Review—contrasting Mitochondrial Genome Organizations and Sequence Affiliations Among Green Algae: Potential Factors, Mechanisms, and Evolutionary Scenarios

Abstract

The three green algal mitochondrial genomes completely sequenced to date-those of Chlamydomonas reinhardtii Dangeard, Chlamydomonas eugametos Gerloff, and Prototheca wickerhamii Soneda & Tubaki-revealed very different mitochondrial genome organizations and sequence affiliations. The Chlamydomonas genomes resemble the ciliate/fungal/animal counterparts, and the Prototheca genome resembles land plant homologues. This review points out that all the green algal mitochondrial genomes examined to date resemble either the Chlamydomonas or the Prototheca mitochondrial genome; the Chlamydomonas-like mitochondrial genomes are small and have a reduced gene content (no ribosomal protein or 5S rRNA genes and only a few protein-coding and tRNA genes) and fragmented and scrambled rRNA coding regions, whereas the Prototheca-like mitochondrial genomes are larger and have a larger set of protein-coding genes (including ribosomal protein genes), more tRNA genes, and 5S rRNA and conventional continuous smallsubunit (SSU) and large-subunit (LSU) rRNA coding regions. It appears, therefore, that the differences previously observed between the mitochondrial genomes of C. reinhardtii and P. wickerhamii extend to the two green algal mitochondrial lineages to which they belong and are significant enough to raise questions about the causes and mechanisms responsible for such contrasting evolutionary strategies among green algae. This review suggests an integrative approach in explaining the occurrence of distinct evolutionary strategies and apparent phylogenetic affiliations among the known green algal mitochondrial lineages. The observed differences could be the result of distinct genetic potentials differentiated during the previous evolutionary history of the flagellate ancestors and/or of subsequent changes in habitat and life history of the more advanced green algal lineages.

Mitochondrial genomes of the green macroalga Ulva pertusa (Ulvophyceae, Chlorophyta): novel insights into the evolution of mitogenomes in the Ulvophyceae

“…, Achaz et al. ) and play an important role in promoting genome rearrangement and gene deletions by acting as substrates for recombination (Nedelcu ). Low content of IRs in Ulva mtDNAs would decrease the possibility of rearrangement and ensure a more economic transcription mode that all genes could be transcribed from one DNA strand.…”

Phylogeny and Molecular Evolution of the Green Algae

“…Some are believed to be transposable elements, and there are examples of similar types of repeats being found in both the mitochondrial and plastid compartments of the same species (Pombert et al, 2005;Smith & Lee, 2009). It has also been argued that in some green algal lineages organelle repeats have played a role in fashioning the mitochondrial and plastid genomes by acting as catalysts for genome fragmentation and reorganization as well as gene splitting and scrambling (Boer & Gray, 1991;Nedelcu, 1998;Nedelcu & Lee, 1998;Maul et al, 2002). Moreover, certain repeats, especially those that can be folded into secondary structures, are thought to be involved in gene regulation and processing (Boer & Gray, 1986;Jiao et al, 2004;Smith & Lee, 2008).…”

The Complete Mitochondrial DNA Sequence of Scenedesmus obliquus Reflects an Intermediate Stage in the Evolution of the Green Algal Mitochondrial Genome

“…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 proteincoding 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.…”

“…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.…”