Diversification of a chimaeric algal group, the chlorarachniophytes: Phylogeny of nuclear and nucleomorph small-subunit rRNA genes

Chlorarachniophytes are a group of algae that acquired their chloroplasts b y a eukaryote-eukaryote endosymbiosis (secondary endosymbiosis) between a p rotozoan and a green alga. The green algal endosymbiont still keeps its own nucleus as a reduced form, called a nucleomorph, that contains the smalles t eukaryotic genome. We sequenced both nuclear and nucleomorph small-subuni t ribosomal RNA (SSU rRNA) genes from seven chlorarachniophyte strains. In order to examine the origins of this algal group in more detail and clarify their phylogenetic relationship and morphological diversification, we perf ormed molecular phylogenetic analyses of their nuclear and nucleomorph SSU rRNA genes with maximum-likelihood, maximum-parsimony, and neighbor-joining methods. The results show that chlorarachniophytes evolved from a single s econdary endosymbiosis and suggest that the endosymbiont was an ulvophycean green alga. They also confirm that the host was related to monadofilosans (sarcomonad flagellates and euglyphid amoebae). Nuclear and nucleomorph tre es are largely congruent, and both show the same five major chlorarachnioph yte lineages. However, nucleotide substitution rates of nucleomorph rRNA ge nes were much higher than those of the nuclear genes. The four known types of pyrenoid ultrastructure map onto the molecular tree in such a way that e ach had only a single origin, indicating that these ultrastructural differe nces among the endosymbionts are reliable indicators of their phylogenetic relationship. Mapping overall cell morphology onto the tree suggests that a t least four losses of the amoeboid stage of the life cycle, two losses of cell walls, and two losses of phagotrophy may have occurred independently i n the evolution of the chlorarachniophytes.