Oncorhynchus gorbuscha, (Walbaum, 1792) (Walbaum, 1792)

Denys, Gaël P. J., Josset, Quentin, Ferreira, Amélie Verde & Dettaï, Agnès, 2024, The complete mitochondrial genome of a new invader fish in France, the pink salmon Oncorhynchus gorbuscha (Walbaum, 1792) (Teleostei, Salmonidae), Cybium 48 (2), pp. 111-120 : 114-116

RESULTS AND DISCUSSION

Sequence description and phylogenetic analysis

The newly obtained mitogenome has a total length of 16,695 bp and follows the standard vertebrate order, similar to already published mitogenome of O. gorbuscha : 13 protein-coding genes including six coding with an incomplete codon stop (COII, ATP6, COIII, NADH3, NADH4 and Cytb), 22 transfer RNA genes including two tRNA-Leu and 2 tRNA-Ser, two ribosomal RNA genes and a control region ( Fig. 2 ; Appendix 3). Intergenic spaces and overlapping sequences were found. The base composition of the entire genome was 27.9% for A, 26.4% for T, 28.7% for C and 17.0% for G. As for the two sequences of O. gorbuscha available on GenBank, the mitogenome CM029873 is reversed in the database and had to be reverse complemented to align with the dataset in standard order. The control region of the mitogenome EF455489 does not have the same length (1131 bp vs. 1041 bp). Previous genetic studies already highlighted length heteroplasmy among pink salmon populations with this marker with insertions and deletions ( Brykov et al., 1999; Churikov and Gharrett, 2002; Sato and Urawa, 2017).

Alignment of our sequence with all CR sequences from GenBank provided a 100% match with the haplotype OGDL-8 (sequence LC191999), one of the haplotypes widespread in Japan ( Sato and Urawa, 2017).

The ML phylogeny ( Fig. 3 ) is consistent with Shedko et al. (2013) on mitochondrial data showing generally high support values for nodes as well as with the nuclear RAG1 marker topology ( Shedko et al., 2012). It differs from phylogenetic trees of Horreo (2017) and Gong et al. (2017) by the position of O. masou , which is not at a basal position within the Oncorhynchus spp. but with a weak robustness. Crespi and Fulton (2004) already demonstrated that the position of O. masou depends to the markers analysed and the phylogenetic reconstruction method. Our O. gorbuscha mitogenome groups well with the two other sequences available on GenBank, corroborating its identification.

Finally, we tested metabarcoding markers of four genes (12S, 16S, COI, Cytb) in order to know if O. gorbuscha can easily be distinguished from the four other Oncorhynchus species used for restocking in non-American areas. O. gorbuscha is distinguished over these four genes by 10 diagnostic sites on the 12S (Table III), 34 on the 16S (Table IV), 82 on the COI ( Table V ) and 61 on the Cytb (Table VI). MiFish ( Miya et al., 2015) and Teleo2 primers ( Taberlet et al., 2018) between the positions 246/250 and 416 differentiate all 4 species (Table III). However, the fragments corresponding to the 12V-5 primers ( Riaz et al., 2011) between the positions 444 and 543 and the Teleo primers ( Valentini et al., 2016) between the positions 849 and 912, while they discriminate well O. gorbuscha from other Oncorhynchus species, have the exact same sequence for two (12V-5) or all three (Teleo) other species making their distinction impossible. For the other markers used for 16S, COI and Cytb genes, all species are distinguishable (Tables IV-VI).

Thus, this mitogenome can be used as a sequence of reference for different molecular expertise using multiple markers such as eDNA or control of mislabelling food ( Wang et al., 2021).

Figures

Figure 2. – Coverage depending on position in the mitogenome assembly.

Figure 3. – Maximum Likelihood phylogenet- ic tree of Oncorhynchus mitogenomes; boot- strap values beside the nodes.