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

Abstract

The complete mitochondrial genome of Gyrodactylus kobayashii was 14 786 bp in length, containing 12 protein-coding genes (lacking Atp8), 22 tRNA genes, two rRNA genes and two major non-coding regions (NC1 and NC2). The overall A + T content of mitochondrial genome was 71.6%. A close relationship between G. kobayashii and the three Gyrodactylus species (G. salaris, G. thymalli and G. derjavinoides) was uncovered in the phylogenetic tree based on amino acid sequences.

Gyrodactylus kobayashii was the most common Gyrodactylus species on the fins and gills of goldfish Carassius auratus. The worm was collected on goldfish from Wuhan (30°31'23”N, 114°23'01”E), China, and was identified by morphology and ITS molecular marker (Li et al. 2013).

The complete mitochondrial genome of G. kobayashii (GenBank accession no. KU057942) was sequenced by using long PCR and Sanger method of DNA sequencing. The circular mitogenome was 14 786 bp long and contained 12 protein-coding genes (PCGs, lacking Atp8), 22 tRNA genes, two rRNA genes and two major non-coding regions (NC1 and NC2) (Table 1). All the genes were transcribed from the same strand. The base composition was 41.9% T, 11.1% C, 29.7% A and 17.3% G. The disproportionally overall A + T content was 71.6%, which was higher than any of the three Gyrodactylus species (G. salaris, 62.3%; G. thymalli 62.8% and G. derjavinoides, 68.2%) (Huyse et al. 2007; Plaisance et al. 2007; Huyse et al. 2008). The gene order of G. kobayashii matched exactly with the three Gyrodactylus species.

Table 1.

Organization of the mitochondrial genome of Gyrodactylus kobayashii.

Gene/region	Position		Size	Intergenic nucleotides	Codon		Anti-codon
	Start	Stop			Start	Stop
Cox3	1	639	639		ATG	TAA
tRNAHis	646	712	67	6			GTG
Cytb	716	1789	1074	3	ATG	TAA
Nad4L	1789	2037	249	–1	ATG	TAA
Nad4	2010	3218	1209	–28	ATG	TAA
tRNAPhe	3221	3285	65	2			GAA
NC1	3286	4063	778
Atp6	4064	4576	513		ATG	TAG
Nad2	4585	5442	858	8	ATG	TAG
tRNAVal	5443	5506	64				TAC
tRNAAla	5508	5579	72	1			TGC
tRNAAsp	5582	5646	65	2			GTC
Nad1	5647	6534	888		ATG	TAG
tRNAAsn	6534	6600	67	–1			GTT
tRNAPro	6601	6663	63				TGG
tRNAIle	6660	6724	65	–4			GAT
tRNALys	6726	6789	64	1			CTT
Nad3	6791	7138	348	1	ATG	TAG
tRNASer(AGN)(S1)	7139	7196	58				GCT
tRNATrp	7206	7270	65	9			TCA
Cox1	7275	8822	1548	4	ATG	TAA
tRNAThr	8831	8895	65	8			TGT
16S rRNA	8895	9849	955	–1
tRNACys	9854	9914	61	4			GCA
12S rRNA	9915	10 621	707
Cox2	10 622	11 203	582		ATG	TAA
tRNAGlu	11 315	11 386	72	111			TTC
Nad6	11 390	11 872	483	3	ATG	TAA
tRNATyr	11 893	11 960	68	20			GTA
tRNALeu(CUN)(L1)	11 967	12 032	66	6			TAG
tRNAGln	12 041	12 104	64	8			TTG
tRNAMet	12 105	12 169	65				CAT
NC2	12 170	12 952	783
tRNASer(UCN)(S2)	12 953	13 011	59				TGA
tRNALeu(UUR)(L2)	13 014	13 081	68	2			TAA
tRNAArg	13 085	13 151	67	3			TCG
Nad5	13 152	14 705	1554		ATG	TAG
tRNAGly	14 718	14 783	66	12			TCC
	14 787	14 786		3

The length of 12 PCGs was 9945 bp, with 71.6% A + T content. ATG was the unique start codon. Nad5, Nad3, Nad2, Nad1 and Atp6 appeared to use TAG as stop codon, whereas the rest of the PCGs used the stop codon TAA, and no premature stop codon (TA or T) was found. Total length of the 22 tRNA genes was 1436 bp, varying from 58 bp (tRNA^Ser(AGN)) to 72 bp (tRNA^Glu and tRNA^Ala). All tRNAs could be fold into the conventional secondary structure, except for three unorthodox tRNAs, tRNA^Ser(AGN), tRNA^Ser(UCN) and tRNA^Cys lacked DHU arms. The rrnL and rrnS were 955 bp and 707 bp in size, respectively. They were flanked by tRNA^Thr and Cox2, and separated by tRNA^Cys, as demonstrated in the monopisthocotyleans (Huyse et al. 2007; Plaisance et al. 2007; Huyse et al. 2008; Perkins et al. 2010; Ye et al. 2014; Zhang et al. 2014a,b).

There were five cases of overlapping regions within the mitogenome. The overlap between Nad4L and Nad4 was common in metazoan mtDNAs (von Nickisch-Rosenegk et al. 2001), with the exception of Benedenia hoshinai and B. seriolae (Perkins et al. 2010). There were 21 short intergenic regions ranging from 1 bp to 111 bp. In addition, the two long non-coding regions, NC1 (between tRNA^Phe and Atp6) and NC2 (between tRNA^Met and tRNA^Ser(UCN)) were 778 bp and 783 bp long, 67.0% and 68.2% for the AT content, respectively. The high similarity over 686 bp sequences was found between NC1 and NC2, with the differences in eight substitutions and three indels.

The phylogenetic analysis was performed with 2858 homologous concatenated amino acid sequences representing 12 protein-coding genes from nine available mitochondrial genomes and G. kobayashii mitogenome (this study), implementing maximum-likelihood (ML) and Bayesian inference (BI) analyses. Both the phylogenetic methods produced the same tree topology in the branching patterns. Gyrodactylus kobayashii was closely relate to the three Gyrodactylus species with extremely high bootstrap resampling (ML) and posterior probability (BI) values (Figure 1).

Figure 1.

Phylogenetic tree of Gyrodactylus kobayashii and selected monopisthocotyleans based on the concatenated amino acids representing 12 mitochondrial protein-coding genes. The MtZoa model for maximum-likelihood analysis and MtREV model for Bayes analysis are selected according to AIC criterion. Scale bar represents the estimated number of substitutions per site. The numbers at the nodes indicate posterior probability (upper value) and bootstrap probability (lower value).

Disclosure statement

The authors report no conflict of interest. The authors alone are responsible for the content and writing of the manuscript.

Funding information

This work was supported by the Earmarked Fund for China Agriculture Research System (CARS-46-08), the National Natural Science Foundation of China (31272695 and 31572658) and the major scientific and technological innovation project of Hubei Province (2015ABA045).