Comparative analyses of chloroplast genomes provide insights into the Trentepohliales (Chlorophyta) adaptive evolution
Trentepohliales species occupy diverse habitats, including subaerial, epiphytic, and parasitic, which makes them ideal candidates for studying evolutionary adaptations to various habitats. In this study, we sequenced and assembled three Cephaleuros chloroplast genomes. The complete chloroplast genomes of C. lagerheimii Schmidle, C. diffusus Thompson &amp; Wujek, and C. virescens Kunze were 480,613, 383,846, and 472,444 bp in length, respectively. Notably, these genomes lacked inverted repeat regions. The sequenced chloroplast genome encompassed a total of 94 genes, comprising three rRNA, 27 tRNA, and 64 protein-coding genes. We performed a comprehensive comparative analysis of Trentepohliales. The variation in genome size among Trentepohliales was mainly attributed to the length of intergenic spacer regions, and followed by introns. Synteny analysis revealed numerous inversions and rearrangements occurred not only in the intergenic regions but also in some genes related to photosynthesis. Codon bias analysis indicated the codon use pattern was mainly affected by natural selection. Selective pressure analysis demonstrated that the majority of chloroplast genes in Trentepohliales species underwent purifying selection, while six chloroplast protein-coding genes exhibited positive selection using the branch-site model. These genes, involved in photosynthesis and ATP synthase, likely reflect adaption to the parasitic habitat. Our findings provided valuable insights into the diversity of Trentepohliales and the genomic evolutionary events of parasitic algae.