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Open Access Research article

Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias

Sergey Ovchinnikov and Susan E Masta*

Author Affiliations

Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207, USA

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BMC Evolutionary Biology 2012, 12:31  doi:10.1186/1471-2148-12-31

Published: 12 March 2012

Additional files

Additional file 1:

List of taxa used in this study. List of taxa used in this study, arranged by their Linnaean taxonomy, with GenBank accession numbers for their mitochondrial genome sequence.

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Additional file 2:

Nucleotide use and AT and CG skew in chelicerate mitochondrial protein-coding genes. Genes are arranged in the linearized order that they occur in the mitochondrial genome. Orange shading indicates genes found on the major strand, whereas gold indicates genes located on the minor strand. Nucleotide use and skew is shown for each of the three codon positions for each gene. The red to blue shading in the AT skew and CG skew columns indicate the degree of skew they possess, with the darker shading indicating greater skew. Blue indicates and excess of that nucleotide, red indicates a deficiency of that nucleotide.

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Additional file 3:

Graph of nucleotide skew at 3rd codon positions of mitochondrial protein-coding genes of arthropods. CG skew is plotted along the Y-axis, and AT skew is plotted on the X-axis. Skew was calculated following Perna and Kocher [65], and described in the Methods. The red square bounds the taxa we considered to not have a pronounced CG or AT nucleotide skew, that is, within the range of -0.2 to +0.2. These taxa have purple branches leading to them in Figure 6. The two purple dots depict the pseudoscorpions, the dark green dots depict the other chelicerates, and the light green dots depict the arthropod outgroup taxa analyzed in this study. The taxa used to create this graph are given in Additional file 1.

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