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{ Category Archives } research articles

Organization of the Mitochondrial Genome in the Dinoflagellate Amphidinium cartera (Nash et al., 2007)

The dinoflagellate Amphidinium has just like Oxyrrhis only a few (3) mitochondrial genes as shown here (only abstract). It also describes the organization of the genome, with fragmented genes of the only 3 functional genes and a large number of inverted repeats. This is important for two reasons: 1) in an endosymbiotic origin I would expect […]

The Highly Reduced and Fragmented Mitochondrial Genome of the Early-branching Dinoflagellate Oxyrrhis marina Shares Characteristics with both Apicomplexan and Dinoflagellate Mitochondrial Genomes (Slamovits et al., 2007)

This is an article about the genome of the Dinoflagellate Oxyrrhis with a small genome. Keeling’s group keeps referring to it as reduced, but that only holds if the endosymbiotic theory is correct. The problem is that the entire article is based (biased) on this, which makes it difficult to assess its real value. What […]

Mitochondrial genome diversity: evolution of the molecular architecture and replication strategy (Nosek and Tomaska 2003)

This is a nice article that could explain the easy interconversion from circular to linear DNA. The plasmid or transposon that inserts itself in the circle automatically provides the protection against the end replication problem. The nuclear chromosomes have a complete machinery for this ‘task’ which make sit unlikely that their origin is the same. Anyway, […]

A Genome Phylogeny for Mitochondria Among alpha-Proteobacteria and a Predominantly Eubacterial Ancestry of Yeast Nuclear Genes (Esser et al., 2004)

This article that uses compares nuclear genes with prokaryotic genes in order to look at the origin of mitochondria. They have some interesting results, basically showing that many eukaryotic genes have a prokaryotic counterpart. Also, the trees are far from clear and interestingly, they use the endosymbiotic theory as a control for the data. So, […]

The dual origin of the yeast mitochondrial proteome. (Karlbert et al., 2000)

Andersson’s group here describes more data on Rickettsia and mitochondrial origin. He directly attributes homologous sequences to a alpha-proteo bacterial origin and assumes the endosymbiotic theory to be true and therefore all of his remarks has to be seen in this respect. He habitually mixes homology with origin, although phylogenetic analyses cannot give a direction […]

Do orthologous gene phylogenies really support tree-thinking? (Bapteste 2003)

An interesting article from important evolutionists that investigates the use of phylogenetic studies. They conclude that these studies are often not in agreement with tree-thinking and warn for the a priori assumption of a tree and using only a selection of markers in phylogenetic analyses. 
We conclude that we simply cannot determine if a large portion of […]

Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: A Streamlined Genome Overrun by Mobile Genetic Elements (Wu et al., 2003)

This article by Wu looks at Wolbachia, intracellular bacteria of Drosophila melanogaster, but also makes a comparison with Rickettsia and mitochondria. In contrast to the original study of Andersson, they did not find evidence for a grouping with Rickettsia, although many genes did relate to a-proteobacteria, but not all. They discuss the error proneness of […]

The genome sequence of Rickettsia prowazekii and the origin of mitochondria (Andersson et al., 1998)

This article is gives full genome phylogenetic evidence that Rickettsia is most related to mitochondria. Btw, I always found it very strange that of all the bacterial species that we know, we picked the right one from the beginning. An endosymbiont that infects higher animals and some arthropods. As you will see from the abstract, […]

Plant mitochondria actively import DNA via the permeability transition pore complex (Koulintchenko et al., 2003)

I stumbled on this article when I was pursuing a scenario in which mitochondria could have gained DNA that was derived from the nucleus, maybe some kind of plasmid (senDNAs?).
 
Abstract Plant mitochondria are remarkable with respect to their content in foreign, alien and plasmid-like DNA, raising the question of the transfer of this information into […]

An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus (Turmel et al., 2007)

This article shows that mitochondrial genomes can be quite different between organisms, especially in early branching organisms. I am not too familiar with plants, but this reported genome look more eukaryotic-like than bacterial-like. At the moment just for reference, don’t know what to make from it, short of a good predictive model for the acquisition of […]