Organization of the Mitochondrial Genome in the Dinoflagellate Amphidinium carterae

Abstract

We have characterized the mitochondrial genome of the dinoflagellate Amphidinium carterae. It contains just 3 identifiable protein-coding genes: cox1, cox3, and cob. No evidence for rRNA or tRNA genes was found. Expressed sequence tags (EST) sequences for the 3 genes suggest that RNA editing occurs in 2 cases removing an in-frame stop codon. Two of the transcripts (cob and cox1) lack a stop codon at the end of the gene. The genome contains a large amount of noncoding DNA including many fragmented copies of all the 3 genes and large numbers of inverted repeats. The genome, which contains about 70% AT, has undergone extensive recombination, possibly due to the inverted repeats. The highly reduced mitochondrial gene content supports the relationship of the dinoflagellates and apicomplexa as sister groups.

Functional remodeling of RNA processing in replacement chloroplasts by pathways retained from their predecessors

“…For each reaction, 200 ng total cellular RNA was reverse-transcribed with SuperScript II reverse transcriptase (Invitrogen). For circular RT-PCR, RNA was precircularized using T4 RNA ligase as previously described (33,35). PCRs were performed using GoTaq polymerase (Promega) as previously described (33,35).…”

“…For circular RT-PCR, RNA was precircularized using T4 RNA ligase as previously described (33,35). PCRs were performed using GoTaq polymerase (Promega) as previously described (33,35). For the initial diagnostic oligo(dA) RT-PCR, PCR forward primers directed against the interior of each gene were used, whereas for whole-gene substitution mapping, PCR forward primers that annealed against the 5′ end of each gene were used (Dataset S1).…”

“…To confirm the structure and composition of the poly(U) tracts, we carried out RT-PCR on circularized transcripts of psbA and psbC ( Fig. S2 and Dataset S1) (35,36). We found that the poly(U) tracts observed were generally between 15 and 30 nt in length, homopolymeric, and on the 3′ end of each transcript (as opposed to an internal insertion).…”

The Highly Reduced and Fragmented Mitochondrial Genome of the Early-branching Dinoflagellate Oxyrrhis marina Shares Characteristics with both Apicomplexan and Dinoflagellate Mitochondrial Genomes

“…16 The third major alveolate lineage, the dinoflagellates, is the most poorly studied, but emerging evidence suggests that their mitochondrial genomes are by far the most unusual. So far, the same three protein-coding genes found in Plasmodium have been identified, [17][18][19][20] and several rRNA fragments that are similar to those of apicomplexans have also been characterized. 21 However, there are also two major differences.…”

Cascades of convergent evolution: The corresponding evolutionary histories of euglenozoans and dinoflagellates

“…Although A to G is the most common substitution, several others have been observed (U 3 C, G 3 C, G 3 A, A 3 C, and C 3 U), suggesting a highly flexible and sophisticated editing mechanism (38,48). Fragments of edited gene sequences have been found in dinoflagellate mitochondrial genomes, prompting the suggestion that they employ gRNAs similar to that of kinetoplastids (49). However, the genomes are prone to recombination, so the significance of these fragments remains unclear; overall, there is no direct evidence for any particular editing mechanism at present.…”