This study determined the transcriptomes of eight Oedogoniales species, including six species from Oedogonium and two species from Oedocladium to conduct phylotranscriptomic and evolutionary analyses. 155,952 gene families and 192 single-copy orthogroups were detected. Phylotranscriptomic analyses based on single-copy orthogroups were conducted using supermatrix and coalescent-based approaches. The phylotranscriptomic analysis results revealed that Oedogonium is polyphyletic, and Oedocladium clustered with Oedogonium. Together with the transcriptomes of the OCC clade in the public database, the phylogenetic relationship of the three orders (Oedogoniales, Chaetophorales, Chaetopeltidales) is discussed. The non-synonymous (dN) to synonymous substitution (dS) ratios of single-copy orthogroups of the terrestrial Oedogoniales species using a branch model of phylogenetic analysis by maximum likelihood were estimated, which showed that 92 single-copy orthogroups were putative rapidly evolving genes. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses results revealed that some of the rapidly evolving genes were associated with photosynthesis, implying that terrestrial Oedogoniales species experienced rapid evolution to adapt to terrestrial habitats. The phylogenetic results combined with evolutionary analyses suggest that the terrestrialization process of Oedogoniales may have occured more than once.

Oedogoniales comprises the three genera Oedogonium, Oedocladium, and Bulbochaete, which include more than 600 described species. The classification of Oedogoniaceae is currently based on morphology, and the complicated morphological characteristics make species identification difficult, with the limited molecular data also restricting the phylogenetic analysis. In the present study, we collected 47 Oedogonium specimens from China and sequenced 18S rDNA, ITS2, ITS (ITS1 + 5.8S + ITS2), and rbcL sequences to conduct phylogenetic analyses. We selected nine morphological characteristics, most of which were considered important in traditional systematics, for comparison with the molecular phylogeny results. All the topologies based on different datasets showed similar results; Oedogonium was a paraphyletic group, and Oedocladium and Bulbochaete clustered with Oedogonium. The morphological characteristics matching the phylogenetic results showed that the types of sexual differentiation, characteristics of the oogonium (including shape, types of aperture, and ornamentation of oospore wall), division types of antheridial, and number of sperm of each antheridial, which are considered the most important morphological characteristics in traditional taxonomy of Oedogonium, did not form monophyletic lineages respectively, indicating that traditional systematics may not reflect the real phylogeny of the genus Oedogonium. In addition, a new taxonomical classification of the genus Oedogonium was presented according to the shapes of basal cells, which matched well with the phylogenetic topologies. In addition, we propose to divide the genus Oedogonium into two sections, section Globosum and section Elongatum, representing the species with spherical or sub-hemispherical basal cells and elongated basal cells, respectively.

Several quadriflagellate genera were revealed as the members of deep branches in Chlamydomonadales. However, the phylogenetic relationships among these quadriflagellate genera remained unresolved, and little information is known about the chloroplast genome structure for the chlamydomonadalean early-diverging lineages due to the limited data. In this study, we conducted phylogenetic and comparative genomic analyses with 6 newly sequenced quadriflagellate chlamydomonadalean chloroplast genomes. Four phylogenetic inferences based on different datasets recovered the robust topology, with Staurocarteria-Hafniomonas as the earliest-diverging lineage, followed by Corbierea within Chlamydomonadales and Spermatozopsis included in Sphaeropleales. The amino acid dataset combined with the site-heterogeneous model received the highest support for key nodes and may better fit the inferences of the deep relationships in Chlamydomonadales. Moreover, Sp. similis chloroplast genome is also more structurally similar to its close relatives than to other quadriflagellate chlamydomonadaleans. Phylogeny and genome structure features both indicated the taxonomic position of Spermatozopsis should be reconsidered. The loss of large inverted repeats (IRs) was first reported in chlamydomonadaleans (Co. pseudopalmata), and may occur at least 4 times in Chlamydomonadales. Comparative genome analyses demonstrated the highly divergent large IRs and a high level of rearrangements across the entire genome. IR expansions/contractions and inversions contribute to changes in gene content and gene order in this region. This study provides a foundation for future research on the phylogenetic relationships as well as chloroplast genomic features and evolution of the entire Chlamydomonadales.

The order Oedogoniales (Chlorophyceae, Chlorophyta) comprises over 600 described species, divided into three genera—Oedogonium, Oedocladium, and Bulb