Comparative Genomic Analysis of Microcystis Strain Diversity Using Conserved Marker Genes

Microcystis-dominated cyanobacterial harmful algal blooms (cHABs) have a global impact on aquatic ecosystems and human health. Diverse Microcystis strains have been observed to have different ecophysiological functions, including toxin production. While shotgun sequencing methods enable tracking of strain diversity and functions in the field, they are costly and require intensive data analysis. In contrast, amplicon sequencing of single genes is high-throughput and efficient but to date has been hindered by a lack of understanding of relationships between single gene sequences, whole genome content, and phenotype of Microcystis strains. Here we evaluated how phylogenies based on single conserved Microcystis genes compare to multi-gene phylogenies and the extent to which they represent the broader gene content of 159 publicly available Microcystis genomes as of June 1, 2020. Phylogenetic trees of 10 individual conserved marker genes did not accurately reflect phylogenies constructed from multiple genes. Regression analysis of phylogenetic distance of individual marker genes versus genes shared between genomes showed weak or no relationships between marker gene similarity and genome content. The results suggest that whole genome or multi-gene approaches are required to accurately assess genome content. Our current analysis is focused on assessing whether single gene markers provide information about gene content.