title: Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias.
abstract: BACKGROUND
  Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes.
  
  
  RESULTS
  We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis.The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13 mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites.
  
  
  CONCLUSIONS
  The well-supported phylogenetic placement of pseudoscorpions as sister to Acariformes differs from some previous analyses based on morphology. However, these two lineages share multiple molecular evolutionary traits, including substantial mitochondrial genome rearrangements, extensive nucleotide substitution, and loss of helices in their inferred tRNA and rRNA structures.
authors.affiliation: Department of Biology, Portland State University, Portland, OR 97207, USA.
authors.forename: Sergey
authors.initials: S
authors.lastname: Ovchinnikov
authors.forename: Susan E
authors.initials: SE
authors.lastname: Masta
mesh_terms: D000818:Animals; D001097:Arachnida / Q000235:genetics*; D001482:Base Composition; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics; D023061:Gene Order; D015321:Gene Rearrangement; D020459:Genes, rRNA / Q000235:genetics; D016678:Genome / Q000235:genetics*; D008928:Mitochondria / Q000235:genetics*; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012313:RNA / Q000235:genetics*; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics
chemical_list: D004272:DNA, Mitochondrial; D012313:RNA; D012343:RNA, Transfer