Mitogenomic Characterization and Phylogenetic Placement of African Hind, Cephalopholis taeniops: Shedding Light on the Evolution of Groupers (Serranidae: Epinephelinae)

Abstract

The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The generated mitogenome spans 16,572 base pairs and exhibits a gene order analogous to that of the ancestral teleost’s, featuring 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. The mitogenome of C. taeniops displays an AT bias (54.99%), aligning with related species. The majority of PCGs in the mitogenome initiate with the start codon ATG, with the exceptions being COI (GTG) and atp6 (TTG). The relative synonymous codon usage analysis revealed the maximum abundance of leucine, proline, serine, and threonine. The nonsynonymous/synonymous ratios were <1, which indicates a strong negative selection among all PCGs of the Cephalopholis species. In C. taeniops, the prevalent transfer RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), which lacks a dihydrouracil (DHU) stem. A comparative examination of conserved domains and sequence blocks across various Cephalopholis species indicates noteworthy variations in length and nucleotide diversity. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic analyses, employing the concatenated PCGs and a combination of PCGs + rRNAs, distinctly separate all Cephalopholis species, including C. taeniops. Overall, these findings deepen our understanding of evolutionary relationships among serranid groupers, emphasizing the significance of structural considerations in mitogenomic analyses.

Complete Mitochondrial Genomes of Nannostomus Pencilfish: Genome Characterization and Phylogenetic Analysis

“…Previous studies have documented the occurrence of atypical initiation codons in Characiformes, such as Astyanax paranae and Hemigrammus armstrongi [ 13 , 40 ]. Most of the gene overlap regions appeared between PCGs and PCGs, with the largest overlaps all located between ATP8 and ATP6 , consistent with other fish mitogenomes [ 41 , 42 , 43 , 44 ]. Apart from ND3 , the Ka/Ks ratios of other PCGs were lower than 1.…”

Structure, Evolution, and Mitochondrial Genome Analysis of Mussel Species (Bivalvia, Mytilidae)

“…To the author's best knowledge, the most thorough attempt to detect the impact of molecular variability on the fitness (W) components (W = Wv + Wf, where Wv and Wf are fitness in terms of viability and fertility, respectively) made in research on allozyme polymorphism in Drosophila by Kojima and coauthors [45], where no definite allele effects in the numerous generations were obtained after nearly ten years of laborious laboratory experimentation. The conclusions in favor of selection occurring quite frequently are available in the literature sources on molecular markers [47][48][49], but little attention is paid to the complications, as stressed above.…”