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Kiledal EA, Reitz LA, Kuiper EQ, Evans J, Siddiqui R, Denef VJ, Dick GJ. Comparative genomic analysis of Microcystis strain diversity using conserved marker genes. HARMFUL ALGAE 2024; 132:102580. [PMID: 38331539 DOI: 10.1016/j.hal.2024.102580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/10/2024]
Abstract
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.
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Affiliation(s)
- E Anders Kiledal
- Department of Earth and Environmental Sciences, University of Michigan, 2534 North University Building, 1100 North University Avenue Ave, Rm. 2004, Ann Arbor, MI 48109-1005, USA.
| | - Laura A Reitz
- Department of Earth and Environmental Sciences, University of Michigan, 2534 North University Building, 1100 North University Avenue Ave, Rm. 2004, Ann Arbor, MI 48109-1005, USA
| | - Esmée Q Kuiper
- Department of Earth and Environmental Sciences, University of Michigan, 2534 North University Building, 1100 North University Avenue Ave, Rm. 2004, Ann Arbor, MI 48109-1005, USA
| | - Jacob Evans
- Department of Ecology and Evolutionary Biology, University of Michigan, 2220 Biological Sciences Building, 1105 North University Avenue, Ann Arbor, MI 48109-1005, USA
| | - Ruqaiya Siddiqui
- Microbiome Core, University of Michigan, 1500 MSRB 1, 1150W Medical Center Drive, Ann Arbor, MI 48109-5666, USA
| | - Vincent J Denef
- Department of Ecology and Evolutionary Biology, University of Michigan, 2220 Biological Sciences Building, 1105 North University Avenue, Ann Arbor, MI 48109-1005, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, 2534 North University Building, 1100 North University Avenue Ave, Rm. 2004, Ann Arbor, MI 48109-1005, USA; Cooperative Institute for Great Lakes Research, University of Michigan, 4040 Dana Building, 440 Church Street, Ann Arbor, MI 48109-1041, USA
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