Phylogenomic and Pangenomic Assessment of a Mediterranean Strain of Raphidiopsis raciborskii Extends Knowledge of the Global Distribution and Characteristics of a Potentially Toxigenic Cyanobacterium

TL;DR

This study analyzes a Mediterranean strain of Raphidiopsis raciborskii, a potentially harmful cyanobacterium, to better understand its global spread and genetic traits.

Contribution

The first taxonomic and functional assessment of a Mediterranean R. raciborskii strain, filling a gap in its global distribution and characteristics.

Findings

The Mediterranean strain shows strong genetic similarity to North American R. raciborskii genomes.

The genome lacks gene clusters for known cyanotoxins or emerging toxigenic compounds.

The open pangenome suggests adaptation to diverse environments through specialized genes.

Abstract

Among potentially toxigenic cyanobacteria, Raphidiopsis raciborskii has attracted considerable attention due to its ability to produce massive blooms and its recent spread to temperate regions. In this work, we reported for the first time a taxonomic and functional assessment of a R. raciborskii strain isolated from the Mediterranean region, contributing to filling a gap in the global distribution and characteristics of this species. The strain LT_0923 was isolated from Lake Trasimeno, a large and shallow lake in central Italy. The phylogenomic analyses based on selected marker genes and the core genome obtained from a pangenomic analysis based on a selection of available high‐quality genomes showed a strong correspondence of the Lake Trasimeno strain with the North American and, at a lower average nucleotide identity, with the South American genomes. The LT_0923 genome did not show the presence of gene clusters encoding legacy cyanotoxins or emerging toxigenic compounds. The open pangenome and the large fraction of distinct gene families identified in the cloud and partly shell genome, enriched with genes specialised in environmental‐specific functions and defence mechanisms, are consistent with the development of Raphidiopsis in geographically distinct regions.

The potentially toxigenic cyanobacterium Raphidiopsis raciborskii has spread to temperate regions and produces massive blooms. This study reports the first taxonomic and functional metagenomic assessment of a strain from the Mediterranean, thus filling a significant gap in global distribution. The Lake Trasimeno strain shows similarities to North and South American genomes.

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