Plastomes provide new insights into phylogeny and evolution in Chlorellaceae (Chlorophyta, Trebouxiophyceae).

Background: The family Chlorellaceae is a key focus of research on resource microalgae due to its potential applications and economic value. Despite its significance, the phylogenetic relationships and evolution among its members remain poorly understood. Plastomes, which offer numerous informative nucleotide sites for phylogenetic analysis, are expected to provide valuable reference information.

Results: In this study, 21 Chlorellacean plastomes were newly sequenced and combined with 37 previously published plastome data, resulting in a total of 58 plastomes representing all major clades. Phylogenomic analysis was conducted to reveal relationships among the members. Furthermore, plastome characteristics were compared to analyze Chlorellacean evolution. The results revealed well-resolved phylogenomic relationships among the clade level and genera level, with the inverted repeat (IR) region displaying interesting evolutionary patterns. Finally, adaptive changes in plastome size, gene content, and codon usage bias were observed in obligate heterotrophic taxa compared to autotrophic and mixotrophic taxa.

Conclusions: This study resolved the phylogenetic relationships among the main lineages within the Chlorellaceae. Additionally, our research highlighted prevalent structural variations in the evolution of Chlorellacean plastomes, emphasizing notable adaptive changes in plastome size, gene content, and codon usage bias in obligate heterotrophic taxa compared with autotrophic and mixotrophic taxa. This work not only enhances our understanding of the phylogenetic relationship within the Chlorellaceae but also enriches our comprehension of its evolutionary diversity.