Phylogenetic Analyses of <i>Pristipomoides</i> (Perciformes: Lutjanidae) Based on New Mitochondrial Genomes
The species in the genus <i>Pristipomoides</i> are commercial fishes with high economic value. There are few studies on the phylogenetic relationship within the genus <i>Pristipomoides</i> at present. mtDNA has the characteristics of maternal inheritance, close gene arrangeme...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-06-01
|
| Series: | Fishes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2410-3888/8/7/343 |
| _version_ | 1827733029487902720 |
|---|---|
| author | Chunhui Liu Dezhao Li Yue Zhang Maxime Péré Zhibo Zhuang Jingyu Liu Haolang Zhou Xiao Chen |
| author_facet | Chunhui Liu Dezhao Li Yue Zhang Maxime Péré Zhibo Zhuang Jingyu Liu Haolang Zhou Xiao Chen |
| author_sort | Chunhui Liu |
| collection | DOAJ |
| description | The species in the genus <i>Pristipomoides</i> are commercial fishes with high economic value. There are few studies on the phylogenetic relationship within the genus <i>Pristipomoides</i> at present. mtDNA has the characteristics of maternal inheritance, close gene arrangement, and a high evolutionary rate, which is an excellent tool to study the phylogeny of the species. In this study, the mitochondrial genomes of five species in the genus <i>Pristipomoides</i> were sequenced using the Sanger sequencing method and analyzed for their features. The mitochondrial genome length of the five species ranged from 16,499 to 16,530 bp. The start codon was ATG\GTG, and the stop codon was TAA\TAG\T--\AGG. The ratio of Ka and Ks for protein-coding genes ranged from 0 to 0.117, suggesting a strong purifying selection acting on the 13 protein-coding genes (PCGs). The gene with the highest diversity was <i>nd2</i> (NADH dehydrogenase subunit 2), suggesting the highest evolutionary rate. Phylogenetic analysis of five <i>Pristipomoides</i> species with other species of Lutjanidae was conducted using maximum likelihood (ML) and Bayesian Inference (BI). The results showed that <i>P. zonatus</i> and <i>P. auricilla</i> were closely related to <i>P. argyrogrammicus</i> and <i>P. sieboldii</i>, respectively, and <i>P. filamentosus</i> and <i>P. multidens</i> clustered together. Furthermore, <i>A. rutilans</i> is deeply nested within the <i>Pristipomoides</i> genus, indicating a close phylogenetic relationship with the species in the <i>Pristipomoides</i> genus. Based on this evidence, we suggest that <i>A. rutilans</i> should be classified under the <i>Pristipomoides</i> genus and recommend a revision in its taxonomy. The molecular data and phylogenetic analysis provided in this study would be helpful for the species identification and phylogenetic studies of the family Lutjanidae. |
| first_indexed | 2024-03-11T01:05:19Z |
| format | Article |
| id | doaj.art-05fb144535f94c8387cb8954dff6f0e0 |
| institution | Directory Open Access Journal |
| issn | 2410-3888 |
| language | English |
| last_indexed | 2024-03-11T01:05:19Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Fishes |
| spelling | doaj.art-05fb144535f94c8387cb8954dff6f0e02023-11-18T19:17:59ZengMDPI AGFishes2410-38882023-06-018734310.3390/fishes8070343Phylogenetic Analyses of <i>Pristipomoides</i> (Perciformes: Lutjanidae) Based on New Mitochondrial GenomesChunhui Liu0Dezhao Li1Yue Zhang2Maxime Péré3Zhibo Zhuang4Jingyu Liu5Haolang Zhou6Xiao Chen7College of Marine Sciences, South China Agricultural University, Guangzhou 510642, ChinaCollege of Marine Sciences, South China Agricultural University, Guangzhou 510642, ChinaCollege of Marine Sciences, South China Agricultural University, Guangzhou 510642, ChinaCollege of Marine Sciences, South China Agricultural University, Guangzhou 510642, ChinaCollege of Marine Sciences, South China Agricultural University, Guangzhou 510642, ChinaCollege of Marine Sciences, South China Agricultural University, Guangzhou 510642, ChinaGuangxi Mangrove Research Center, Beihai 536000, ChinaCollege of Marine Sciences, South China Agricultural University, Guangzhou 510642, ChinaThe species in the genus <i>Pristipomoides</i> are commercial fishes with high economic value. There are few studies on the phylogenetic relationship within the genus <i>Pristipomoides</i> at present. mtDNA has the characteristics of maternal inheritance, close gene arrangement, and a high evolutionary rate, which is an excellent tool to study the phylogeny of the species. In this study, the mitochondrial genomes of five species in the genus <i>Pristipomoides</i> were sequenced using the Sanger sequencing method and analyzed for their features. The mitochondrial genome length of the five species ranged from 16,499 to 16,530 bp. The start codon was ATG\GTG, and the stop codon was TAA\TAG\T--\AGG. The ratio of Ka and Ks for protein-coding genes ranged from 0 to 0.117, suggesting a strong purifying selection acting on the 13 protein-coding genes (PCGs). The gene with the highest diversity was <i>nd2</i> (NADH dehydrogenase subunit 2), suggesting the highest evolutionary rate. Phylogenetic analysis of five <i>Pristipomoides</i> species with other species of Lutjanidae was conducted using maximum likelihood (ML) and Bayesian Inference (BI). The results showed that <i>P. zonatus</i> and <i>P. auricilla</i> were closely related to <i>P. argyrogrammicus</i> and <i>P. sieboldii</i>, respectively, and <i>P. filamentosus</i> and <i>P. multidens</i> clustered together. Furthermore, <i>A. rutilans</i> is deeply nested within the <i>Pristipomoides</i> genus, indicating a close phylogenetic relationship with the species in the <i>Pristipomoides</i> genus. Based on this evidence, we suggest that <i>A. rutilans</i> should be classified under the <i>Pristipomoides</i> genus and recommend a revision in its taxonomy. The molecular data and phylogenetic analysis provided in this study would be helpful for the species identification and phylogenetic studies of the family Lutjanidae.https://www.mdpi.com/2410-3888/8/7/343phylogeny<i>Pristipomoides</i>mtDNAclassificationmitochondrial structures<i>Aphareus</i> |
| spellingShingle | Chunhui Liu Dezhao Li Yue Zhang Maxime Péré Zhibo Zhuang Jingyu Liu Haolang Zhou Xiao Chen Phylogenetic Analyses of <i>Pristipomoides</i> (Perciformes: Lutjanidae) Based on New Mitochondrial Genomes Fishes phylogeny <i>Pristipomoides</i> mtDNA classification mitochondrial structures <i>Aphareus</i> |
| title | Phylogenetic Analyses of <i>Pristipomoides</i> (Perciformes: Lutjanidae) Based on New Mitochondrial Genomes |
| title_full | Phylogenetic Analyses of <i>Pristipomoides</i> (Perciformes: Lutjanidae) Based on New Mitochondrial Genomes |
| title_fullStr | Phylogenetic Analyses of <i>Pristipomoides</i> (Perciformes: Lutjanidae) Based on New Mitochondrial Genomes |
| title_full_unstemmed | Phylogenetic Analyses of <i>Pristipomoides</i> (Perciformes: Lutjanidae) Based on New Mitochondrial Genomes |
| title_short | Phylogenetic Analyses of <i>Pristipomoides</i> (Perciformes: Lutjanidae) Based on New Mitochondrial Genomes |
| title_sort | phylogenetic analyses of i pristipomoides i perciformes lutjanidae based on new mitochondrial genomes |
| topic | phylogeny <i>Pristipomoides</i> mtDNA classification mitochondrial structures <i>Aphareus</i> |
| url | https://www.mdpi.com/2410-3888/8/7/343 |
| work_keys_str_mv | AT chunhuiliu phylogeneticanalysesofipristipomoidesiperciformeslutjanidaebasedonnewmitochondrialgenomes AT dezhaoli phylogeneticanalysesofipristipomoidesiperciformeslutjanidaebasedonnewmitochondrialgenomes AT yuezhang phylogeneticanalysesofipristipomoidesiperciformeslutjanidaebasedonnewmitochondrialgenomes AT maximepere phylogeneticanalysesofipristipomoidesiperciformeslutjanidaebasedonnewmitochondrialgenomes AT zhibozhuang phylogeneticanalysesofipristipomoidesiperciformeslutjanidaebasedonnewmitochondrialgenomes AT jingyuliu phylogeneticanalysesofipristipomoidesiperciformeslutjanidaebasedonnewmitochondrialgenomes AT haolangzhou phylogeneticanalysesofipristipomoidesiperciformeslutjanidaebasedonnewmitochondrialgenomes AT xiaochen phylogeneticanalysesofipristipomoidesiperciformeslutjanidaebasedonnewmitochondrialgenomes |