harmful algal blooms.

以微囊藻为主的蓝藻有害藻华 (cyanoHAB) 对淡水环境具有全球影响，影响野生动物和人类健康。现场样品和实验室培养物中微囊藻的多样性和功能可以通过对培养分离株或自然种群的整个基因组进行测序来确定，但这些方法在计算和经济上仍然昂贵。标记基因的扩增子测序是一种成本更低、通量更高的替代方案，可用于表征混合样品中的菌株组成和多样性。然而，选择合适的标记基因区域和引物需要事先了解单基因基因型、全基因组内容和表型之间的关系。为了确定微囊藻菌株多样性的系统发育标记，我们将由 2,351 个单独核心基因构建的系统发育树与已建立的系统发育进行了比较，并评估了这些核心基因预测全基因组内容和生物活性化合物基因型的能力。我们鉴定出的单拷贝核心基因比之前鉴定的标记基因能够更好地解析微囊藻系统发育。我们开发了适合当前基于 Illumina 的扩增子测序的引物，几乎完全覆盖了可用的微囊藻基因组，并证明它们优于评估微囊藻菌株组成的现有选项。结果表明，遗传标记可用于推断微囊藻基因含量和表型，例如生物活性化合物的潜在产量，尽管标记性能因生物活性化合物基因和序列相似性而异。最后，我们证明这些标记可用于表征实验室或现场样品的微囊藻菌株组成，例如为微囊藻为主的蓝藻有害藻华的监测和建模而收集的样品。