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Monophyly of Primary Photosynthetic Eukaryotes: Green Plants, Red Algae, and Glaucophytes
TLDR
These analyses provide the first strong support for a single endosymbiotic event that gave rise to primary photosynthetic eukaryotes, the Plantae, which are present in green plants, red algae, and glaucophytes. Expand
The tree of eukaryotes.
TLDR
Recent progress in assembling the tree of eukaryotes is reviewed, describing the major evidence for each supergroup, and where gaps in the authors' knowledge remain. Expand
Mitochondrial genomes: anything goes.
TLDR
In addition to outlining the extraordinary diversity of mtDNA, this review highlights the divergent trends in mitochondrial genome evolution in the various eukaryotic lineages, and examines the relationship between mitochondrial and nuclear genome Evolution in a given organism. Expand
The origin and early evolution of mitochondria
TLDR
Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available and confirm that the mitochondrial genome originated from a eubacterial ancestor but raise questions about the evolutionary antecedents of the mitochondrial proteome. Expand
Mitochondrial introns: a critical view.
TLDR
This work set out to identify all mitochondrial group I and II introns in published sequences, and developed and applied a new search approach: RNAweasel, which results in a comprehensive picture of mitochondrialGroup I introns, including a modified (reduced) consensus RNA secondary structure and a concise phylogeny-based subclassification. Expand
An ancestral mitochondrial DNA resembling a eubacterial genome in miniature
TLDR
Feature of gene content together with eubacterial characteristics of genome organization and expression not found before in mitochondrial genomes indicate that R. americana mtDNA more closely resembles the ancestral proto-mitochondrial genome than any other mtDNA investigated to date. Expand
The Closest Unicellular Relatives of Animals
TLDR
Trees inferred from multiple concatenated mitochondrial protein sequences demonstrate that animals are specifically affiliated with two morphologically dissimilar unicellular protist taxa and propose the new taxonomic group Holozoa, comprising Ichthyosporea, Choanoflagellata, and Metazoa. Expand
Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication
TLDR
The order and genomic arrangement of the duplicated gene pairs and their common phylogenetic origin provide evidence for an ancestral whole-genome duplication (WGD) event that resulted in the expansion of multiple gene families related to cell growth and signal transduction, as well as secreted aspartic protease and subtilase protein families, which are known fungal virulence factors. Expand
AutoFACT: An Automatic Functional Annotation and Classification Tool
TLDR
This work presents AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence and determines the most informative functional description by combining multiple BLAST reports from several user-selected databases. Expand
Strikingly Bacteria-Like and Gene-Rich Mitochondrial Genomes throughout Jakobid Protists
TLDR
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. Expand
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