International Journal of Marine Science, 2025, Vol.15, No.2, 107-117 http://www.aquapublisher.com/index.php/ijms 108 genome, mitochondrial genome, nuclear genome and transcriptome has greatly enriched the information that can be used for phylogenetic analysis. Through these technical means, researchers began to reconstruct phylogenetic trees including prokaryotic algae (cyanobacteria) and various eukaryotic algae, and explore the origin and evolution of algae. At present, algae research has accumulated a large amount of molecular and genomic data, but there are still many unsolved mysteries. For example, algae are not single-line groups, and there are complex factors such as endosynthetic events and horizontal gene transfer among different groups, which pose challenges to phylogenetic analysis. Different researchers also have certain disputes about the classification system and evolutionary history of algae, and need to systematically integrate multiple aspects of evidence to explain it. In this context, this study aims to review the phylogenetic relationship and evolutionary history of major algae lineages, and comprehensively review relevant research progress from multiple angles such as classification, molecular evidence, chloroplast origin, time scale and environmental drivers, providing a reference for understanding algae diversity and evolutionary mechanisms. 2 Overview of Classification of Major Algae Lineages 2.1 Prokaryotic algae: characteristics and systemic status of cyanobacteria (cyanobacteria) Cyanobacteria is one of the oldest photosynthetic organisms on Earth, with Gram-negative prokaryotic cell structure, without nuclear membrane enclosure, photosynthesis releases oxygen. Traditionally, cyanobacteria have been classified as a primitive algae (blue-green algae) in the plant world, but it has been clearly stated that it belongs to the bacterial domain, unlike eukaryotic algae. The photosynthetic pigments of cyanobacteria are mainly chlorophyll a and phycobilidin. They are extremely extensive in freshwater and marine environments, forming various colorful and changeable biological symbiotic or coherence groups, such as snow algae, solidified algae, etc. Due to its diverse and ancient morphology, cyanobacteria are extremely complex in classification, and their classification system has undergone many revisions. Komárek et al. proposed a modern multiphase classification system for cyanobacteria, which divided cyanobacteria into many families, each containing fewer species, based on model species (Komárek et al., 2014). In terms of molecular systems, 16S rDNA, ITS sequence and functional genes (such as nitrogen fixation gene nifH, etc.) are widely used in the study of the evolutionary relationship of cyanobacteria. The current consensus is that cyanobacteria constitute an independent lineage of bacterial domains, and their chloroplasts originate from a cyanobacteria ancestor and become an important part of eukaryotic photosynthetic organisms. However, under the concept of algae, cyanobacteria and eukaryotic algae are not monophyletic, and should be regarded as independent branches of prokaryotic photosynthetic organisms. 2.2 The main groups of eukaryotic algae: green algae, brown algae, red algae, etc. There are many species of eukaryotic algae and can be divided into multiple lineages. Green algae (Chlorophyta and Charophyta) together with terrestrial plants (Embryophyta) form the phylum of green plants (Viridiplantae). Most green algae contain chlorophyll a and b, the cell wall is mostly cellulose, the habitat covers freshwater and oceans, and most of them are single-cell, filamentous or large-scale groups; among them, Charophyta are close relatives of terrestrial plants. Brown algae (Phaeophyceae) belongs to the varicosome group of pigments originating from red algae (Ochromophyta). It is mainly dellate, nude algae, green algae, and other micro-groups, while the latter mainly refers to large seaweeds suchistributed on the cold temperate coast. It is known for its multicellular giant kelp and sea fog. It contains chlorophyll a, c and the co-pigmented fucoxanthin, and has complex morphology (Friedl and Rybalka, 2012). Red algae (Rhodophyta) mainly consists of marine red tide algae, lilac, etc., containing chlorophyll a and red algae (phycoerythrin, phycocyanin), and belongs to the primary membrane chloroplast group. In addition, there are a series of eukaryotic microalgae groups that obtain chloroplasts by secondary or tertiary endosymbiosis: such as diatoms (Bacillariophyceae), Chrysophyceae/Xanthophyceae), Cryptophyta, Dinophyta, nude algae (Euglenophyta), etc. Some experts have divided algae into "microalgae" and "macroalgae": the former includes cyanobacteria, diatoms, golden algae, zooxanthaceae, cryptoalgae, dinoflag as red algae, brown algae and streptaceae.
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