The complete mitochondrial DNA sequence of Scenedesmus obliquus reflects an intermediate stage in the evolution of the green algal mitochondrial genome

Abstract

Two distinct mitochondrial genome types have been described among the green algal lineages investigated to date: a reduced-derived, Chlamydomonas-like type and an ancestral, Prototheca-like type. To determine if this unexpected dichotomy is real or is due to insufficient or biased sampling and to define trends in the evolution of the green algal mitochondrial genome, we sequenced and analyzed the mitochondrial DNA (mtDNA) of Scenedesmus obliquus. This genome is 42,919 bp in size and encodes 42 conserved genes (i.e., large and small subunit rRNA genes, 27 tRNA and 13 respiratory protein-coding genes), four additional free-standing open reading frames with no known homologs, and an intronic reading frame with endonuclease/maturase similarity. No 5S rRNA or ribosomal protein-coding genes have been identified in Scenedesmus mtDNA. The standard protein-coding genes feature a deviant genetic code characterized by the use of UAG (normally a stop codon) to specify leucine, and the unprecedented use of UCA (normally a serine codon) as a signal for termination of translation. The mitochondrial genome of Scenedesmus combines features of both green algal mitochondrial genome types: the presence of a more complex set of protein-coding and tRNA genes is shared with the ancestral type, whereas the lack of 5S rRNA and ribosomal protein-coding genes as well as the presence of fragmented and scrambled rRNA genes are shared with the reduced-derived type of mitochondrial genome organization. Furthermore, the gene content and the fragmentation pattern of the rRNA genes suggest that this genome represents an intermediate stage in the evolutionary process of mitochondrial genome streamlining in green algae.

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, Trebouxiophyceae, and Chlorophyceae). The two deeply diverging chlorophycean lineages defined by flagellar apparatus configuration (CW, clockwise; DO, directly opposed) are shown. The Prasinophyceae is a non-monophyletic assemblage of primitive green algae, some of which are of uncertain phylogenic affiliation (dashed lines). All the green plants for which complete mtDNA sequences have been determined are indicated, with the exception of Pedinomonas minor, a primitive unicellular green flagellate whose phylogenetic position has not yet been established.

Figure 2

Physical and genome map of the S. obliquus mtDNA. Genes, exons, and non-intronic ORFs are depicted as black blocks, introns are indicated as light-gray blocks, and intronic ORFs are shown as dark-gray blocks. Gene abbreviations are listed in Table 2. Gene blocks outside and inside the circle are transcribed in clockwise and counterclockwise directions, respectively. Transfer RNA genes are shown as thin black bars, with letters indicating amino acid specificity (see Table 2), and numbers denoting different genes specific for the same amino acid. The anticodons (lowercase letters enclosed in parentheses) of the numbered tRNA genes are: I1, (uau); I2, (gau); L1, (cag); L2, (aag); L3, (caa); L4, (cua); R1, (acg); R2, (ccu); R3, (ucu); S1, (gcu); S2, (gga). Me and Mf denote the elongator and initiator trnM(cau), respectively.

Figure 3

Mitochondrial rRNA structure in green algae. Ribosomal RNA fragmentation patterns are depicted for chlorophyte algae whose mitochondrial genomes have been completely sequenced; the rRNAs are represented to the scale of the covalently continuous E. coli homologs. Arrows indicate the positions of breakpoints that occur in corresponding variable regions in the C. reinhardtii, C. eugametos, Chlorogonium, and S. obliquus rRNAs; S₁–S₄ and L₁–L₈ denote SSU and LSU rRNA fragments, respectively.

Figure 4

Best tree derived from a phylogenetic analysis of concatenated mitochondrial sequences representing seven respiratory protein-coding genes (1949 amino acid positions) common to all of the green algal mitochondrial genomes sequenced to date. Abbreviations are as in the text.