The mitochondrial genome of Paragyrodactylus variegatus (Platyhelminthes: Monogenea): differences in major non-coding region and gene order compared to Gyrodactylus

Abstract

BackgroundParagyrodactylus 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.MethodsThe 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.ResultsThe 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.ConclusionThe 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.

Comparative analyses within Gyrodactylus (Platyhelminthes: Monogenea) mitochondrial genomes and conserved polymerase chain reaction primers for gyrodactylid mitochondrial DNA

“…variegatus was considered to be the putative control region (Ye et al . ). Although typical control regions are not readily identifiable within mitochondrial genomes of flatworms, the possibility of control regions in NCR for Gyrodactylus cannot be neglected.…”

The complete mitochondrial genome of Gyrodactylus gurleyi (Platyhelminthes: Monogenea)

“…The rrnL and rrnS were 954 bp and 710 bp in size, respectively. They were adjacent to tRNA Thr (upstream) and Cox2 (downstream), and separated by tRNA Cys , as described with other reported monopisthocotyleans (Huyse et al 2007;Plaisance et al 2007;Huyse et al 2008;Perkins et al 2010;Ye et al 2014;Zhang et al 2014aZhang et al , 2014bZhang et al , 2016. In addition, there were 37 bp overlapping sequences and 1763 space sequences, among which the biggest were NC1 (783 bp) and NC2 (783 bp).…”

“…All the genes were transcribed from the same strand. The nucleotide composition was computed at 29.2%A, 16.9% G, 42.9% T and 11.1% C. The AT content of 72.1% was lower than that of Paragyrodactylus variegatus (76.3%), but higher than that of other four Gyrodactylus species (G. salaris, 62.3%; G. thymalli, 62.8%; G. derjavinoides, 68.2%; G. kobayashii, 71.6%) (Huyse et al 2007;Plaisance et al 2007;Huyse et al 2008;Ye et al 2014;Zhang et al 2016).…”

Three new Diplozoidae mitogenomes expose unusual compositional biases within the Monogenea class: implications for phylogenetic studies

“…The high level of conservation in the DHU stem can be explained by the fact that DHU stem probably acts as a recognition site for the aminoacyl-tRNA synthetase [58]. Notably, the anticodon sequences of 21 tRNAs perfectly conformed to that of other monogeneans [15, 42, 50, 55, 59–61]. The only exception was trnR , which uses the ACG anticodon in Eudiplozoon sp.…”