Extreme genome diversity and cryptic speciation in a harmful algal-bloom-forming eukaryote

Wisecaver, Jennifer H.; Auber, Robert; Pendleton, Amanda L.; Watervoort, Nathan F.; Fallon, Timothy R.; Riedling, Olivia L.; Manning, Schonna R.; Moore, Bradley S.; Driscoll, William W.

doi:10.1016/j.cub.2023.05.003

Cited by 9 publications

(20 citation statements)

References 134 publications

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“…(strain ID 3408, CCAC, University Duisburg-Essen), a haptophyte from the Pavlovaceae family. Short read genome assemblies of other P. parvum genomes from Wisecaver et al 16 were downloaded from the corresponding figshare repository and aligned to the ODER1 chloroplast genome by Minimap2. 22 Alignments were converted to maf format (paftools.js view -f maf) and screened for ortholog matches using last-split.…”

Section: Prymnesium Parvum Phylogeny Based On Chloroplast Dnamentioning

confidence: 99%

“…The two haploid assemblies were aligned to each other with Minimap2 and stringent mapping parameters "-x asm5" for genomes with divergence of less than 5%, 22,32 results were plotted in a dotplot fashion using minidot. 33 The haploid assemblies were also compared to the P. parvum 12B1 type A reference genome 16 (Minimap2, minidot but using less stringent alignment parameters: -x mapont). A genome browser for the ODER1 assembly has been established at http://genomes.igbberlin.de:8081/ (will be made publicly available upon acceptance of the manuscript).…”

Section: Diploid Genome Assemblymentioning

confidence: 99%

“…10 These compounds consist of a ladder-frame polyether backbone, whose length defines the type, as well as various pentose and/or hexose units. 10,12 More recently, flow-cytometry, transcriptomics, 13,14 and whole genome sequencing 15,16 indicate that P. parvum s.l. is a complex of at least 40 genetically distinct strains (i.e., forms within types A, B, C) that differ in genome size and/or ploidy and produce typespecific prymnesins and even strain-specific mixtures of differently glycosylated/halogenated prymnesin variants.…”

Section: Introductionmentioning

confidence: 99%

“…is a complex of at least 40 genetically distinct strains (i.e., forms within types A, B, C) that differ in genome size and/or ploidy and produce typespecific prymnesins and even strain-specific mixtures of differently glycosylated/halogenated prymnesin variants. 15,16 The polyketide-like chemical nature of these prymnesins suggests that polyketide synthases (PKSs) contribute to their biosynthesis, 14,17 while glycosyltransferases are essential for polysaccharide modifications.…”

Section: Introductionmentioning

confidence: 99%

“…Thus, to uncover the hidden diversity of P. parvum s.l., unambiguous identification of these harmful bloom-forming algae requires genomic data. 16 This will also facilitate the identification of the prymnesin types, which is of particular interest as not only its structure but also its toxicity is type-dependent. 18 To understand how the genes of the major protein families enable strain-specific toxin production and evolution, comparative genomics involving additional chromosome-scale high-quality reference genomes of P. parvum are essential.…”

Section: Introductionmentioning

confidence: 99%

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The haplotype-resolved Prymnesium parvum (type B) microalga genome reveals the genetic basis of its fish-killing toxins

Kuhl,

Strassert,

Čertnerova

et al. 2024

Preprint

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The catastrophic loss of aquatic life in the Central European Oder River in 2022, caused by a toxic bloom of the haptophyte microalga Prymnesium parvum (in a wide sense, s.l.), underscores the need to improve our understanding of the genomic basis of the toxin. Previous morphological, phylogenetic, and genomic studies have revealed cryptic diversity within P. parvum s.l. and uncovered three clade-specific (types A, B, C) prymnesin toxins. Here, we used state-of-the-art long-read sequencing and assembled the first haplotype-resolved diploid genome of a P. parvum type B, the strain responsible for the Oder disaster. Comparative analyses with type A genomes uncovered a genome-size expansion driven by repetitive elements in type B. We also found conserved chromosomal synteny but divergent evolution in several polyketide synthase (PKS) genes, which are known to underlie toxin production in combination with environmental cues. We identified a specific, approximately 20 kilobase pair comprising deletion in the largest PKS gene of type B that we link to differences of the chemical structure of types A and B prymnesins. Electron-microscopy and flow cytometry confirmed diploidy in the Oder River strain and differences to closely related strains in morphology and ploidy. Our results provide unprecedented resolution of strain diversity in P. parvum and a better understanding of the genomic basis of toxin variability in haptophytes. The reference-quality genome will help to understand changes to microbial diversity in the face of increasing environmental pressures, and provides a basis for strain-level monitoring of invasive Prymnesium in the future.

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Section: Prymnesium Parvum Phylogeny Based On Chloroplast Dnamentioning

confidence: 99%