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Modern ultrastructural and molecular studies have provided important information that has led to a reassessment of the evolution of algae.
The evolution of algae and land plants and their photosynthetic machineries is intimately linked to the extended light-harvesting complex (LHC) protein superfamily.
Given its extraordinary metabolic plasticity, it is not surprising that some of these characteristics of cyanobacteria seem to have been transferred into the heterotrophic eukaryote during this process leading to the evolution of algae and higher plants (Margulis 1970; Reyes-Prieto et al. 2007).
Only two other convincing cases of horizontal gene transfer in the chloroplast have been documented thus far; both events took place early during the evolution of algae and involved the replacement of native chloroplast genes (the rbcL and rbcS pair and rpl36) by bacterial genes [ 58, 59].
To investigate the potential effect of the protein domain density (domain%, see Results and Discussion) on the evolution of algae proteins, we used C. reinhardtii protein domain annotations (JGI v.4) downloaded from SUPERFAMILY (v.1.75) (Wilson et al. 2007).
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In addition, the fossil record for some groups of algae has hindered evolutionary studies, and the realization that some algae are more closely related to protozoa or fungi than they are to other algae came late, producing confusion in evolutionary thought and delays in understanding the evolution of the algae.
The endosymbiotic uptake of an ancient cyanobacterial ancestor by a eukaryotic cell initiated the evolution of phototrophic algae and plants.
It is likely that adaptation to freshwater habitats involved multiple, independent events in the evolution of red algae.
A fundamental question in the evolution of chlorarachniophyte algae is the nature of the green algal endosymbiont that gave rise to the plastid and nucleomorph.
Being the closest relatives to land plants, studying the evolution of streptophyte algae has prompted the sequencing of multiple genomes from charophycean lineages [ 1– 5].
Interestingly, two cyp97a genes were predicted in C. reinhardtii and O. lucimarinus, indicating that lineage-specific gene duplications occurred during the evolution of these algae.
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