1
|
Liao X, Shih Y, Jia C, Gao T. Complete Mitochondrial Genome of Four Peristediidae Fish Species: Genome Characterization and Phylogenetic Analysis. Genes (Basel) 2024; 15:557. [PMID: 38790187 PMCID: PMC11121196 DOI: 10.3390/genes15050557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
The systematic revision of the family Peristediidae remains an unresolved issue due to their diverse and unique morphology. Despite the popularity of using mitochondrial genome research to comprehensively understand phylogenetic relationships in fish, genetic data for peristediid fish need to be included. Therefore, this study aims to investigate the mitochondrial genomic characteristics and intra-family phylogenetic relationships of Peristediidae by utilizing mitochondrial genome analysis. Therefore, this study aims to investigate the phylogenetic relationship of Peristediidae by utilizing mitochondrial genome analysis. The mitochondrial genome of four species of Peristediidae (Peristedion liorhynchus, Satyrichthys welchi, Satyrichthys rieffeli, and Scalicus amiscus) collected in the East China Sea was studied. The mitochondrial gene sequence lengths of four fish species were 16,533 bp, 16,526 bp, 16,527 bp, and 16,526 bp, respectively. They had the same mitochondrial structure and were all composed of 37 genes and one control region. Most PCGs used ATG as the start codon, and a few used GTG as the start codon. An incomplete stop codon (TA/T) occurred. The AT-skew and GC-skew values of 13 PCGs from four species were negative, and the GC-skew amplitude was greater than that of AT-skew. All cases of D-arm were found in tRNA-Ser (GCT). The Ka/Ks ratio analysis indicated that 13 PCGs were suffering purifying selection. Based on 12 PCGs (excluding ND6) sequences, a phylogenetic tree was constructed using Bayesian inference (BI) and maximum likelihood (ML) methods, providing a further supplement to the scientific classification of Peristediidae fish. According to the results of divergence time, the four species of fish had apparent divergence in the Early Cenozoic, which indicates that the geological events at that time caused the climax of species divergence and evolution.
Collapse
Affiliation(s)
- Xianhui Liao
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Yijia Shih
- Fisheries College, Jimei University, Xiamen 361021, China;
| | - Chenghao Jia
- School of Ecology and Environment, Hainan University, Haikou 570228, China;
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China;
| |
Collapse
|
2
|
Glacier lanternfish (Benthosema glaciale) first found on the continental slope of the Pacific Arctic. Polar Biol 2022. [DOI: 10.1007/s00300-021-02988-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
3
|
Smith WL, Ghedotti MJ, Domínguez-Domínguez O, McMahan CD, Espinoza E, Martin RP, Girard MG, Davis MP. Investigations into the ancestry of the Grape-eye Seabass (Hemilutjanus macrophthalmos) reveal novel limits and relationships for the Acropomatiformes (Teleostei: Percomorpha). NEOTROPICAL ICHTHYOLOGY 2022. [DOI: 10.1590/1982-0224-2021-0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract For 175 years, an unremarkable bass, the Grape-eye Seabass (Hemilutjanus macrophthalmos), has been known from coastal waters in the Eastern Pacific. To date, its phylogenetic placement and classification have been ignored. A preliminary osteological examination of Hemilutjanus hinted that it may have affinities with the Acropomatiformes. To test this hypothesis, we conducted a phylogenetic analysis using UCE and Sanger sequence data to study the placement of Hemilutjanus and the limits and relationships of the Acropomatiformes. We show that Hemilutjanus is a malakichthyid, and our results corroborate earlier studies that have resolved a polyphyletic Polyprionidae; accordingly, we describe Stereolepididae, new family, for Stereolepis. With these revisions, the Acropomatiformes is now composed of the: Acropomatidae; Banjosidae; Bathyclupeidae; Champsodontidae; Creediidae; Dinolestidae; Epigonidae; Glaucosomatidae; Hemerocoetidae; Howellidae; Lateolabracidae; Malakichthyidae; Ostracoberycidae; Pempheridae; Pentacerotidae; Polyprionidae; Scombropidae; Stereolepididae, new family; Symphysanodontidae; Synagropidae; and Schuettea. Finally, using our new hypothesis, we demonstrate that acropomatiforms repeatedly evolved bioluminescence and transitioned between shallow waters and the deep sea.
Collapse
|
4
|
Li H, Yang F, Wang X, Li Y, Zhang N, Zhang R, Liu C, Zhang H, Lin L, Song P. Demersal fish diversity and molecular taxonomy in the Bering Sea and Chukchi Sea. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01241-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
5
|
Naeem Z, Masud S, Hassan S, Naeem M. Molecular approach for identification of Catla catla using mitochondrial CO1 from Pakistan. Mitochondrial DNA B Resour 2020; 5:3000-3003. [PMID: 33458033 PMCID: PMC7782247 DOI: 10.1080/23802359.2020.1768913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 05/09/2020] [Indexed: 11/01/2022] Open
Abstract
DNA barcoding is a rapid, precise, and effective way of species identification. A short and standard target gene marker is used to create sequence profile of identified species. Specific tag or marker is used, which is derived from mitochondrial COI for identification. Effectiveness of this method axes the degree of divergence among species. Identification is necessary for their representation. In the present work, Catla catla was used to study by using Cytochrome C Oxidase 1.The genetic distances were computed, and Neighbor Joining tree was constructed based on the Kimura 2 Parameter method. GenBank and BOLD revealed definitive identity matches. Conspecific and congeneric K2P nucleotide divergence was estimated. Evolutionary tree was analyzed clearly by relating their species to phylogenetic tree, as same as species were bunched under same tree node, while species were differently clustered under distinct nodes. These findings conclude that the gene sequence may serve as a milestone for identification and phylogenetic history of related species at molecular level.
Collapse
Affiliation(s)
- Zara Naeem
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Samrah Masud
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Shoaib Hassan
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Naeem
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| |
Collapse
|
6
|
Xing B, Chen X, Zhang Z, Sun R, Xiang P, Lin M, Wang C. Genetic identification of ophichthid fishes through DNA barcoding. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1756940] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Bingpeng Xing
- Third Institute of Oceanography Ministry of Natural Resources, Xiamen, Fujian, China
| | - Xiaoyin Chen
- Third Institute of Oceanography Ministry of Natural Resources, Xiamen, Fujian, China
| | - Zhilan Zhang
- Third Institute of Oceanography Ministry of Natural Resources, Xiamen, Fujian, China
| | - Rouxin Sun
- Third Institute of Oceanography Ministry of Natural Resources, Xiamen, Fujian, China
| | - Peng Xiang
- Third Institute of Oceanography Ministry of Natural Resources, Xiamen, Fujian, China
| | - Mao Lin
- Third Institute of Oceanography Ministry of Natural Resources, Xiamen, Fujian, China
| | - Chunguang Wang
- Third Institute of Oceanography Ministry of Natural Resources, Xiamen, Fujian, China
| |
Collapse
|
7
|
Bañón R, Barros‐García D, Arronte JC, Comesaña ÁS, Sánchez‐Ruiloba L, Carlos A. Deep‐sea anglerfishes (Lophiiformes: Ceratioidei) from the western North Atlantic: Testing the efficacy ofDNAbarcodes. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rafael Bañón
- Instituto de Investigaciones MarinasConsejo Superior de Investigaciones CientíficasIIM‐CSIC Vigo Spain
| | - David Barros‐García
- Programa de Doctorado en Metodología y Aplicaciones en Ciencias de la VidaFacultad de BioloxíaUniversidade de Vigo Vigo Spain
| | | | - Ángel Sebastián Comesaña
- Centro de Apoyo Científico y Tecnológico a la Investigación (CACTI)Universidade de Vigo – Campus Lagoas Marcosende Vigo Spain
| | - Lucía Sánchez‐Ruiloba
- Instituto de Investigaciones MarinasConsejo Superior de Investigaciones CientíficasIIM‐CSIC Vigo Spain
| | - Alejandro Carlos
- Departamento de Bioquímica, Xenética e InmunoloxíaFacultade de BioloxíaUniversidade de Vigo Vigo Spain
| |
Collapse
|
8
|
Ghedotti MJ, Gruber JN, Barton RW, Davis MP, Smith WL. Morphology and evolution of bioluminescent organs in the glowbellies (Percomorpha: Acropomatidae) with comments on the taxonomy and phylogeny of Acropomatiformes. J Morphol 2018; 279:1640-1653. [DOI: 10.1002/jmor.20894] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/09/2018] [Accepted: 08/22/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | | | - Ryan W. Barton
- Department of Biology; Regis University; Denver Colorado
| | - Matthew P. Davis
- Department of Biological Sciences; St. Cloud State University; St. Cloud Minnesota
| | - W. Leo Smith
- Department of Ecology and Evolutionary Biology and Biodiversity Institute; University of Kansas; Lawrence Kansas
| |
Collapse
|
9
|
Bingpeng X, Heshan L, Zhilan Z, Chunguang W, Yanguo W, Jianjun W. DNA barcoding for identification of fish species in the Taiwan Strait. PLoS One 2018; 13:e0198109. [PMID: 29856794 PMCID: PMC5983523 DOI: 10.1371/journal.pone.0198109] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/14/2018] [Indexed: 11/30/2022] Open
Abstract
DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species.
Collapse
Affiliation(s)
- Xing Bingpeng
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Lin Heshan
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Zhang Zhilan
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Wang Chunguang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Wang Yanguo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Wang Jianjun
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
- * E-mail:
| |
Collapse
|