Diplodiscus spp

An, Qi, Qiu, Yang-Yuan, Lou, Yan, Jiang, Yan, Qiu, Hong-Yu, Zhang, Zhong-Huai, Li, Ben, Zhang, Ai-Hui, Wei, Wei, Chen, Ying-Yu, Gao, Jun-Feng & Wang, Chun-Ren, 2022, Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication, International Journal for Parasitology: Parasites and Wildlife 19, pp. 9-17 : 15-16

3.4. Diversity and mutation rate among Diplodiscus spp . Mitogenomes

To determine the highly conserved and variable mitochondrial genes among 11 Paramphistomoidea trematodes, a sliding window analysis was conducted by the concatenated nucleotide sequence of 12 PCGs. The results showed obvious differences in 12 PCGs of 11 Paramphistomoidea trematodes. By computing the number of variable positions per unit

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length of gene, the curve indicated that cox 1 was the lowest variable gene, while nad 2, nad 4, nad 5 and cox 3 showed high sequence divergence ( Fig. 4 ). The gene cox 1 was considered to be a useful barcode for metazoans, and widely employed for trematode studies ( Hebert et al., 2003; Brabec et al., 2015). The mitochondrial genes cox 1 has also been used to study the population genetic structure of Diplostomum spp. on a local and global scale ( Brabec et al., 2015). As shown in Fig. 5 , non-synonymous/synonymous (dN/dS) mutation rates among the 12 PCGs of the three Diplodiscus mitogenomes were analyzed. It was clearly showed that all PCGs were under negative (purifying) selection (dN/dS <0.5), and cox 1 had the lowest dN/dS value in 12 PCGs, which was similar with Gyrodactylus derjavinoides reported by Huyse et al. (2008). Because the stronger purification selection pressure has the smaller value of dN/dS, which further corroborates that cox 1 has higher synonymous variation. Additionally, the relatively looser selection pressure (0.3 <dN/dS <0.5), which may due to the accu-mulation of non-synonymous substitutions. These results suggest that the cox 1 gene should be considered as optimal candidates for genetic marker to be used for population genetics and species identification studies in the superfamily Paramphistomoidea species.

Figures

Fig. 4. Sliding window analysis of the complete mt genome sequences of 11 Paramphistomoidea trematodes. A sliding window of 300 bp (in 10 bp overlapping steps) was used to estimate nucleotide diversity Pi (π) across the alignments. Nucleotide diversity was plotted against the mid-point positions of each window. Each gene boundary is identified.

Fig. 5. Proportions between rates of non-synonymous (dN) and synonymous (dS) nucleotide substitutions (dN/dS). Bar chart for pairwise proportions of dN/dS for each of the mitochondrial subunits of the Diplodiscus spp.