Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution

Abstract

Background The order Oedogoniales within the single family Oedogoniaceae comprised of three genera, Oedogonium, Oedocladium, and Bulbochaete based on traditional morphological criteria. While several molecular phylogenetic studies have suggested that both Oedogonium and Oedocladium may not be monophyletic, broader taxon sampling and large amounts of molecular data acquisition could help to resolve the phylogeny and evolutionary problems of this order. This study determined five chloroplast (cp) genomes of Oedogonium species and aimed to provide further information on cp genome for a better understanding of the phylogenetic and evolutionary relationships of the order Oedogoniales. Results The five Oedogonium cp genomes showed typical quadripartite and circular structures, and were relatively conserved in their structure, gene synteny, and inverted repeats boundaries in general, except for small variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses based on 54 cp protein-coding genes examined by maximum likelihood and Bayesian analyses using amino acid and nucleotide datasets indicated that both Oedocladium and Oedogonium are polyphyletic groups. A positively selected gene (psbA) was identified in the two Oedocladium species and the terrestrial Oedogonium species, indicating that terrestrial Oedogoniales taxa may have undergone adaptive evolution to adjust to the difference in light intensity between aquatic and terrestrial habitats. Conclusions Our results enrich the data on cp genomes of the genus Oedogonium. The availability of these cp genomes can help in understanding the cp genome characteristics and resolve phylogenetic and evolutionary relationships of the order Oedogoniales.

Phylotranscriptomic and Evolutionary Analyses of Oedogoniales (Chlorophyceae, Chlorophyta)

“…Based on both the GO enrichment and KEGG pathway analyses, the function of the putative rapidly evolving genes is related to photosynthesis, considering the differences between aquatic and terrestrial habitats, we speculated that the terrestrial Oedogoniales species underwent rapid evolution to adapt to the varying conditions, especially for the terrestrialization process. This observation is consistent with the findings of a previous study that was based on chloroplast protein-coding genes [22]. A previous study revealed that the transition from water to land occurred several times and across different taxa, ranging from microorganisms to lichens and green plants, and later, arthropods, mollusks, annelids, and vertebrates [84].…”

“…The phylogenetic results based on the three kinds of dataset (18S rDNA, 99/29 singlecopy orthologues based on Oedogoniales and the OCC clade respectively) showed the same results that Oedogonium was polyphyletic and Oedocladium species formed a separate clade clustering with Oedogonium. At the same time, with C. reinhardtii as an outgroup, a BI tree based on 99 single-copy orthologues determined by the supermatrix method showed results similar to those of the ST analyzed by ASTRAL, which is consistent with the phylogenetic results based on 18S rDNA sequences, internal transcribed spacers (ITS), and chloroplast protein coding genes [21,22]. The inconsistency in the results observed with regard to the position of Oe.…”

“…However, the researchers suggested that the phylogeny required further investigation based on larger sampling of such taxa, particularly those of Oedocladium and Bulbochaete. Phylogenetic and evolutionary analyses based on chloroplast genome protein-coding genes have showed that both Oedocladium and Oedogonium are polyphyletic groups [21,22].…”

“…The genus Oedocladium (terrestrial) was presumed to have partly originated from Oedogonium species, which grow on moist soil surfaces and present underground filaments with slightly unbranched rhizoids [9]. The Oedocladium and the terrestrial Oedogonium species were detected to have positively selected positions in psbA, suggesting that terrestrial Oedogoniales taxa may have undergone adaptive evolution to adjust to the variations in light intensity between aquatic and terrestrial habitats [21,22]. dN/dS analysis in Oedogoniales would further contribute to revealing the evolutionary relationships in this group of algae.…”

Comparative plastome analysis of Musaceae and new insights into phylogenetic relationships

“…The parameters in CODEML control file were set as follow: (1) F3 × 4 model for codon frequencies; (2) “model = 0” for allowing a single dN/dS value to vary among branches; (3) “cleandata = 1” to remove gaps; (4) default settings for other parameters (as alternative model, “fix_omega = 0” and “omega = 2”) [ 64 ]. For the potential positive selection gene, a null model (set “fix_omega = 1” and “omega = 1” in the control file) was additionally performed following Xiong et al [ 93 ]. LRT were used to test model fit and a Chi-square test was conducted to calculate the P value.…”