Nephroselmis

Abstract: One major lineage of green plants, the Chlorophyta, is represented by the green algal classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae, and Chlorophyceae. The Prasinophyceae occupies the most basal position in the Chlorophyta, but the branching order of the Ulvophyceae, Trebouxiophyceae, and Chlorophyceae remains unresolved. The chloroplast genome sequences currently available for representatives of three chlorophyte classes have revealed that this genome is highly plastic, with Chlamydomonas (Chlorophyceae) and Chlorella (Trebouxiophyceae) showing fewer ancestral features than Nephroselmis (Prasinophyceae). We report the 195,867-bp chloroplast DNA (cpDNA) sequence of Pseudendoclonium akinetum (Ulvophyceae), a member of the class that has not been previously examined for detailed cpDNA analysis. This genome shares common evolutionary trends with its Chlorella and Chlamydomonas homologs. The gene content, number of ancestral gene clusters, and abundance of short dispersed repeats in Pseudendoclonium cpDNA are intermediate between those observed for Chlorella and Chlamydomonas cpDNAs. Although Pseudendoclonium cpDNA features a large inverted repeat, its quadripartite structure is unusual in displaying an rRNA operon transcribed toward the large single-copy (LSC) region and a small single-copy region containing 14 genes that are normally found in the LSC region. Twenty-seven group I introns lie in nine genes and fall within four subgroups (IA1, IA2, IA3, and IB); 19 encode putative homing endonucleases, and 7 have homologs at identical insertion sites in other chlorophyte or streptophyte organelle genomes. The high similarity observed among the 14 IA1 and 7 IA2 introns and their encoded endonucleases suggests that many introns arose from intragenomic proliferation of a few founding introns in the lineage leading to Pseudendoclonium. Interestingly, one intron (in atpA) and some of the dispersed repeats also reside in Pseudendoclonium mitochondria, providing strong evidence for interorganellar lateral transfer of these genetic elements. Phylogenetic analyses of 58 cpDNA-encoded proteins and genes support the hypothesis that the Ulvophyceae is sister to the Trebouxiophyceae but cannot eliminate the hypothesis that the Ulvophyceae is sister to the Chlorophyceae. We favor the latter hypothesis because it is strongly supported by phylogenetic analyses of gene order data and by independent structural evidence based on shared gene losses and rearrangement break points within ancestrally conserved gene clusters.

Abstract: Two distinct mitochondrial genome types have been described among the green algal lineages investigated to date. The Chlamydomonas-like type displays a reduced-derived organizational pattern characterized by small genome size (16–25 kb), limited gene content (no ribosomal protein or 5S rRNA genes and only a few respiratory protein and tRNA genes), and the presence of fragmented and scrambled rRNA coding regions. The Prototheca-like type represents an ancestral form of green algal mitochondrial genome that features a larger size (45–55 kb), a more complex set of protein-coding genes (including ones for ribosomal proteins), a complete or almost complete set of tRNA genes, and 5S rRNA as well as conventional continuous rRNA genes (Nedelcu 1998; Gray et al. 1998; Turmel et al. 1999). To date, six green algal mitochondrial genomes have been completely sequenced. Of these, four belong to the reduced–derived type (i.e., Chlamydomonas reinhardtii [Michaelis et al. 1990; Boer and Gray 1991; Vahrenholz et al. 1993], Chlamydomonas eugametos [Denovan-Wright et al. 1998], Chlorogonium elongatum [Kroymann and Zetsche 1998], and Pedinomonas minor [Turmel et al. 1999]), and two are members of the ancestral type (i.e., Prototheca wickerhamii [Wolff et al. 1994] and Nephroselmis olivacea [Turmel et al. 1999]). In phylogenetic analyses using mitochondrial rDNA sequences (Denovan-Wright et al. 1996) the above two types of mitochondrial genome fail to affiliate with each other. Furthermore, whereas in mitochondrial protein trees the ancestral mitochondrial sequences directly affiliate, as expected, with their land plant counterparts, the reduced–derived (fast-evolving) sequences form a clade separate from both ancestral green algal and land plant homologs (Turmel et al. 1999). The causes, factors, and mechanisms responsible for the extensive changes sustained by the mitochondrial genome in different green algal lineages are not known yet, although some suggestions have been made (Nedelcu 1998; Nedelcu and Lee 1998a,b). To decipher the processes involved in the evolution of the green algal mitochondrial genome in particular, and to understand the mechanisms involved in the evolution of the mitochondrial genome in general, we need more knowledge about the extent of mitochondrial genome diversity and the specific evolutionary trends in mitochondrial genome organization within each lineage. The phylogeny of green algae continues to undergo revision. Green algal lineages are distributed between two phyla, Chlorophyta and Streptophyta (see Bremer 1985) (Figure ​(Figure1).1). The reduced-derived green algal mitochondrial genomes sequenced to date belong to lineages placed in the Chlorophyceae (i.e., Chlamydomonas spp. and Chlorogonium) and Pedinophyceae (i.e., Pedinomonas), whereas the ancestral-like mitochondrial genomes belong to the trebouxiophyte (i.e., Prototheca) and prasinophyte (i.e., Nephroselmis) lineages (Fig. ​(Fig.1).1). Comparisons among the gene contents of ancestral and reduced–derived mitochondrial genomes show that most of the derived features shared by all of the Chlamydomonas-like mitochondrial genomes (such as lack of ribosomal protein and 5S rRNA genes and the presence of fragmented and scrambled rRNA coding regions) are also found in the primitivelike taxon, Pedinomonas; however, the rRNA genes are less fragmented and a slightly larger number of genes are encoded in the mitochondrial genome of this taxon, relative to other Chlamydomonas-like counterparts. Do these observations mean that the evolutionary processes leading to the very peculiar type of mitochondrial genome organization in Chlamydomonas were initiated long before the divergence of the chlorophycean group, namely in a Pedinomonas-like green flagellate ancestor, and continued since? Alternatively, is the similarity in organization between the pedinophycean and chlorophycean mitochondrial genomes an example of convergent evolution? Figure 1 Evolutionary relationships among green plants (green algae and land plants). The two main evolutionary branches depict the two sister phyla (Chlorophyta and Streptophyta) into which all green plants fall. Chlorophyta comprises three classes (Ulvophyceae, ... The goals of our work were to determine whether the observed split in mitochondrial genome organization and sequence affiliation in green algae is real or is due to insufficient or biased sampling, and to define trends in mitochondrial genome evolution within the green algal group. The chlorophycean group consists of two very distinct evolutionary lineages that diverged early (Wilcox et al. 1992; Steinkotter et al. 1994) (Fig. ​(Fig.1).1). Because all of the chlorophycean mitochondrial genomes sequenced to date belong to only one lineage and feature reduced–derived organizational types, we decided to investigate mitochondrial genome organization within the other lineage. The specific questions addressed by this study follow: Do the mitochondrial genomes in the two (early diverged) chlorophycean lineages resemble each other and are they of the reduced–derived mitochondrial genome type? Alternatively, are the mitochondrial genomes very different between the two evolutionarily distinct chlorophycean lineages? Will the acquisition of information about mitochondrial genome organization from both chlorophycean lineages contribute to suggesting evolutionary mechanisms and pathways in the streamlining process leading toward the derived chlamydomonadalean mitochondrial genome? Could mitochondrial genome traits help decipher phylogenetic relationships among green algal lineages? In light of available data on phylogenetic affiliation (Wilcox et al. 1992; Steinkotter et al. 1994), mitochondrial genome size (Kuck 1989), and rRNA gene organization (Nedelcu et al. 1996; Nedelcu 1997) for Scenedesmus obliquus, we decided to determine the entire mitochondrial genome sequence of this green alga.

Abstract: A new species provisionally attributed to the genus Nephroselmis has been described with the aid of light- and electron-microscopy. Significant features include the presence of a single layer of scales over the flagellar and cell surfaces as in Micromonas squamata Manton & Parke, though the morphology of the flagellar scales is as in the outer scale layer of Pyramimonas and Halosphaera. Reasons are given for rejection of Thalassomonas on the grounds of nomen confusum and for homologizing various representatives of it with Micromonas squamata.Some additional facts about the latter include details of the imbrication of the flagellar scales and demonstration, made possible by the use of lead staining of sections, of a close association between golgi bodies and the scale-producing vesicles.