Complete Mitochondrial Genome of <i>Niphon spinosus</i> (Perciformes: Niphonidae): Genome Characterization and Phylogenetic Analysis

The species <i>Niphon spinosus</i> (Cuvier, 1829) is the only representative of the family Niphonidae and the genus <i>Niphon</i>, and its taxonomic history is complicated; it is still unclear in a phylogenetic sense. In this study, we report the complete mitochondrial genome...

Full description

Saved in:
Bibliographic Details
Main Authors: Maheshkumar Prakash Patil, Jong-Oh Kim, Seung Hyun Yoo, Jiyoung Shin, Ji-Young Yang, Kyunghoi Kim, Gun-Do Kim
Format: Article
Language:English
Published: MDPI AG 2025-01-01
Series:Biomolecules
Subjects:
Online Access:https://www.mdpi.com/2218-273X/15/1/52
Tags: Add Tag
No Tags, Be the first to tag this record!
_version_ 1832588890499710976
author Maheshkumar Prakash Patil
Jong-Oh Kim
Seung Hyun Yoo
Jiyoung Shin
Ji-Young Yang
Kyunghoi Kim
Gun-Do Kim
author_facet Maheshkumar Prakash Patil
Jong-Oh Kim
Seung Hyun Yoo
Jiyoung Shin
Ji-Young Yang
Kyunghoi Kim
Gun-Do Kim
author_sort Maheshkumar Prakash Patil
collection DOAJ
description The species <i>Niphon spinosus</i> (Cuvier, 1829) is the only representative of the family Niphonidae and the genus <i>Niphon</i>, and its taxonomic history is complicated; it is still unclear in a phylogenetic sense. In this study, we report the complete mitochondrial genome of <i>N. spinosus</i> (OP391482), which was determined to be 16,503 bp long with biased A + T contents (53.8%) using next-generation technology. The typical set of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and one control region (D-loop) are included in the mitochondrial genome. The H-strand encoded 28 genes (14 tRNA, 2 rRNA, and 12 PCGs), and D-loop, whereas the L-strand encoded the remaining 9 genes (8 tRNA and <i>ND6</i>). Its nucleotide composition, gene arrangement, codon usage patterns, and tRNA secondary structures are identical with other members of the Percoidei suborder. Furthermore, we reconstructed phylogenetic trees based on the 13 PCGs. The resulting phylogenetic trees showed <i>N. spinosus</i> placing as a separate lineage within the family Niphonidae, its close relationship to <i>Trachinus draco</i> (Trachinidae), and the clustering of major subfamilies like Luciopercinae and Percinae of the Percoidei suborder. These findings will contribute to future studies on the evolutionary history, population genetics, molecular taxonomy, and phylogeny of <i>N. spinosus</i> and related species.
format Article
id doaj-art-2518714cdfeb4a65b5ea79987b847734
institution Kabale University
issn 2218-273X
language English
publishDate 2025-01-01
publisher MDPI AG
record_format Article
series Biomolecules
spelling doaj-art-2518714cdfeb4a65b5ea79987b8477342025-01-24T13:25:00ZengMDPI AGBiomolecules2218-273X2025-01-011515210.3390/biom15010052Complete Mitochondrial Genome of <i>Niphon spinosus</i> (Perciformes: Niphonidae): Genome Characterization and Phylogenetic AnalysisMaheshkumar Prakash Patil0Jong-Oh Kim1Seung Hyun Yoo2Jiyoung Shin3Ji-Young Yang4Kyunghoi Kim5Gun-Do Kim6Industry-University Cooperation Foundation, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of KoreaDepartment of Microbiology, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of KoreaSchool of Marine and Fisheries Life Science, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of KoreaInstitute of Food Science, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of KoreaDepartment of Food Science and Technology, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of KoreaDepartment of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of KoreaDepartment of Microbiology, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of KoreaThe species <i>Niphon spinosus</i> (Cuvier, 1829) is the only representative of the family Niphonidae and the genus <i>Niphon</i>, and its taxonomic history is complicated; it is still unclear in a phylogenetic sense. In this study, we report the complete mitochondrial genome of <i>N. spinosus</i> (OP391482), which was determined to be 16,503 bp long with biased A + T contents (53.8%) using next-generation technology. The typical set of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and one control region (D-loop) are included in the mitochondrial genome. The H-strand encoded 28 genes (14 tRNA, 2 rRNA, and 12 PCGs), and D-loop, whereas the L-strand encoded the remaining 9 genes (8 tRNA and <i>ND6</i>). Its nucleotide composition, gene arrangement, codon usage patterns, and tRNA secondary structures are identical with other members of the Percoidei suborder. Furthermore, we reconstructed phylogenetic trees based on the 13 PCGs. The resulting phylogenetic trees showed <i>N. spinosus</i> placing as a separate lineage within the family Niphonidae, its close relationship to <i>Trachinus draco</i> (Trachinidae), and the clustering of major subfamilies like Luciopercinae and Percinae of the Percoidei suborder. These findings will contribute to future studies on the evolutionary history, population genetics, molecular taxonomy, and phylogeny of <i>N. spinosus</i> and related species.https://www.mdpi.com/2218-273X/15/1/52<i>Niphon spinosus</i>PercoideiPerciformesmitogenomephylogenetic analysissawedged perch
spellingShingle Maheshkumar Prakash Patil
Jong-Oh Kim
Seung Hyun Yoo
Jiyoung Shin
Ji-Young Yang
Kyunghoi Kim
Gun-Do Kim
Complete Mitochondrial Genome of <i>Niphon spinosus</i> (Perciformes: Niphonidae): Genome Characterization and Phylogenetic Analysis
Biomolecules
<i>Niphon spinosus</i>
Percoidei
Perciformes
mitogenome
phylogenetic analysis
sawedged perch
title Complete Mitochondrial Genome of <i>Niphon spinosus</i> (Perciformes: Niphonidae): Genome Characterization and Phylogenetic Analysis
title_full Complete Mitochondrial Genome of <i>Niphon spinosus</i> (Perciformes: Niphonidae): Genome Characterization and Phylogenetic Analysis
title_fullStr Complete Mitochondrial Genome of <i>Niphon spinosus</i> (Perciformes: Niphonidae): Genome Characterization and Phylogenetic Analysis
title_full_unstemmed Complete Mitochondrial Genome of <i>Niphon spinosus</i> (Perciformes: Niphonidae): Genome Characterization and Phylogenetic Analysis
title_short Complete Mitochondrial Genome of <i>Niphon spinosus</i> (Perciformes: Niphonidae): Genome Characterization and Phylogenetic Analysis
title_sort complete mitochondrial genome of i niphon spinosus i perciformes niphonidae genome characterization and phylogenetic analysis
topic <i>Niphon spinosus</i>
Percoidei
Perciformes
mitogenome
phylogenetic analysis
sawedged perch
url https://www.mdpi.com/2218-273X/15/1/52
work_keys_str_mv AT maheshkumarprakashpatil completemitochondrialgenomeofiniphonspinosusiperciformesniphonidaegenomecharacterizationandphylogeneticanalysis
AT jongohkim completemitochondrialgenomeofiniphonspinosusiperciformesniphonidaegenomecharacterizationandphylogeneticanalysis
AT seunghyunyoo completemitochondrialgenomeofiniphonspinosusiperciformesniphonidaegenomecharacterizationandphylogeneticanalysis
AT jiyoungshin completemitochondrialgenomeofiniphonspinosusiperciformesniphonidaegenomecharacterizationandphylogeneticanalysis
AT jiyoungyang completemitochondrialgenomeofiniphonspinosusiperciformesniphonidaegenomecharacterizationandphylogeneticanalysis
AT kyunghoikim completemitochondrialgenomeofiniphonspinosusiperciformesniphonidaegenomecharacterizationandphylogeneticanalysis
AT gundokim completemitochondrialgenomeofiniphonspinosusiperciformesniphonidaegenomecharacterizationandphylogeneticanalysis