International Journal of Marine Science, 2025, Vol.15, No.2, 107-117 http://www.aquapublisher.com/index.php/ijms 110 as genomic structural rearrangement, gene family expansion or contraction, and assist in clarifying lineage branches. Transcriptome data (phylogenetic transcriptomics) can also be used to infer kinship, and in dinoflagellate studies, transcriptome studies of the genus Cyclone revealed the main phylogenetic turning points in the evolution of this group (Jia, 2014). At the same time, metagenomic and environmental genome analysis has been gradually used in the diversity and phylogenetic research of algae communities. Figure 1 Maximum-Likelihood tree inferred from 58 protein-coding sequences– 13 mitochondrial and 45 plastid genes. Bootstrap value from ML and posterior probability from Bayesian inference are shown at the node. The scale bar represents the estimated number of nucleotide substitution per site (Adopted from Mekvipad and Satjarak, 2019) 4 The Origin of Chloroplasts and The Evolution of Algae Photosynthetic Pigments 4.1 Primary endosymbiotic events and the formation of primitive photosynthetic eukaryotes The origin of chloroplasts can be traced to primary endosymbiosis between eukaryotes and cyanobacteria ancestors. The study pointed out that after primary endosymbiosis occurs, three independent primary photosynthetic eukaryotic branches emerge: gray algae, red algae and green algae (including terrestrial plants), which are collectively called primitive photosynthetic organisms (Archaepastida). In this event, a heterotrophic eukaryotic host cell engulfs a cyanobacteria containing photosynthetic capacity, which eventually evolved into the first chloroplasts (Chan and Bhattacharya, 2011). Gray algae contains three outer membranes, a small amount of chlorophyll and chromophyll; red algae and green algae have evolved different combinations of pigment systems (red algae contains phycobiliproteins, and green algae contains chlorophyll a/b). After that, red algae, green algae and gray algae each evolve independently, and one branch of the green algae family eventually landed to form terrestrial plants. This primary symbiotic event laid the foundation for all photosynthetic eukaryotes, allowing eukaryotes to have the ability to perform photosynthesis. 4.2 Secondary and tertiary endosymbiosis and their impact on algae diversity After primary endosymbiosis, chloroplasts further spread to other algae groups through eukaryotic-eukaryotic endosymbiosis, forming so-called complex chloroplasts (with additional membrane numbers). In secondary endosymbiosis, some native eukaryotic algae are again engulfed by other eukaryotic cells. For example, members of Cryptophyta and Cyclophyta obtained complex chloroplasts from red algae, while Ochromophyta (including brown algae, diatoms, etc.) came from the homologous pigment of red algae (Grisdale ad Archibald, 2016). Tertiary endosymbiosis occurs when algae containing complex chloroplasts are engulfed by higher eukaryotic cells, such as some Dinophyta that have obtained chloroplasts transferred from Dinoflagellates or Cryptoalgae. The chloroplasts of these multilayer membranes often retain the nucleus (nuclear matrix) of the endosymbol,
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