Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Reef Fish Family Holocentridae (Holocentriformes)
To understand the molecular mechanisms and adaptive strategies of holocentrid fish, we sequenced the mitogenome of eight species within the family Holocentridae and compared them with six other holocentrid species. The mitogenomes were found to be 16,507–16,639 bp in length and to encode 37 typical...
| المؤلفون الرئيسيون: | , , , , |
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| التنسيق: | مقال |
| اللغة: | English |
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MDPI AG
2023-09-01
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| سلاسل: | Biology |
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| الوصول للمادة أونلاين: | https://www.mdpi.com/2079-7737/12/10/1273 |
| _version_ | 1827721658928988160 |
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| author | Qin Tang Yong Liu Chun-Hou Li Jin-Fa Zhao Teng Wang |
| author_facet | Qin Tang Yong Liu Chun-Hou Li Jin-Fa Zhao Teng Wang |
| author_sort | Qin Tang |
| collection | DOAJ |
| description | To understand the molecular mechanisms and adaptive strategies of holocentrid fish, we sequenced the mitogenome of eight species within the family Holocentridae and compared them with six other holocentrid species. The mitogenomes were found to be 16,507–16,639 bp in length and to encode 37 typical mitochondrial genes, including 13 PCGs, two ribosomal RNAs, and 22 transfer RNA genes. Structurally, the gene arrangement, base composition, codon usage, tRNA size, and putative secondary structures were comparable between species. Of the 13 PCGs, <i>nad6</i> was the most specific gene that exhibited negative AT-skews and positive GC-skews. Most of the genes begin with the standard codon ATG, except <i>cox1</i>, which begins with the codon GTG. By examining their phylogeny, <i>Sargocentron</i> and <i>Neoniphon</i> were verified to be closely related and to belong to the same subfamily Holocentrinae, while <i>Myripristis</i> and <i>Ostichthys</i> belong to the other subfamily Myripristinae. The subfamilies were clearly distinguished by high-confidence-supported clades, which provide evidence to explain the differences in morphology and feeding habits between the two subfamilies. Selection pressure analysis indicated that all PCGs were subject to purifying selection. Overall, our study provides valuable insight into the habiting behavior, evolution, and ecological roles of these important marine fish. |
| first_indexed | 2024-03-10T21:25:09Z |
| format | Article |
| id | doaj.art-15119853a4f24293a7d55331baebaa42 |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-10T21:25:09Z |
| publishDate | 2023-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-15119853a4f24293a7d55331baebaa422023-11-19T15:42:57ZengMDPI AGBiology2079-77372023-09-011210127310.3390/biology12101273Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Reef Fish Family Holocentridae (Holocentriformes)Qin Tang0Yong Liu1Chun-Hou Li2Jin-Fa Zhao3Teng Wang4College of Fisheries, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, ChinaKey Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, ChinaKey Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, ChinaKey Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, ChinaTo understand the molecular mechanisms and adaptive strategies of holocentrid fish, we sequenced the mitogenome of eight species within the family Holocentridae and compared them with six other holocentrid species. The mitogenomes were found to be 16,507–16,639 bp in length and to encode 37 typical mitochondrial genes, including 13 PCGs, two ribosomal RNAs, and 22 transfer RNA genes. Structurally, the gene arrangement, base composition, codon usage, tRNA size, and putative secondary structures were comparable between species. Of the 13 PCGs, <i>nad6</i> was the most specific gene that exhibited negative AT-skews and positive GC-skews. Most of the genes begin with the standard codon ATG, except <i>cox1</i>, which begins with the codon GTG. By examining their phylogeny, <i>Sargocentron</i> and <i>Neoniphon</i> were verified to be closely related and to belong to the same subfamily Holocentrinae, while <i>Myripristis</i> and <i>Ostichthys</i> belong to the other subfamily Myripristinae. The subfamilies were clearly distinguished by high-confidence-supported clades, which provide evidence to explain the differences in morphology and feeding habits between the two subfamilies. Selection pressure analysis indicated that all PCGs were subject to purifying selection. Overall, our study provides valuable insight into the habiting behavior, evolution, and ecological roles of these important marine fish.https://www.mdpi.com/2079-7737/12/10/1273Holocentridaemitogenomecodon usagegene rearrangementphylogenyselection pressure |
| spellingShingle | Qin Tang Yong Liu Chun-Hou Li Jin-Fa Zhao Teng Wang Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Reef Fish Family Holocentridae (Holocentriformes) Biology Holocentridae mitogenome codon usage gene rearrangement phylogeny selection pressure |
| title | Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Reef Fish Family Holocentridae (Holocentriformes) |
| title_full | Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Reef Fish Family Holocentridae (Holocentriformes) |
| title_fullStr | Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Reef Fish Family Holocentridae (Holocentriformes) |
| title_full_unstemmed | Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Reef Fish Family Holocentridae (Holocentriformes) |
| title_short | Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Reef Fish Family Holocentridae (Holocentriformes) |
| title_sort | comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the reef fish family holocentridae holocentriformes |
| topic | Holocentridae mitogenome codon usage gene rearrangement phylogeny selection pressure |
| url | https://www.mdpi.com/2079-7737/12/10/1273 |
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