Comparative genomic and phylogenetic analysis of mitochondrial genomes of the Pseudo-nitzschia HAB species

The genus Pseudo-nitzschia within Bacillariophyta (diatoms) is best known for its rich collection of toxigenic harmful algal bloom (HAB) species capable of producing the neurotoxin domoic acid (DA), which causes amnesic shellfish poisoning (ASP) in humans. Molecular markers such as 18S rDNA, ITS1, and ITS2 have been applied to facilitate Pseudo-nitzschia species identification because morphology-based methods often could not adequately distinguish different species due to their morphological similarities and plasticity. In this study, we constructed mitochondrial genomes (mtDNAs) for 11 Pseudo-nitzschia species and assessed their utility as "super-barcodes" for species identification and evolutionary analysis. These mtDNAs exhibited conserved genome structures despite variability in repeat regions. A potential tatA-tatC gene fusion event was observed in a single Pseudonitzschia species P. brasiliana. We also observed intron variability in cox1 genes. Phylogenetic analyses of mtDNAs, chloroplast genomes (cpDNAs), and nuclear ribosomal DNA (nrDNA) arrays revealed consistent results, supporting the closely related but distinct clustering of the genera Fragilariopsis and Pseudo-nitzschia. We further designed a high-resolution molecular marker tatA for species identification based on the comparative analysis of these mtDNAs, which could be used to track Pseudo-nitzschia diversity. These findings offer new genome resources and new insights into the genetic evolution and classification of Pseudo-nitzschia, underscoring the need for continued research in this field.