Six Newly Sequenced Chloroplast Genomes From Quadriflagellate Chlamydomonadales (Chlorophyceae): Phylogeny and Comparative Genome Analyses

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.