title: The mitochondrial genome of Paragyrodactylus variegatus (Platyhelminthes: Monogenea): differences in major non-coding region and gene order compared to Gyrodactylus.
abstract: BACKGROUND
  Paragyrodactylus Gvosdev and Martechov, 1953, a viviparous genus of ectoparasite within the Gyrodactylidae, contains three nominal species all of which infect Asian river loaches. The group is suspected to be a basal lineage within Gyrodactylus Nordmann, 1832 sensu lato although this remains unclear. Further molecular study, beyond characterization of the standard Internal Transcribed Spacer region, is needed to clarify the evolutionary relationships within the family and the placement of this genus.
  
  
  METHODS
  The mitochondrial genome of Paragyrodactylus variegatus You, King, Ye and Cone, 2014 was amplified in six parts from a single worm, sequenced using primer walking, annotated and analyzed using bioinformatic tools.
  
  
  RESULTS
  The mitochondrial genome of P. variegatus is 14,517 bp, containing 12 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a major non-coding region (NCR). The overall A + T content of the mitochondrial genome is 76.3%, which is higher than all reported mitochondrial genomes of monogeneans. All of the 22 tRNAs have the typical cloverleaf secondary structure, except tRNACys, tRNASer1 and tRNASer2 that lack the dihydrouridine (DHU) arm. There are six domains (domain III is absent) and three domains in the inferred secondary structures of the large ribosomal subunit (rrnL) and small ribosomal subunit (rrnS), respectively. The NCR includes six 40 bp tandem repeat units and has the double identical poly-T stretches, stem-loop structure and some surrounding structure elements. The gene order (tRNAGln, tRNAMet and NCR) differs in arrangement compared to the mitochondrial genomes reported from Gyrodactylus spp.
  
  
  CONCLUSIONS
  The Duplication and Random Loss Model and Recombination Model together are the most plausible explanations for the variation in gene order. Both morphological characters and characteristics of the mitochondrial genome support Paragyrodactylus as a distinct genus from Gyrodactylus. Considering their specific distribution and known hosts, we believe that Paragyrodactylus is a relict freshwater lineage of viviparous monogenean isolated in the high plateaus of central Asia on closely related river loaches.
authors.forename: Fei
authors.initials: F
authors.lastname: Ye
authors.forename: Stanley D
authors.initials: SD
authors.lastname: King
authors.forename: David K
authors.initials: DK
authors.lastname: Cone
authors.affiliation: Co-Innovation Center for Qinba regions' sustainable development, College of Life Science, Shaanxi Normal University, Xi'an 710062, China. youping@snnu.edu.cn.
authors.forename: Ping
authors.initials: P
authors.lastname: You
mesh_terms: D000818:Animals; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000235:genetics; D023061:Gene Order; D054629:Genome, Mitochondrial; D015801:Helminth Proteins / Q000235:genetics / Q000378:metabolism; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction; D012335:RNA, Ribosomal; D012343:RNA, Transfer; D013045:Species Specificity; D014200:Trematoda / Q000145:classification / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial; D015801:Helminth Proteins; D012335:RNA, Ribosomal; D012343:RNA, Transfer