Insights into the structural features, codon usage patterns and phylogenetic analysis in Neoniphon argenteus (Teleostei: Holocentriformes) based on complete mitochondrial genome

Insights into the structural features, codon usage patterns and phylogenetic analysis in Neoniphon argenteus (Teleostei: Holocentriformes) based on complete mitochondrial genome | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 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Data may be preliminary. 12 May 2026 V1 Latest version Share on Insights into the structural features, codon usage patterns and phylogenetic analysis in Neoniphon argenteus (Teleostei: Holocentriformes) based on complete mitochondrial genome Authors : Lei Xie [email protected] , Nan Chen [email protected] , Qi Qiao [email protected] , Xuedong Xie [email protected] , Bozhu Huang [email protected] , Lu Songhui [email protected] , Dong Yuelei [email protected] , and Lei Cui 0000-0003-4365-5173 [email protected] Authors Info & Affiliations https://doi.org/10.22541/authorea.15003168/v1 Under Review Ecology and Evolution Peer review timeline 8 views 9 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Neoniphon argenteus is a widely distributed species within the nocturnal coral reef fish family and plays 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, codon usage patterns, and phylogenetic relationship of N. argenteus were examined using its complete mitochondrial genome. With a total length of 16,569 bp (GenBank accession number: 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), which lacks the dihydrouridine (DHU) arm. 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. Analysis of relative synonymous codon usage (RSCU) revealed 32 frequently used codons (RSCU > 1) across the 13 PCGs, with a pronounced preference for NNA and NNC codons. Selection pressure analysis using site-specific models implemented in EasyCodeML revealed that all PCGs were predominantly under purifying selection, with no statistically significant evidence of pervasive positive selection. ND6 exhibited elevated non-synonymous/synonymous substitution ratios in pairwise comparisons, consistent with reduced selective constraint rather than adaptive evolution. Phylogenetic analysis of 19 Holocentriformes species assigned all taxa to two subfamilies (Holocentrinae and Myripristinae), 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. Supplementary Material File (supplement material.doc) supplement material Download 4.12 MB Information & Authors Information Version history V1 Version 1 12 May 2026 Peer review timeline Under Review Ecology and Evolution 13 May 2026 Under Review Collection Ecology and Evolution Authors Affiliations Lei Xie [email protected] Jinan University, Guangzhou, China, 510632 View all articles by this author Nan Chen [email protected] Jinan University, Guangzhou, China, 510632 View all articles by this author Qi Qiao [email protected] Jinan University, Guangzhou, China, 510632 View all articles by this author Xuedong Xie [email protected] Jinan University, Guangzhou, China, 510632 View all articles by this author Bozhu Huang [email protected] Jinan University, Guangzhou, China, 510632 View all articles by this author Lu Songhui [email protected] Jinan University, Guangzhou, China, 510632 View all articles by this author Dong Yuelei [email protected] Jinan University, Guangzhou, China, 510632 View all articles by this author Lei Cui 0000-0003-4365-5173 [email protected] Jinan University, Guangzhou, China, 510632 View all articles by this author Metrics & Citations Metrics Article Usage 8 views 9 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Lei Xie, Nan Chen, Qi Qiao, et al. Insights into the structural features, codon usage patterns and phylogenetic analysis in Neoniphon argenteus (Teleostei: Holocentriformes) based on complete mitochondrial genome. Authorea . 12 May 2026. DOI: https://doi.org/10.22541/authorea.15003168/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . 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