The first two complete mitochondrial genomes for the family Triglidae and implications for the higher phylogeny of Scorpaeniformes

Abstract

The mitochondrial genome (mitogenome) can provide useful information for analyzing phylogeny and molecular evolution. Scorpaeniformes is one of the most diverse teleostean orders and has great commercial importance. To develop mitogenome data for this important group, we determined the complete mitogenomes of two gurnards Chelidonichthys kumu and Lepidotrigla microptera of Triglidae within Scorpaeniformes for the first time. The mitogenomes are 16,495 bp long in C. kumu and 16,610 bp long in L. microptera. Both the mitogenomes contain 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and two non-coding regions. All PCGs are initiated by ATG codons, except for the cytochrome coxidase subunit 1 (cox1) gene. All of the tRNA genes could be folded into typical cloverleaf secondary structures, with the exception of tRNASer(AGN) lacks a dihydrouracil (DHU) stem. The control regions are both 838 bp and contain several features common to Scorpaeniformes. The phylogenetic relationships of 33 fish mitogenomes using Bayesian Inference (BI) and Maximum Likelihood (ML) based on nucleotide and amino acid sequences of 13 PCGs indicated that the mitogenome sequences could be useful in resolving higher-level relationship of Scorpaeniformes. The results may provide more insight into the mitogenome evolution of teleostean species.

The First Complete Mitochondrial Genome of the Flathead Cociella crocodilus (Scorpaeniformes: Platycephalidae) and the Phylogenetic Relationships within Scorpaeniformes Based on Whole Mitogenomes

“…Most of the tRNAs were folded into an ordinary cloverleaf secondary structure (Figure S2), except trnS2 (AUN), which lacked a DHU stem. This phenomenon is identical to other mitogenomes of teleost fishes, including the Scorpaeniformes species [12,35]. The standard structure of the amino acid acceptor stem was 7 bp, while trnaV, trnF, and trnaL1 (UUR) were 9 bp.…”

“…The best supported phylogenetic relationships of Scorpaeniformes are as follows: (Synanceiidae + (Platycephalidae + ((Scorpaenidae + Sebastidae) + ((Triglidae + Peristediidae) + (Agonidae + (Hexagrammidae + (Anoplopomatidae + Cottidae))))))). There was a conflict with our work based on complete mitogenomes [12]. In a previous study, Synanceiidae was as a sister to Scorpaenidae + Sebastidae.…”

“…To obtain the complete C. crocodilus mitogenome sequence, PCR amplification was performed with several primer pairs designed based on aligned mitogenome sequences of Chelidonichthys kumu (GenBank: KY379222) and Lepidotrigla microptera (GenBank: KY012348.1) (Table S1) [12]. All PCR reactions were conducted with LA Taq DNA polymerase using Premix LA Taq (Takara, Dalian, China) according to the following cycling conditions: beginning with an initial denaturation step at 95 °C for 1 min, followed by 35 cycles of denaturation at 95 °C for 20 s, annealing at 55 °C for 45 s and elongation at 72 °C for 1–5 min depending on the length of the segment.…”

“…However, only one complete mitogenome from Platycephalidae, Platycephalus indicus , has been sequenced. We previously used the mitochondrial genome to study the genetic relationships of Scorpaeniformes [12], which does not include the Platycephalidae family, although phylogenetic trees based on nuclear genes and partial mitochondrial gene sequences were constructed to analyze interspecies relationships with Scorpaeniformes in previous research. Nevertheless, the difference between whether flatheads or scorpionfishes are ‘the most basal clade’ of Scorpaeniformes was studied [13,14,15].…”

Comparative Analysis of the Complete Mitochondrial Genomes for Development Application

“…The cellular injury will release mitochondria “damage-associated molecular patterns” DAMPs (formyl-peptides and circular mtDNA) into the circulation with functional critical immune consequences, and this is believed to be the link between trauma, inflammation, and systemic inflammatory response syndrome (SIRS) (Zhang et al, 2010 ). The mitochondrial genome of fish is a circular double-stranded molecule which is about 15 to 19 kb in length (Cui et al, 2017 ). Mitochondria play a central role in metabolism (Brand, 1997 ), including oxidative phosphorylation (Smeitink et al, 2001 ), apoptosis (Kroemer et al, 1998 ), diseases (Graeber and Muller, 1998 ), aging (Wei, 1998 ), and also different other biochemical functions.…”