Characterization of complete mitochondrial genome and ribosomal operon forCarassotrema koreanumPark, 1938 (Digenea: Haploporidae) by means of next-generation sequencing data

Abstract

AbstractWe obtained new data on the complete mitochondrial DNA (mtDNA) and the ribosomal operon of the trematodeCarassotrema koreanum(Digenea: Haploporata: Haploporidae), an intestinal parasite ofCarassius auratus, using next-generation sequencing. The mtDNA ofC.koreanumcontained 13,965 bp, including 12 protein-coding genes, two ribosomal genes, 22 transport RNA (tRNA) genes and a non-coding region. The ribosomal operon ofC.koreanumwas 10,644 bp in length, including ETS1 (1449 bp), 18S ribosomal RNA (rRNA) gene (1988 bp), ITS1 ribosomal DNA (rDNA) (558 bp), 5.8S rRNA gene (157 bp), ITS2 rDNA (274 bp), 28S rRNA gene (4152 bp) and ETS2 (2066 bp). Phylogenetic analysis based on mtDNA protein-coding regions showed thatC.koreanumwas closely related toParasaccocoelium mugili, a species from the same suborder Haploporata. Bayesian phylogenetic tree topology was the most reliable and confirmed the validity of the Haploporata. The results of sequence cluster analysis based on codon usage bias demonstrated some agreement with the results of the phylogenetic analysis. In particular,Schistosomaspp. were differentiated from the other members of Digenea and the members of Pronocephalata were localized within the same cluster.Carassotrema koreanumandP.mugilifell within different clusters. The grouping ofC.koreanumandP.mugiliwithin the same cluster was obtained on the basis of frequencies of 13 specified codons, of which three codon pairs were degenerate. A similarity was found between two haploporid species and twoDicrocoeliumspp. in the presence of TTG start codon of the mitochondrialnad5 gene. Our results confirmed the taxonomical status of the Haploporata identified in the previous studies and revealed some characteristic features of the codon usage in its representatives.