Category: Papers by CGEB labs

Gene-content evolution in discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa.
Genome Biol Evol. 2014 Jan 21;
Authors: Kamikawa R, Kolisko M, Nishimura Y, Ya…

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SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles.
Bioinformatics. 2013 Aug 1;29(15):1858-64
Authors: Porter MS, Beiko RG
Abstract
BACKGROUND: Homology…

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The site-wise log-likelihood score is a good predictor of genes under positive selection.
J Mol Evol. 2013 May;76(5):280-94
Authors: Wang HC, Susko E, Roger AJ
Abstract
The strength and direc…

The spliceosomal catalytic core arose in the RNA world… or did it?

Genome Biol. 2013 Dec 13;14(12):141

Authors: Doolittle WF

Abstract
A new study adds to the evidence for a common evolutionary origin of the spliceosome and group II introns, but RNA-world questions remain.

PMID: 24330866 [PubMed – as supplied by publisher]

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Treetrimmer: a method for phylogenetic dataset size reduction.
BMC Res Notes. 2013;6:145
Authors: Maruyama S, Eveleigh RJ, Archibald JM
Abstract
BACKGROUND: With rapid advances in genome seq…

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Comprehensive ultrastructure of Kipferlia bialata provides evidence for character evolution within the Fornicata (Excavata).
Protist. 2013 May;164(3):423-39
Authors: Yubuki N, Simpson AG, Leander BS
…

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The flagellar apparatus of Breviata anathema, a eukaryote without a clear supergroup affinity.

Eur J Protistol. 2013 Aug;49(3):354-72

Authors: Heiss AA, Walker G, Simpson AG

Abstract
Breviata anathema is an anaerobic amoeboid flagellate that does not branch within any established ‘supergroup’. Molecular phylogenies suggest affinities to Amoebozoa, Opisthokonta, or apusomonads. Here we describe its flagellar apparatus ultrastructure. Breviata has two basal bodies. The flagellated anterior basal body (AB) is associated with a fan of ∼18 microtubules and a short singlet microtubular root. Three microtubular roots associate with the posterior basal body. One, the right root (RR), is initially a triplet that splits into two parts. The other two are singlets: the left root (LR), and the middle root (MR), which arises on the posterior side of the basal body. The MR, LR and smaller part of RR support the left ventral side of the cell, while the larger part of RR runs down the right. Outer dynein arms were not observed on the flagellar axoneme. The mitochondrion-like organelle sometimes contains some tubular cristae. The posterior flagellar apparatus resembles that of several eukaryotic lineages, particularly apusomonads, ancyromonads, excavates, and myxogastrid amoebozoans. This comparison suggests that the complex flagellar apparatus of myxogastrids is actually plesiomorphic within Amoebozoa. The widely distributed splitting right root and posterior singlet (MR in Breviata) may be plesiomorphies in many eukaryotic lineages, and thus could be features of the last eukaryotic common ancestor.

PMID: 23523042 [PubMed – indexed for MEDLINE]

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Inference of functional divergence among proteins when the evolutionary process is non-stationary.
J Mol Evol. 2013 Apr;76(4):205-15
Authors: Bay RA, Bielawski JP
Abstract
Functional shifts d…

Carl R. Woese (1928–2012).

Curr Biol. 2013 Mar 4;23(5):R183-5

Authors: Doolittle WF

PMID: 23596635 [PubMed – indexed for MEDLINE]

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Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists.

Genome Biol Evol. 2013;5(2):418-38

Authors: Burger G, Gray MW, Forget L, Lang BF

Abstract
The most bacteria-like mitochondrial genome known is that of the jakobid flagellate Reclinomonas americana NZ. This genome also encodes the largest known gene set among mitochondrial DNAs (mtDNAs), including the RNA subunit of RNase P (transfer RNA processing), a reduced form of transfer-messenger RNA (translational control), and a four-subunit bacteria-like RNA polymerase, which in other eukaryotes is substituted by a nucleus-encoded, single-subunit, phage-like enzyme. Further, protein-coding genes are preceded by potential Shine-Dalgarno translation initiation motifs. Whether similarly ancestral mitochondrial characters also exist in relatives of R. americana NZ is unknown. Here, we report a comparative analysis of nine mtDNAs from five distant jakobid genera: Andalucia, Histiona, Jakoba, Reclinomonas, and Seculamonas. We find that Andalucia godoyi has an even larger mtDNA gene complement than R. americana NZ. The extra genes are rpl35 (a large subunit mitoribosomal protein) and cox15 (involved in cytochrome oxidase assembly), which are nucleus encoded throughout other eukaryotes. Andalucia cox15 is strikingly similar to its homolog in the free-living α-proteobacterium Tistrella mobilis. Similarly, a long, highly conserved gene cluster in jakobid mtDNAs, which is a clear vestige of prokaryotic operons, displays a gene order more closely resembling that in free-living α-proteobacteria than in Rickettsiales species. Although jakobid mtDNAs, overall, are characterized by bacteria-like features, they also display a few remarkably divergent characters, such as 3′-tRNA editing in Seculamonas ecuadoriensis and genome linearization in Jakoba libera. Phylogenetic analysis with mtDNA-encoded proteins strongly supports monophyly of jakobids with Andalucia as the deepest divergence. However, it remains unclear which α-proteobacterial group is the closest mitochondrial relative.

PMID: 23335123 [PubMed – indexed for MEDLINE]