Insights into the structural features, optimal codons and phylogenetic analysis in Neoniphon argenteus (Teleostei: Holocentriformes) based on complete mitochondrial genome
Year: 2025
Type: preprint
Abstract: Neoniphon argenteus as one of widely distributed species within the nocturnal coral reef fish family and play an important role in maintaining the health of coral reef ecosystems. However, there is currently insufficient data regarding its phylogenetic position. To bridge this gap, the mitochondrial structure, optimal codon usage, and phylogenetic relationship of N. argenteus were examined using its complete mitochondrial genome. With a total length of 16,569 bp (GenBank PP190474.1), the complete mitogenome encodes 13 protein-coding genes, 22 tRNAs, and two rRNAs, along with two intergenic spacers. All tRNA sequences were able to adopt the anticipated cloverleaf secondary structures, with the exception of tRNA-Ser (AGN). Additionally, the palindromic motifs TACAT and ATGTA within the control region showed a propensity to adopt secondary structures resembling hairpins, whereas a conserved sequence motif (5’-GCCGG-3’) was observed in the OL region. △RSCU (Relative Synonymous Codon Usage) method revealed 11 optimal codons (AGG, GCA, GAA, GGC, AUU, CUA, UUA, CCA, CGA, ACA, GUC). Selection pressure analysis revealed purifying selection acting on all protein-coding genes with the exception of ND6. All species were assigned to two subfamilies (Holocentrinae and Myripristinae) based on phylogenetic analysis, which aligned with the known morphological and dietary differences. This study provides valuable molecular insight for further exploration of the evolutionary history of N. argenteus and other members of Holocentriformes
Authors: Lei Xie, Nan Chen, Qi Qiao, Xuedong Xie, Bozhu Huang, Lu Songhui, Dong Yuelei, Lei Cui
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W4414490762
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