Mitochondrial genome of the garfish Hyporhamphus quoyi (Beloniformes: Hemiramphidae) and phylogenetic relationships within Beloniformes based on whole mitogenomes

Abstract

Mitochondrial DNA (mtDNA) can provide genome-level information (e.g. mitochondrial genome structure, phylogenetic relationships and codon usage) for analyzing molecular phylogeny and evolution of teleostean species. The species in the order Beloniformes have commercial importance in recreational fisheries. In order to further clarify the phylogenetic relationship of these important species, we determined the complete mitochondrial genome (mitogenome) of garfish Hyporhamphus quoyi of Hemiramphidae within Beloniformes. The mitogenome was 16,524 bp long and was typical of other teleosts mitogenomes in size and content. Thirteen PCGs started with the typical ATG codon (with exception of the cytochrome coxidase subunit 1 (cox1) gene with GTG). All tRNA sequences could be folded into expected cloverleaf secondary structures except for tRNASer (AGN) which lost a dihydrouracil (DHU) stem. The control region was 866 bp in length, which contained some conserved sequence blocks (CSBs) common to Beloniformes. The phylogenetic relationship between 26 fish Beloniformes species was analyzed based on the complete nucleotide and amino acid sequences of 13 PCGs by two different inference methods (Maximum Likelihood and Bayesian Inference). Phylogenetic analyses revealed Hemiramphidae as the sister group to Exocoetidae and it is a paraphyletic grouping. Our results may provide useful information on mitogenome evolution of teleostean species.

Stronger selective constraints on the mitochondrial genome in flying fishes

“…In this study, based on the results of phylogenetic trees from previous studies (Toyama et al, 2020;Daane et al, 2021), the classification information from the NCBI Taxonomy Browser (Schoch et al, 2020) was adopted, which divided the sauries (Scomberesocidae) into the family Belonidae and also gave family status (Zenarchopteridae) to the freshwater halfbeaks. The phylogenetic trees based on 13 concatenated PCGs showed a similar topology to the previous molecular phylogenetic analyses based on mitochondrial genome sequences (Cui et al, 2018;Lü et al, 2018;Zhu et al, 2018;Tan et al, 2019), showing that the ricefishes (Adrianichthyidae) were at the base of the phylogenetic tree, the freshwater halfbeaks (Zenarchopteridae) were nested within the needlefishes (Belonidae), and the flying fishes (Exocoetidae) were nested within the marine halfbeaks (Hemiramphidae). However, the results of research by Lovejoy (2000); Lovejoy (2004) based on mtDNA and nuclear loci, revealed a sister relationship between needlefishes and the freshwater halfbeaks, which was consistent with the morphologically based analysis of Beloniformes phylogenetic relationships (Toyama et al, 2020) and the reconstruct the phylogeny of the Beloniformes based on 4683 genes (Daane et al, 2021).…”

Complete mitochondrial genome of Buffon’s river garfish Zenarchopterus buffonis (Valenciennes, 1847)

“…The result (Figure 1) supports that Z. buffonis forms a monophyletic cluster with Dermogenys pusilla, Ablennes hians, Tylosurus acus, Strongylura anastomella, and Cololabis saira. The topology relationships of Beloniformes was consistent with the previous work (Cui et al 2018), but the relationships among Belonidae, Zenarchopteridae, and Sconberesocidae is still not clear, which required more mitogenomes data to demonstrate in the future.…”

Draft Genome of the Mirrorwing Flyingfish (Hirundichthys speculiger)

“…The two core genes, eevs and mt-ox , in zebrafish are flanked by four transcription factor genes [ frmd4B, mitf , mdfic , and foxp1 (Osborn et al, 2015 )], which is not consistent with the loss of mdfic in Japanese medaka [ Oryzias latipes (Kim et al, 2018 )]. Phylogenetic analysis using mitochondrial genes in Beloniformes had inferred a close relationship between the mirrorwing flyingfish and medaka (Lovejoy et al, 2004 ; Cui et al, 2018 ). Whether the mirrorwing flyingfish contains the complete gene cluster as zebrafish or incomplete cluster as medaka is valuable for checking the possible lineage-specific gene rearrangement of eevs -like cluster.…”