Multiple Independent Changes in Mitochondrial Genome Conformation in Chlamydomonadalean Algae

Abstract

Chlamydomonadalean green algae are no stranger to linear mitochondrial genomes, particularly members of the Reinhardtinia clade. At least nine different Reinhardtinia species are known to have linear mitochondrial DNAs (mtDNAs), including the model species Chlamydomonas reinhardtii. Thus, it is no surprise that some have suggested that the most recent common ancestor of the Reinhardtinia clade had a linear mtDNA. But the recent uncovering of circular-mapping mtDNAs in a range of Reinhardtinia algae, such as Volvox carteri and Tetrabaena socialis, has shed doubt on this hypothesis. Here, we explore mtDNA sequence and structure within the colonial Reinhardtinia algae Yamagishiella unicocca and Eudorina sp. NIES-3984, which occupy phylogenetically intermediate positions between species with opposing mtDNA mapping structures. Sequencing and gel electrophoresis data indicate that Y. unicocca has a linear monomeric mitochondrial genome with long (3 kb) palindromic telomeres. Conversely, the mtDNA of Eudorina sp., despite having an identical gene order to that of Y. unicocca, assembled as a circular-mapping molecule. Restriction digests of Eudorina sp. mtDNA supported its circular map, but also revealed a linear monomeric form with a matching architecture and gene order to the Y. unicocca mtDNA. Based on these data, we suggest that there have been at least three separate shifts in mtDNA conformation in the Reinhardtinia, and that the common ancestor of this clade had a linear monomeric mitochondrial genome with palindromic telomeres.

Does mitochondrial DNA replication in Chlamydomonas require a reverse transcriptase?

“…NIES‐3984 is a close relative of Y. unicocca and both algae have identical mitochondrial gene orders. Eudorina sp., however, has a primarily circularly mapping genome and, most importantly, is missing rtl (Hamaji et al ., 2017), supporting the notion that this gene is involved in mitochondrial telomere maintenance. The only other well‐studied example of linear mtDNAs from the Chlamydomonadales is Polytomella .…”

“…Letters Forum 1193 C. reinhardtii and C. incerta mitochondrial telomeres, for example, share only c. 65% nucleotide identity, not including gaps. This is significant because it means that it is not a specific telomeric sequence that is being maintained in these linear mtDNAsa common feature of linear organelle genomes but rather a specific genomic architecture, one in which the ends of the genome match to an internal site and one that likely existed in the most recent common ancestor of the core Reinhardtinia clade (Hamaji et al, 2017).…”

Anisogamy evolved with a reduced sex-determining region in volvocine green algae

“…unicocca and male and female strains of Eudorina sp. were performed using PacBio and Illumina technologies as described previously 34 . Briefly, genomic DNA was sheared using a DNA shearing tube, g-TUBE (Covaris).…”

Biochemical and phylogenetic characterization of the wastewater tolerant Chlamydomonas biconvexa Embrapa|LBA40 strain cultivated in palm oil mill effluent

“…It can be observed that there is a wide genome architecture variation, including both linear and circular conformations and a wide range of mtDNA sizes, number of genes and GC content. This diversity is characteristic of Chlamydomonadalean algae [64]. It has been proposed that at least three conformational changes (from linear to circular and vice-versa) occurred during evolutionary divergence within this clade.…”