Phylogenetic and evolutionary insights into Oedogoniales from nine newly sequenced chloroplast genomes

The order Oedogoniales (Chlorophyceae, Chlorophyta) comprises over 600 described species, divided into three genera-Oedogonium, Oedocladium, and Bulbochaete-based on the presence of branches and hairs. Current classification relies primarily on morphological traits, yet the complex morphological features make species identification challenging. Moreover, limited molecular data have hindered phylogenetic analyses, leaving the phylogeny of Oedogonium problematic. A previous study proposed a new taxonomic classification of the genus Oedogonium based on basal cell shape, splitting it into two sections: section Globosum and section Elongatum. In the present study, we sequenced nine chloroplast (cp.) genomes of Oedogoniales, including four from section Globosum and five from section Elongatum, and performed comparative analyses to elucidate the phylogenetic and evolutionary relationships between these two sections.

The nine newly sequenced Oedogoniales cp. genomes exhibited highly conserved structures and gene numbers, identical to those previously reported for this order. Nevertheless, variations in genome size, AT content, introns, repeats, and some structural rearrangements were observed. Phylogenetic analyses based on 64 cp. protein‑coding genes, using Bayesian inference and ASTRAL species trees constructed from amino acid and nucleotide datasets, consistently supported the division of Oedogoniales into two sections according to basal cell shape, with the genus Oedocladium clustering within section Elongatum. Evolutionary analysis revealed that 27 genes showed significant differences in dN and dS between the two sections, and three genes-psbA, atpA, and psbC-were identified as undergoing rapid evolution and positive selection. These findings suggest that species of section Globosum experienced rapid radiation and have retained ancestral morphological characteristics since their divergence from the ancestral lineage.

Our results enrich the data on cp. genomes of the Oedogoniales. The availability of these cp. genomes can help in understanding the cp. genome characteristics and resolve phylogenetic and evolutionary relationships of the order Oedogoniales.