The signals of selective constraints on the mitochondrial non-coding control region: insights from comparative mitogenomics of Clupeoid fishes

Insights into the structural features and phylogenetic implications of the complete mitochondrial genome of Fasin rainbow fish (Melanotaenia fasinensis)

The Fasin rainbow fish, scientifically named Melanotaenia fasinensis, is highly prized by aquarium enthusiasts for its vibrant colors and adaptability to artificial aquatic environments. This species is endemic to the karst landscape of the Bird's Head region in Papua, Indonesia, and belongs to the family Melanotaeniidae. Discovered relatively recently in 2010, this species was designated as endangered by the International Union for Conservation of Nature (IUCN) in 2021. However, there is currently insufficient data regarding its phylogenetic position. To address this gap, our study employed next-generation sequencing (NGS) to analyze the entire mitochondrial genome of M. fasinensis. The mitochondrial genome comprises 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, with a total length of 16,731 base pairs. The base composition of the mitogenome revealed percentages of 27.76% adenine (A), 27.34% thymine (T), 16.15% guanine (G), and 28.75% cytosine (C) residues. Our phylogenetic analysis based on sequence data indicated that all species of the Melanotaeniidae family clustered together on the same branch. Furthermore, the intergeneric and interspecific taxonomic positions were explicit and clear. Phylogenetically, Melanotaeniidae were more closely related to the family Isonidae than to the family Atherinomorus. The phylogenetic position of M. fasinensis was relatively basal within the genus Melanotaenia. This study provides valuable molecular insights for further exploration of the phylogeography and evolutionary history of M. fasinensis and other members of the genus Melanotaenia.

Comparative mitogenomics and phylogenetics of the family Carangidae with special emphasis on the mitogenome of the Indian Scad Decapterus russelli

Carangids are abundant and commercially important marine fish that contribute to a significant portion of the fisheries in many parts of the world. In the present study, we characterized the complete mitogenome of the Indian scad, Decapterus russelli and performed a comprehensive comparative mitogenomic analysis of the family Carangidae. The comparative mitogenomics provided valuable insights into the structure, variability, and features of the coding and non-coding regions that evolved across species over millions of years. The structural features of tRNAs revealed changes in the frequency of mismatched and wobble base pairs, which is reflected in the base composition of H and L strands. The highly conserved sequence motif of the mTERF binding site in carangids over the ~ 400 MYA of their divergence demonstrated the functional importance of these sites. The control region of carangids was characterized by the presence of discontinuous repeat units with a high rate of sequence divergence in the form of base substitutions, insertions, and deletions. The maintenance of secondary structures in the control region independent of the rapid evolution of primary structure suggested the effect of selective constraints on their maintenance. Maximum likelihood (ML) and Bayesian inference (BI) phylogeny revealed a similar topology consistent with previous taxonomic studies. The extant carangids diverged through the evolutionary events experienced during the Cretaceous, Paleogene, and Neogene periods.