Taxonomic re-examination of six species of Nitella (Charales, Charophyceae) from Asia, and phylogenetic relationships within the genus based on rbcL and atpB gene sequences

Six taxa of Nitella (Charales, Charophyceae), collected from Asia, were investigated using light and scanning electron microscopy (SEM) for the oospores, and sequencing of the gene encoding the large subunit of Rubisco (rbcL), in order to improve our understanding of their taxonomic status. Our SEM observations demonstrated that the oospore morphology of four taxa belonging to the subgenus Tieffallenia [N.megaspora (J.Groves) Sakayama, comb. nov. (= N.pseudoflabellata f.megaspora), N.tumulosa (= N.furcata f.tumulosa), N.gracillima (= N.gracilis f.gracillima) and N.axilliformis (= N.translucens f.axilliformis)] is distinctly different from that of the species N.pseudoflabellata, N.furcata, N.gracilis and N.translucens, respectively, to which R.D.Wood assigned them as infraspecific taxa. Our rbcL sequence data showed that N.megaspora is separated phylogenetically from N.pseudoflabellata, N.tumulosa from N.furcata and N.axilliformis from N.translucens. In addition, to re-examine the taxonomic system of Nitella proposed by R.D.Wood, who treated oospore wall ornamentations as diagnostic at the infraspecific level, we carried out molecular phylogenetic analyses using the combined sequence data set for the gene encoding the beta subunit of ATP synthase (atpB) and the rbcL gene of these six species, as well as eleven species of Nitella studied previously. The combined sequence data resolved five robust clades within the subgenus Tieffallenia that were characterized by differences in oospore wall ornamentation. However, the species and sectional diagnoses of R.D.Wood, such as the form and cell number of dactyls in vegetative thalli, were variable within the clades. Therefore, R.D.Wood\u27s taxonomic system appears unnatural, at least within subgenus Tieffallenia

Taxonomic re-examination of Nitella (Charales, Charophyceae) from Japan, based on microscopical studies of oospore wall ornamentation and rbcL gene sequences

Nine taxa of Nitella (Charales, Charophyceae) from Japan, including five Japanese or east Asian endemics, were examined to improve understanding of their taxonomic status. The approaches used were light and scanning electron microscopy (SEM) of the oospores and sequencing of the gene (rbcL) encoding the large subunit of Rubisco. The species delineated were N.pulchella (= N.dualis f.pulchella), N.furcata, N.inversa (= N.furcata f.inversa), N.gracilens (= N.furcata f.gracilens), N.pseudoflabellata, N.hyalina, N.spiciformis (= N.gracilis f.spiciformis), N.moriokae (= N.rigida f.moriokae) and N.axillaris (= N.translucens var.axillaris). SEM observations showed that the oospore morphology of four taxa - N.inversa, N.gracilens, N.spiciformis and N.axillaris - was distinctly different from that of the species (N.furcata, N.furcata, N.gracilis and N.translucens, respectively) to which R.D.Wood assigned them as infraspecific taxa. Furthermore, the rbcL data showed that N.gracilens was separated phylogenetically from N.furcata and N.axillaris from N.translucens. This is the first integration of SEM oospore morphology and molecular phylogenetics in charalean taxonomy, demonstrating the efficiency of both approaches to address problems at lower taxonomic levels

An extended phylogenetic analysis reveals ancient origin of "non-green" phosphoribulokinase genes from two lineages of "green" secondary photosynthetic eukaryotes: Euglenophyta and Chlorarachniophyta

Abstract Background Euglenophyta and Chlorarachniophyta are groups of photosynthetic eukaryotes harboring secondary plastids of distinct green algal origins. Although previous phylogenetic analyses of genes encoding Calvin cycle enzymes demonstrated the presence of genes apparently not derived from green algal endosymbionts in the nuclear genomes of Euglena gracilis (Euglenophyta) and Bigelowiella natans (Chlorarachniophyta), the origins of these "non-green" genes in "green" secondary phototrophs were unclear due to the limited taxon sampling. Results Here, we sequenced five new phosphoribulokinase (PRK) genes (from one euglenophyte, two chlorarachniophytes, and two glaucophytes) and performed an extended phylogenetic analysis of the genes based on a phylum-wide taxon sampling from various photosynthetic eukaryotes. Our phylogenetic analyses demonstrated that the PRK sequences form two genera of Euglenophyta formed a robust monophyletic group within a large clade including stramenopiles, haptophytes and a cryptophyte, and three genera of Chlorarachniophyta were placed within the red algal clade. These "non-green" affiliations were supported by the taxon-specific insertion/deletion sequences in the PRK alignment, especially between euglenophytes and stramenopiles. In addition, phylogenetic analysis of another Calvin cycle enzyme, plastid-targeted sedoheptulose-bisphosphatase (SBP), showed that the SBP sequences from two genera of Chlorarachniophyta were positioned within a red algal clade. Conclusions Our results suggest that PRK genes may have been transferred from a "stramenopile" ancestor to Euglenophyta and from a "red algal" ancestor to Chlorarachniophyta before radiation of extant taxa of these two "green" secondary phototrophs. The presence of two of key Calvin cycle enzymes, PRK and SBP, of red algal origins in Chlorarachniophyta indicate that the contribution of "non-green" algae to the plastid proteome in the "green" secondary phototrophs is more significant than ever thought. These "non-green" putative plastid-targeted enzymes from Chlorarachniophyta are likely to have originated from an ancestral red alga via horizontal gene transfer, or from a cryptic red algal endosymbiosis in the common ancestor of the extant chlorarachniophytes.</p