The complete mitochondrial genome of Gyrodactylus pseudorasborae (Platyhelminthes: Monogenea) with a phylogeny of Gyrodactylidae parasites

Abstract

Background: Gyrodactylus von Nordmann, 1832, a genus of viviparous parasites within the family Gyrodactylidae, contains one of the largest nominal species in the world. Gyrodactylus pseudorasborae Ondračková, Seifertová & Tkachenko, 2023 widely distributed in Europe and China, although its mitochondrial genome remains unclear. This study aims to sequence the mitogenome of G.pseudorasborae and clarify its phylogenetic relationship within the Gyrodactylidea. The mitochondrial genome of G. pseudorasborae was amplified in six parts from a single parasite, sequenced using primer walking, annotated and analyzed using bioinformatic tools.

Results: The mitochondrial genome of G. pseudorasborae is 14,189 bp in length, containing 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and two major non-coding regions (NCR: NC1 and NC2). The overall A + T content of the mitogenome is 73.1%, a medium content compared with all reported mitochondrial genomes of monogeneans. The mitogenome of G. pseudorasborae presents a clear bias in nucleotide composition with a negative AT skew and a positive GC skew except for NCR. All tRNAs have the typical cloverleaf secondary structure except for tRNA^Cys, tRNA^Ser1, and tRNA^Ser2, which lack the dihydrouridine (DHU) arm. Furthermore, one repetitive non-coding region of 32 bp repeats occurred in the NC1 region with poly-T stretch, stem-loop structure, and TAn motif. The gene order is identical to the mitochondrial genomes reported from other Gyrodactylus species except Gyrodactylus nyanzae Paperna, 1973 and Gyrodactylus sp. FZ-2021. Phylogenetic analyses show that G. pseudorasborae and Gyrodactylus parvae You, Easy & Cone, 2008 cluster together with high nodal support based on 12 PCGs sequences and amino acid sequences, Gyrodactylidae forms independent monophyletic clade within Gyrodactylidea.

Conclusion: Both the mitochondrial genome and phylogenetic analyses support G. pseudorasborae is a member of the genus Gyrodactylus and Gyrodactylidae forms an independent monophyletic clade within Gyrodactylidea. Furthermore, the mitochondrial genome of G. pseudorasborae is the shortest in the Gyrodactylidea species compared with size differences in NCR.

Keywords: Gyrodactylus pseudorasborae; Pseudorasbora parva; China; Gyrodactylidea; Mitochondrial genome.

Fig. 1

Graphical map of the mitogenome of Gyrodactylus pseudorasbora. The yellow, pink, and green segments represent protein-coding genes (PCGs); the blue and red segments represent tRNA genes (tRNAs) and rRNA genes (RNAs), respectively. Genes for tRNAs are abbreviated using three letters

Fig. 2

Gene orders (a) and gene synteny analysis (b) are shown among 13 mitogenomes of Gyrodactylidea species. The rearrangements of tRNAs (red rectangle) and PCGs (blue rectangle) occurred in five gyrodactylids, including G. nyanzae, Gyrodactylus sp. FZ-2021, P. variegatus, M. karibae, and A. forficulatus (a). Gene synteny analysis revealed three homologous regions (A-C) (b)

Fig. 3

Secondary structures of tRNAs in the mitochondrial genome of Gyrodactylus pseudorasbora

Fig. 4

Codon and relative synonymous codon usage (RSCU) values of the protein-coding genes (PCGs) in the mitochondrial genomes of Gyrodactylidea are shown in different colors. Grey-colored codon indicates that codon is not present in the genome. A total of 3311, 3279, 3319, 3311, 3309, 3225, 3310, 3274, 3304, 3322, 3329, and 3307 codons for Gyrodactylus pseudorasborae, Gyrodactylus derjavinoides, Gyrodactylus nyanzae, Gyrodactylus gurleyi, Gyrodactylus parvae, Gyrodactylus brachymystacis, Gyrodactylus kobayashii, Gyrodactylus salaris, Gyrodactylus sp. FY-2015, Gyrodactylus sp. FZ-2021, Paragyrodactylus variegatus, and Aglaiogyrodactylus forficulatus were analyzed, respectively, excluding stop codons

Fig. 5

Stem-loop structural elements of one consensus repeat pattern for the mitochondrial major non-coding region 1 (NC1) of Gyrodactylus pseudorasbora

Fig. 6

Sliding window and evolutionary rate analyses of the PCGs of mitogenomes among twelve Gyrodactylidea species. (a) Sliding window analysis was conducted on concatenated alignments of 12 PCGs. The black line represents the value of nucleotide diversity (window size = 200 bp, step size = 20 bp, with the value inserted at its mid-point). Gene names, boundaries, and average nucleotide diversity values are indicated above the graph. (b) Ratios of non-synonymous (dN) to synonymous (dS) substitution rates calculated for protein-coding genes (PCGs)

Fig. 7

Phylogenetic relationships between Gyrodactylus pseudorasborae and related species of Gyrodactylidea based on the concatenated protein-coding genes (PCGs) sequences (a) and amino acid sequences (b) were analyzed with Bayesian inference (BI) and maximum likelihood (ML) methods. The GTR + I + G and MtArt + G + F were selected as the best-fitting models according to the BIC criterion for BI and ML analyses. The scale bar represents the estimated number of substitutions per site. Node numbers represent the Bayesian posterior probabilities and bootstrap values (BI/ML), respectively. The study gyrodactylid and outgroup species are highlighted by a pentagram and a circle, respectively