دورية أكاديمية
Comparative genomic analysis of Microcystis strain diversity using conserved marker genes.
| العنوان: | Comparative genomic analysis of Microcystis strain diversity using conserved marker genes. |
|---|---|
| المؤلفون: | Kiledal EA; 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. Electronic address: kiledal@umich.edu., Reitz LA; 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., Kuiper EQ; 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., Evans J; Department of Ecology and Evolutionary Biology, University of Michigan, 2220 Biological Sciences Building, 1105 North University Avenue, Ann Arbor, MI 48109-1005, USA., Siddiqui R; Microbiome Core, University of Michigan, 1500 MSRB 1, 1150W Medical Center Drive, Ann Arbor, MI 48109-5666, USA., Denef VJ; Department of Ecology and Evolutionary Biology, University of Michigan, 2220 Biological Sciences Building, 1105 North University Avenue, Ann Arbor, MI 48109-1005, USA., Dick GJ; 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. |
| المصدر: | Harmful algae [Harmful Algae] 2024 Feb; Vol. 132, pp. 102580. Date of Electronic Publication: 2024 Jan 11. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Elsevier Country of Publication: Netherlands NLM ID: 101128968 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1878-1470 (Electronic) Linking ISSN: 15689883 NLM ISO Abbreviation: Harmful Algae Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Amsterdam ; New York : Elsevier, c2002- |
| مواضيع طبية MeSH: | Microcystis*/genetics , Cyanobacteria*/genetics, Humans ; Phylogeny ; Harmful Algal Bloom ; Genomics |
| مستخلص: | 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. Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. (Copyright © 2024. Published by Elsevier B.V.) |
| فهرسة مساهمة: | Keywords: Amplicon sequencing; Marker genes; Microcystis; Phylogenetics |
| تواريخ الأحداث: | Date Created: 20240208 Date Completed: 20240214 Latest Revision: 20240214 |
| رمز التحديث: | 20240214 |
| DOI: | 10.1016/j.hal.2024.102580 |
| PMID: | 38331539 |
| قاعدة البيانات: | MEDLINE |
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