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Automatic annotation of organellar genomes with DOGMA
The Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of organellar genomes and allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.
Animal mitochondrial genomes.
  • J. Boore
  • Biology, Medicine
    Nucleic acids research
  • 1 April 1999
The comparison of animal mitochondrial gene arrangements has become a very powerful means for inferring ancient evolutionary relationships, since rearrangements appear to be unique, generally rare events that are unlikely to arise independently in separate evolutionary lineages.
The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants
This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments; acquisition of genes for tolerating terrestrial stresses; and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response.
The Ecoresponsive Genome of Daphnia pulex
The Daphnia genome reveals a multitude of genes and shows adaptation through gene family expansions, and the coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random.
Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate
The hypothesis that the relatively large and complex vertebrate genome was created by two ancient, whole genome duplications has been hotly debated, and the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage is highlighted.
The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins
A draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis, is generated, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development.
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
Phylogenetic trees from multiple methods provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales, and the plastid genome trees also provide strongSupport for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids.
Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis
Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.
Gene translocation links insects and crustaceans
A derived gene rearrangement common to insects and crustaceans but absent in the other arthropod groups is reported, suggesting an insect-crustacean evolutionary lineage that is separate from those leading to myriapods and chelicerates.
Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana
It is shown that N. gaditana has highly favourable lipid yields, and is a promising production organism, and the availability of a genome sequence and transformation methods will facilitate investigations into N. Gaditana lipid biosynthesis and permit genetic engineering strategies to further improve this naturally productive alga.