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

Date Published: November 15, 2018

Publisher: Public Library of Science

Author(s): Lei Cui, Yuelei Dong, Rongbo Cao, Jian Gao, Jingyi Cen, Zhijia Zheng, Songhui Lu, Tzen-Yuh Chiang.

http://doi.org/10.1371/journal.pone.0205025

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.

Partial Text

Mitochondrial DNA (mtDNA) of teleosts is a circular genome ranging from 15 to 19 kbp in length that is generally composed of two ribosomal RNA genes (12S rRNA and 16S rRNA), 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two typical non-coding control regions (origin of the light strand (OL) and control region (CR)) which contain essential regulatory elements for replication and transcription [1, 2]. MtDNA is commonly used for population genetics and phylogenetic molecular evolution due to maternal inheritance, rapid evolution, coding content conservation, and high substitution rates compared to the nuclear genome[3, 4]. In addition, the molecular characteristics of the mitogenome, such as gene rearrangement, tRNA secondary structure and models of the control of mtDNA replication are valuable for deep phylogenetic analysis [5, 6].

 

Source:

http://doi.org/10.1371/journal.pone.0205025

 

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