Cryptomonad

Abstract: ALTHOUGH it is widely accepted that the plastids of plants and algae originated as endosymbionts1, the details of this evolutionary process are unclear2'3. It has been proposed that in organisms whose plastids are surrounded by more than two membranes, the endosymbiont was a eukaryotic alga rather than a photosynthetic prokaryote4. The DNA-containing5 nucleomorph6 of cryptomonad algae appears to be the vestigial nucleus of such an algal endosymbiont7. Eukaryotic-type ribosomal RNA sequences have been localized to a nucleolus-like structure in the nucleomorph8. In support of the hypothesis that cryptomonads are evolutionary chimaeras of two distinct eukaryotic cells, we show here that Cryptomonas Φ contains two phylogenetically separate, nuclear-type small-subunit rRNA genes, both of which are transcriptionally active. We incorporate our rRNA sequence data into phylogenetic trees, from which we infer the evolutionary ancestry of the host and symbiont components of Cryptomonas Φ. Such trees do not support the thesis3 that chromophyte algae evolved directly from a cryp-tomonad-like ancestor.

Abstract: Selective extraction and morphological evidence indicate that the phycobiliproteins in three Cryptophyceaen algae (Chroomonas, Rhodomonas, and Cryptomonas) are contained within intrathylakoidal spaces and are not on the stromal side of the lamellae as in the red and blue-green algae. Furthermore, no discrete phycobilisome-type aggregates have thus far been observed in the Cryptophyceae. Structurally, although not necessarily functionally, this is a radical difference. The width of the intrathylakoidal spaces can vary but is generally about 200-300 A. While the thylakoid membranes are usually closely aligned, grana-type fusions do not occur. In Chroomonas these membranes evidence an extensive periodic display with a spacing on the order of 140-160 A. This periodicity is restricted to the membranes and has not been observed in the electron-opaque intrathylakoidal matrix.

Abstract: Red algae are one of the main photosynthetic eukaryotic lineages and are characterized by primitive features, such as a lack of flagella and the presence of phycobiliproteins in the chloroplast. Recent molecular phylogenetic studies using nuclear gene sequences suggest two conflicting hypotheses (monophyly versus non-monophyly) regarding the relationships between red algae and green plants. Although kingdom-level phylogenetic analyses using multiple nuclear genes from a wide-range of eukaryotic lineages were very recently carried out, they used highly divergent gene sequences of the cryptomonad nucleomorph (as the red algal taxon) or incomplete red algal gene sequences. In addition, previous eukaryotic phylogenies based on nuclear genes generally included very distant archaebacterial sequences (designated as the outgroup) and/or amitochondrial organisms, which may carry unusual gene substitutions due to parasitism or the absence of mitochondria. Here, we carried out phylogenetic analyses of various lineages of mitochondria-containing eukaryotic organisms using nuclear multigene sequences, including the complete sequences from the primitive red alga Cyanidioschyzon merolae. Amino acid sequence data for two concatenated paralogous genes (alpha- and beta-tubulin) from mitochondria-containing organisms robustly resolved the basal position of the cellular slime molds, which were designated as the outgroup in our phylogenetic analyses. Phylogenetic analyses of 53 operational taxonomic units (OTUs) based on a 1525-amino-acid sequence of four concatenated nuclear genes (actin, elongation factor-1alpha, alpha-tubulin, and beta-tubulin) reliably resolved the phylogeny only in the maximum parsimonious (MP) analysis, which indicated the presence of two large robust monophyletic groups (Groups A and B) and the basal eukaryotic lineages (red algae, true slime molds, and amoebae). Group A corresponded to the Opisthokonta (Metazoa and Fungi), whereas Group B included various primary and secondary plastid-containing lineages (green plants, glaucophytes, euglenoids, heterokonts, and apicomplexans), Ciliophora, Kinetoplastida, and Heterolobosea. The red algae represented the sister lineage to Group B. Using 34 OTUs for which essentially the entire amino acid sequences of the four genes are known, MP, distance, quartet puzzling, and two types of maximum likelihood (ML) calculations all robustly resolved the monophyly of Group B, as well as the basal position of red algae within eukaryotic organisms. In addition, phylogenetic analyses of a concatenated 4639-amino-acid sequence for 12 nuclear genes (excluding the EF-2 gene) of 12 mitochondria-containing OTUs (including C. merolae) resolved a robust non-sister relationship between green plants and red algae within a robust monophyletic group composed of red algae and the eukaryotic organisms belonging to Group B. A new scenario for the origin and evolution of plastids is suggested, based on the basal phylogenetic position of the red algae within the large clade (Group B plus red algae). The primary plastid endosymbiosis likely occurred once in the common ancestor of this large clade, and the primary plastids were subsequently lost in the ancestor(s) of the Discicristata (euglenoids, Kinetoplastida, and Heterolobosea), Heterokontophyta, and Alveolata (apicomplexans and Ciliophora). In addition, a new concept of "Plantae" is proposed for phototrophic and nonphototrophic organisms belonging to Group B and red algae, on the basis of the common history of the primary plastid endosymbiosis. The Plantae include primary plastid-containing phototrophs and nonphototrophic eukaryotes that possibly contain genes of cyanobacterial origin acquired in the primary endosymbiosis.