Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History

Abstract

Mitochondrial genome is a powerful molecule marker to explore phylogenetic relationships and reveal molecular evolution in ichthyological studies. Gerres species play significant roles in marine fishery, but its evolution has received little attention. To date, only two Gerres mitochondrial genomes were reported. In the present study, three mitogenomes of Gerres (Gerres filamentosus, Gerres erythrourus, and Gerres decacanthus) were systemically investigated. The lengths of the mitogenome sequences were 16,673, 16,728, and 16,871 bp for G. filamentosus, G. erythrourus, and G. decacanthus, respectively. Most protein-coding genes (PCGs) were initiated with the typical ATG codon and terminated with the TAA codon, and the incomplete termination codon T/TA could be detected in the three species. The majority of AT-skew and GC-skew values of the 13 PCGs among the three species were negative, and the amplitude of the GC-skew was larger than the AT-skew. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, were which most likely due to the difference in their living environment. The phylogenetic tree was constructed by molecular method (Bayesian Inference (BI) and maximum Likelihood (ML)), providing further supplement to the scientific classification of fish. Three Gerres species were differentiated in late Cretaceous and early Paleogene, and their evolution might link with the geological events that could change their survival environment.

Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication

“…The length of P. cupulatus 02 was longer than that of other species, resulting in having the longest mitogenome ( Figure 1 ). There were large length variations across species, even closely related ones, which supports a previous study [ 48 ]. Rapid variation of CRs seemed to provide information for species evolution, but its internal mechanisms need deeper examination.…”

Mitochondrial Genome Structures and Phylogenetic Analyses of Two Tropical Characidae Fishes

“…Eight tRNAs ( trnA , trnC , trnE , trnN , trnP , trnQ , trnS2 , and trnY ) and nad6 were found to be encoded on the L-strand ( Figure 1 ), whereas 14 tRNAs, 12 PCGs, 2 rRNAs, and 1 CR were on the H-strand. Similar to other fish mitogenomes ( Kim et al, 2008 ; Ruan et al, 2020 ), the A + T content in Characidae mitogenomes was highly biased, ranging from 57.1 ( A. paranae ) to 60.1% ( G. bogotensis ) ( Table 4 ). The base composition of a mitogenome is frequently described in terms of the AT skew.…”

“…The sizes of the 16S rRNA genes were 1,678 bp (H. erythrozonus) and 1,671 bp (H. amandae), and the 12S rRNA genes of both mitogenomes were 949 bp. The rRNA genes of Characidae mitogenomes were found to be highly conserved compared with those of other published fish mitogenomes (Javonillo et al, 2010;Zhao et al, 2015;Ruan et al, 2020), with the two rRNA genes located between trnL2 and trnF separated by trnV. The A + T contents of rRNA genes ranged from 55.1 to 57.2% among the 11 Characidae species (Table 4).…”

“…Mitochondria possess mitochondrial DNA (mtDNA), which has a closed circular double-stranded structure and self-replicates semi-conservatively ( Prosdocimi et al, 2012 ; Paz et al, 2014 ). Mitochondrial DNA is considered the second genetic information system of eukaryotic cells ( Kim et al, 2008 ; Cooke et al, 2012 ; Zhao et al, 2015 ; Ruan et al, 2020 ). Compared with nuclear DNA, it is a relatively independent replication unit characterized by a small size, simple structure, maternal inheritance, rapid evolution, limited recombination, and variability in evolutionary rate at different loci ( Harrison, 1989 ; Javonillo et al, 2010 ).…”

Comparative analysis of the complete mitochondrial genomes of three rockfishes (Scorpaeniformes, Sebastiscus) and insights into the phylogenetic relationships of Sebastidae

“…TAA were commonly used as the termination codons, although the incomplete termination codons T or TA were found in ND2, COII, ATP6, COIII, ND3, ND4, and CYTB in all three mitogenomes. The incomplete termination codon has also been found in all other sequenced Osteichthyes species [48][49][50][51][52]. It has been confirmed that the incomplete termination codons could act as the complete functional termination codons in polyadenylation processes and polycistronic transcription cleavage [29,51,53].…”