Strong population genomic structure of the toxic dinoflagellate Alexandrium minutum inferred from meta‐transcriptome samples

Despite theoretical expectations, marine microeukaryote population are often highly structured and the mechanisms behind such patterns remain to be elucidated. These organisms display huge census population sizes, yet genotyping usually requires clonal strains originating from single cells, hindering proper population sampling. Estimating allelic frequency directly from population wide samples, without any isolation step, offers an interesting alternative. Here we validate the use of meta-transcriptome environmental samples to determine the population genetic structure of the dinoflagellate Alexandrium minutum. Strain and meta-transcriptome based results both indicated a strong genetic structure for A. minutum in Western Europe, to the level expected between cryptic species. The presence of numerous private alleles, and even fixed polymorphism, would indicate ancient divergence and absence of gene flow between populations. Single Nucleotide Polymorphisms (SNPs) displaying strong allele frequency differences were distributed throughout the genome, which might indicate pervasive selection from standing genetic variation (soft selective sweeps). However, a few genomic regions displayed extremely low diversity that could result from the fixation of adaptive de novo mutations (hard selective sweeps) within the populations.

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Supplementary Figure 1: Graphical summary illustrating the estimation of allelic ...
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Supplementary Figure 2: Relationship between sequencing strategy and Fst estimates. Five meta-transcriptome samples were....
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Supplementary Figure 3: Reference allele frequency of population diagnostic SNPs. Population diagnostic SNPs (SNPs displaying one allele in all strains from a given population and the alternative ...
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Supplementary Figure 4 : Boxplot indicating the pairwise Fst between and within populations based on meta-transcriptome samples using de novo SNPs. The results ...
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Supplementary Figure 5 : Folded Joint Allele Frequency Spectrum (JAFS) comparing the rare allele frequencies in the three populations using de novo SNPs identified from ...
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Supplementary Figure 6: Genome wide diversity using de novo SNPs identified from meta-transcriptome samples. A. Haplotype diversity (H) moving average (width=100SNPs, steps=20 SNPs) along A. minutum..
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Table S1: Supplementary Tables
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Table S2: Supplementary Tables
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How to cite
Le Gac Mickael, Mary Lou, Metegnier Gabriel, Quéré Julien, Siano Raffaele, Rodríguez Francisco, Destombe Christophe, Sourisseau Marc (2022). Strong population genomic structure of the toxic dinoflagellate Alexandrium minutum inferred from meta‐transcriptome samples. Environmental Microbiology. 24 (12). 5966-5983.,

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