Phylogeny and species delineation in the marine diatomPseudo‐nitzschia(Bacillariophyta) usingcox1,LSU, andITS2rRNAgenes: A perspective in character evolution

Abstract

Analyses of the mitochondrial cox1, the nuclear-encoded large subunit (LSU), and the internal transcribed spacer 2 (ITS2) RNA coding region of Pseudo-nitzschia revealed that the P. pseudodelicatissima complex can be phylogenetically grouped into three distinct clades (Groups I-III), while the P. delicatissima complex forms another distinct clade (Group IV) in both the LSU and ITS2 phylogenetic trees. It was elucidated that comprehensive taxon sampling (sampling of sequences), selection of appropriate target genes and outgroup, and alignment strategies influenced the phylogenetic accuracy. Based on the genetic divergence, ITS2 resulted in the most resolved trees, followed by cox1 and LSU. The morphological characters available for Pseudo-nitzschia, although limited in number, were overall in agreement with the phylogenies when mapped onto the ITS2 tree. Information on the presence/absence of a central nodule, number of rows of poroids in each stria, and of sectors dividing the poroids mapped onto the ITS2 tree revealed the evolution of the recently diverged species. The morphologically based species complexes showed evolutionary relevance in agreement with molecular phylogeny inferred from ITS2 sequence-structure data. The data set of the hypervariable region of ITS2 improved the phylogenetic inference compared to the cox1 and LSU data sets. The taxonomic status of P. cuspidata and P. pseudodelicatissima requires further elucidation.

Phylogenetic relationships of Pseudo-nitzschia subpacifica (Bacillariophyceae) from the Mexican Pacific, and its production of domoic acid in culture

“…A four-helix structure (I-IV) with an additional helix, IIa, was identified, similar to previous findings [7,8,50]. One SNP was found at the base of helix II when compare the Todos Santos PLOS ONE https://doi.org/10.1371/journal.pone.0231902.g001…”

“…Only ITS2 of the ITS region was used in this study. This ITS rDNA sequence was aligned with a total of 141 Pseudo-nitzschia sequences (S1 and S2 Tables) retrieved from the NCBI nucleotide database by 4SALE [68] as detailed in Lim, Tan [8]. The final data set of ITS2 comprised 141 taxa with 1 outgroup.…”

“…The ITS2 analyses were rooted with a sequence of Nitzschia longissima. ML analyses were carried out with Phangorn in which the model parameters was directly estimated from the aligned data set [8,69]. Bootstrap support values were obtained based on 500 bootstrap replicates.…”

“…Bootstrap support values were obtained based on 500 bootstrap replicates. The BI (Bayesian) analyses of ITS2 were carried out using MrBayes v3.2.6 [70] following the parameters outlined in Lim et al [8], with 2,650,000 Markov chain Monte Carlo generations, sample frequency was 100, the number of burn-in generations was 6625, and the best model obtained as detailed in Lim et al [8].…”

“…Pseudo-nitzschia is one of the most common diatom genus, belonging to the Bacillariaceae family. It is a cosmopolitan genus that comprises at least 52 species [7][8][9][10][11][12][13]. It has been documented that many species are capable of producing the neurotoxin domoic acid (DA) under stressed conditions [11].…”