Comparative genomic analysis of Microcystis strain diversity using conserved marker genes

Area of Science:

• Environmental microbiology
• Aquatic ecology
• Genomics

Background:

• Microcystis-dominated cyanobacterial harmful algal blooms (cyanoHABs) pose global threats to freshwater ecosystems and human health.
• Whole genome sequencing is accurate but expensive for characterizing Microcystis diversity.
• Amplicon sequencing offers a cost-effective alternative but requires optimized marker genes and primers.

Purpose of the Study:

• To identify reliable phylogenetic markers for Microcystis strain diversity.
• To assess the ability of these markers to predict whole genome content and bioactive compound genotypes.
• To develop and validate new primers for amplicon sequencing of Microcystis.

Main Methods:

• Phylogenetic analysis of 2,351 core genes against an established Microcystis phylogeny.
• Assessment of marker genes for predicting whole genome content and bioactive compound genotypes.
• Development of Illumina-compatible primers for amplicon sequencing and validation with Microcystis genomes.

Main Results:

• Identified single-copy core genes that provide higher phylogenetic resolution than previously used markers.
• Developed novel primers that offer near-complete genome coverage and outperform existing options for Microcystis strain composition analysis.
• Demonstrated that genetic markers can infer Microcystis gene content and phenotypes, including bioactive compound production, with varying accuracy.

Conclusions:

• New phylogenetic markers and primers enable more accurate and affordable characterization of Microcystis strain diversity.
• These tools are valuable for surveillance and modeling of harmful algal blooms.
• Genetic markers can serve as proxies for Microcystis functional traits and toxin potential.