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Akhter G, Ahmed I, Ahmad SM. Genomic analysis and phylogenetic characterization of Himalayan snow trout, Schizothorax esocinus based on mitochondrial protein-coding genes. Mol Biol Rep 2024; 51:659. [PMID: 38748061 DOI: 10.1007/s11033-024-09622-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 05/07/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) has become a significant tool for exploring genetic diversity and delineating evolutionary links across diverse taxa. Within the group of cold-water fish species that are native to the Indian Himalayan region, Schizothorax esocinus holds particular importance due to its ecological significance and is potentially vulnerable to environmental changes. This research aims to clarify the phylogenetic relationships within the Schizothorax genus by utilizing mitochondrial protein-coding genes. METHODS Standard protocols were followed for the isolation of DNA from S. esocinus. For the amplification of mtDNA, overlapping primers were used, and then subsequent sequencing was performed. The genetic features were investigated by the application of bioinformatic approaches. These approaches covered the evaluation of nucleotide composition, codon usage, selective pressure using nonsynonymous substitution /synonymous substitution (Ka/Ks) ratios, and phylogenetic analysis. RESULTS The study specifically examined the 13 protein-coding genes of Schizothorax species which belongs to the Schizothoracinae subfamily. Nucleotide composition analysis showed a bias towards A + T content, consistent with other cyprinid fish species, suggesting evolutionary conservation. Relative Synonymous Codon Usage highlighted leucine as the most frequent (5.18%) and cysteine as the least frequent (0.78%) codon. The positive AT-skew and the predominantly negative GC-skew indicated the abundance of A and C. Comparative analysis revealed significant conservation of amino acids in multiple genes. The majority of amino acids were hydrophobic rather than polar. The purifying selection was revealed by the genetic distance and Ka/Ks ratios. Phylogenetic study revealed a significant genetic divergence between S. esocinus and other Schizothorax species with interspecific K2P distances ranging from 0.00 to 8.87%, with an average of 5.76%. CONCLUSION The present study provides significant contributions to the understanding of mitochondrial genome diversity and genetic evolution mechanisms in Schizothoracinae, hence offering vital insights for the development of conservation initiatives aimed at protecting freshwater fish species.
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Affiliation(s)
- G Akhter
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190 006, India
| | - I Ahmed
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190 006, India.
| | - S M Ahmad
- Division of Biotechnology, Faculty of Veterinary Sciences & Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology, Srinagar, India.
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Marques-Neto JC, de Lima GM, Maciel CMT, Maciel BR, Abrunhosa FA, Sampaio I, Maciel CR. In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data. BMC Genomics 2023; 24:677. [PMID: 37950193 PMCID: PMC10637016 DOI: 10.1186/s12864-023-09770-y] [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: 07/18/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Macrobrachium amazonicum is a freshwater prawn widely distributed in South America that is undergoing speciation, so the denomination "M. amazonicum complex" is used for it. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used to elucidate this speciation, but heteroplasmies and pseudogenes have been recorded, making separation difficult. Obtaining genes from cDNA (RNA) rather than genomic DNA is an effective tool to mitigate those two types of occurrences. The aim of this study was to assemble in silico the mitochondrial DNA (mtDNA) of the Amazonian coastal population of M. amazonicum inhabiting the state of Pará. RESULTS Sequences were obtained from the prawn's transcriptome using the de novo approach. Six libraries of cDNA from the androgen gland, hepatopancreas, and muscle tissue were used. The mtDNA of M. amazonicum was 14,960 bp in length. It contained 13 protein-coding genes, 21 complete transfer RNAs, and the 12S and 16S subunits of ribosomal RNA. All regions were found on the light strand except tRNAGln, which was on the heavy strand. The control region (D-loop) was not recovered, making for a gap of 793 bp. The cladogram showed the formation of the well-defined Macrobrachium clade, with high support value in the established branches (91-100). The three-dimensional spatial conformation of the mtDNA-encoded proteins showed that most of them were mainly composed of major α-helices that typically shows in those proteins inserted in the membrane (mitochondrial). CONCLUSIONS It was possible to assemble a large part of the mitochondrial genome of M. amazonicum in silico using data from other genomes deposited in GenBank and to validate it through the similarities between its COI and 16S genes and those from animals of the same region deposited in GenBank. Depositing the M. amazonicum mtDNA sequences in GenBank may help solve the taxonomic problems recorded for the species, in addition to providing complete sequences of candidate coding genes for use as biomarkers in ecological studies.
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Affiliation(s)
- Jerônimo Costa Marques-Neto
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Gabriel Monteiro de Lima
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Carlos Murilo Tenório Maciel
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Bruna Ramalho Maciel
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Fernando Araujo Abrunhosa
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Carcinology, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Iracilda Sampaio
- Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Cristiana Ramalho Maciel
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
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Parker SD, Perkin JS, Bean MG, Lutz‐Carrillo D, Acre MR. Temporal distribution modelling reveals upstream habitat drying and downstream non‐native introgression are squeezing out an imperiled headwater fish. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Stephanie D. Parker
- Department of Ecology and Conservation Biology Texas A&M University College Station TX USA
| | - Joshuah S. Perkin
- Department of Ecology and Conservation Biology Texas A&M University College Station TX USA
| | - Megan G. Bean
- Inland Fisheries Texas Parks and Wildlife Department Mountain Home TX USA
| | - Dijar Lutz‐Carrillo
- Analytical Services Laboratory Inland Fisheries Texas Parks and Wildlife Department San Marcos TX USA
| | - Matthew R. Acre
- Department of Ecology and Conservation Biology Texas A&M University College Station TX USA
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Akhtar T, Ali G, Shafi N, Akhtar W, Khan AH, Latif Z, Wali A, Ain-ul-Batool S, Khan AR, Mumtaz S, Altaf SI, Khawaja S, Sadia, Khalid M, Rehman FU, Javid Q. Sequencing and Characterization of Mitochondrial Protein-Coding Genes for Schizothorax niger (Cypriniformes: Cyprinidae) with Phylogenetic Consideration. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5980135. [PMID: 33490246 PMCID: PMC7787735 DOI: 10.1155/2020/5980135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/29/2020] [Accepted: 11/18/2020] [Indexed: 01/05/2023]
Abstract
The present study was conducted to get more information about the genome and locate the taxonomic position of Schizothorax niger in Schizothoracinae through mitochondrial 13 protein-coding genes (PCGs). These PCGs for S. niger were found to be 11409 bps in length ranging from 165 (ATPase 8) to 1824 bps (NADH dehydrogenase subunit 5) and encode 3801 amino acids. In these PCGs, 4 genes overlap on the similar strands, while one shown on the opposite one: ATPase 6+8 and NADH dehydrogenase subunit 4+4L overlap by 7 nucleotides. Similarly, ND5-ND6 overlap by 4 nucleotides, while ATP6 and COIII overlap by 1 nucleotide. Similarly, four commonly used amino acids in S. niger were Leu (15.6 %), Ile (10.12 %), Thr (8.12 %), and Ala (8.7 %). The results presented that COII, COIII, NDI, ND4L, and Cytb had substantial amino acid conservation as compared to the COI gene. Through phylogenetic analysis, it was observed that S. niger is closely linked with S. progastus, S. labiatus, S. plagiostomus, and S. nepalensis with high bootstrap values. The present study provided more genomic data to know the diversity of the mitochondrial genome and its molecular evolution in Schizothoracinae.
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Affiliation(s)
- Tasleem Akhtar
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Ghazanfar Ali
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Nuzhat Shafi
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Wasim Akhtar
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Abdul Hameed Khan
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Zahid Latif
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Abdul Wali
- Faculty of Life Sciences & Informatics, BUITEMS, 87100 Quetta, Pakistan
| | - Syeda Ain-ul-Batool
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Abdul Rehman Khan
- Department of Chemistry, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sadia Mumtaz
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Syed Iftikhar Altaf
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sundus Khawaja
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sadia
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Madiha Khalid
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
- Department of Biotechnology, Women University Bagh, Pakistan
| | - Fazal Ur Rehman
- Department of Microbiology, University of Balochistan, Quetta 87300, Pakistan
| | - Qudir Javid
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
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The complete mitochondrial genome of the surubim Pseudoplatystoma corruscans (Siluriformes: Pimelodidae) and mitochondrial phylogenomics of catfishes confirm monophyly of Siluriformes families. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0717-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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6
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Kappas I, Vittas S, Pantzartzi CN, Drosopoulou E, Scouras ZG. A Time-Calibrated Mitogenome Phylogeny of Catfish (Teleostei: Siluriformes). PLoS One 2016; 11:e0166988. [PMID: 27907107 PMCID: PMC5132296 DOI: 10.1371/journal.pone.0166988] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data. We constructed an ingroup matrix of 62 full-length mitogenome sequences from 20 catfish families together with four cypriniform outgroups, spanning 15,557 positions in total. Partitioned maximum likelihood analyses and Bayesian relaxed clock dating using fossil age constraints provide some useful and novel insights into the evolutionary history of this group. Loricarioidei are recovered as the first siluriform group to diversify, rendering Neotropics the cradle of the order. The next deepest clade is the South American Diplomystoidei placed as a sister group to all the remaining Siluroidei. The two multifamilial clades of "Big Asia" and "Big Africa" are also recovered, albeit nodal support for the latter is poor. Within "Big Asia", Bagridae are clearly polyphyletic. Other interfamilial relationships, including Clariidae + Heteropneustidae, Doradidae + Auchenipteridae and Ictaluridae + Cranoglanididae are robustly resolved. Our chronogram shows that siluriforms have a Pangaean origin, at least as far back as the Early Cretaceous. The inferred timeline of the basal splits corroborates the "Out-of-South America" hypothesis and accords well with the fossil record. The divergence of Siluroidei most likely postdated the final separation of Africa and South America. An appealing case of phylogenetic affinity elaborated by biogeographic dispersal is exemplified by the Early Paleogene split between the Southeast Asian Cranoglanididae and Ictaluridae, with the latter radiating into North America's freshwater realm by Eocene. The end of Cretaceous probably concludes the major bout of diversification at the family level while with the dawn of the Cenozoic a prolific radiation is evident at the generic level.
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Affiliation(s)
- Ilias Kappas
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Spiros Vittas
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Chrysoula N. Pantzartzi
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Elena Drosopoulou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Zacharias G. Scouras
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail:
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Sequencing and characterization of mitochondrial DNA genome for Brama japonica (Perciformes: Bramidae) with phylogenetic consideration. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Diversification of Sisorid catfishes (Teleostei: Siluriformes) in relation to the orogeny of the Himalayan Plateau. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-016-1104-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Ballesteros-Córdova CA, Castañeda-Rivera M, Grijalva-Chon JM, Castillo-Gámez RA, Gutiérrez-Millán LE, Camarena-Rosales F, Ruíz-Campos G, Varela-Romero A. Complete mitochondrial genome of Ictalurus pricei (Teleostei: Ictaluridae) and evidence of a cryptic Ictalurus species in Northwest Mexico. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4439-4441. [PMID: 26405008 DOI: 10.3109/19401736.2015.1089561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The nominal Yaqui catfish, Ictalurus pricei, is a species of Ictaluridae (Siluriformes) often recorded from Northwest Mexico. Southern distribution members of the I. pricei complex in Northwest Mexico include at least one undescribed species that differs from Yaqui catfish in morphological features, herein called "Sinaloa Catfish". Sequencing of four geographical mitogenome haplotypes of Yaqui catfish and Sinaloa catfish showed geographical haplotypes of I. pricei within a clade of specific identity, close to Sinaloa catfish haplotypes. Our molecular phylogeny represents a working hypothesis supporting information on the evolutionary relationships of the Ictalurus species from Western Mexico and Western USA.
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Affiliation(s)
- Carlos A Ballesteros-Córdova
- a Departamento de Investigaciones Científicas y Tecnológicas , Universidad de Sonora , Hermosillo , Sonora , México and
| | - Melissa Castañeda-Rivera
- a Departamento de Investigaciones Científicas y Tecnológicas , Universidad de Sonora , Hermosillo , Sonora , México and
| | - José M Grijalva-Chon
- a Departamento de Investigaciones Científicas y Tecnológicas , Universidad de Sonora , Hermosillo , Sonora , México and
| | - Reyna A Castillo-Gámez
- a Departamento de Investigaciones Científicas y Tecnológicas , Universidad de Sonora , Hermosillo , Sonora , México and
| | - Luis E Gutiérrez-Millán
- a Departamento de Investigaciones Científicas y Tecnológicas , Universidad de Sonora , Hermosillo , Sonora , México and
| | - Faustino Camarena-Rosales
- b Facultad de Ciencias , Universidad Autónoma de Baja California , Ensenada , Baja California , México
| | - Gorgonio Ruíz-Campos
- b Facultad de Ciencias , Universidad Autónoma de Baja California , Ensenada , Baja California , México
| | - Alejandro Varela-Romero
- a Departamento de Investigaciones Científicas y Tecnológicas , Universidad de Sonora , Hermosillo , Sonora , México and
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Zhou C, Li B, Ma L, Zhao Y, Kong X. The complete mitogenome of natural triploidCarassius auratusin Qihe River. ACTA ACUST UNITED AC 2015; 27:605-6. [DOI: 10.3109/19401736.2014.908367] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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11
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Sahoo L, Kumar S, Das SP, Patnaik S, Bit A, Sundaray JK, Jayasankar P, Das P. Complete mitochondrial genome sequence of Heteropneustes fossilis obtained by paired end next generation sequencing. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2485-6. [PMID: 26016883 DOI: 10.3109/19401736.2015.1033710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the present study, the complete mitochondrial genome sequence of Heteropneustes fossilis is reported using massive parallel sequence technology. The complete mitogenome of H. fossilis is obtained by de novo assembly of paired end Illumina sequences using CLC Genomics Workbench version 7.0.4, which is 16,489 bp in length. It comprised of 13 protein- coding genes, 22 tRNAs, 2 rRNA genes and a putative control region along with the gene order and organization, being similar to most of vertebrates. The mitogenome in the present study has 99% similarity to the complete mitogneome sequence of H. Fossilis, as reported earlier. Phylogenetic analysis of Siluriformes depicted that Heteropneustids were closer to Clariids. The mitogenome sequence of H. fossilis contributes better understanding of population genetics, phylogenetics and evolution of Indian catfish species.
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Affiliation(s)
- Lakshman Sahoo
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
| | - Santosh Kumar
- b Fish Conservation Division, ICAR-National Bureau of Fish Genetics Resources , Lucknow , Uttar Pradesh , India
| | - Sofia P Das
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
| | - Siddhi Patnaik
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
| | - Amrita Bit
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
| | - Jitendra Kumar Sundaray
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
| | - P Jayasankar
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
| | - Paramananda Das
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
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Castañeda-Rivera M, Grijalva-Chon JM, Gutiérrez-Millán LE, Ruiz-Campos G, Varela-Romero A. Analysis of theIctalurus priceicomplex (Teleostei: Ictaluridae) in northwest Mexico based on mitochondrial DNA. SOUTHWEST NAT 2015. [DOI: 10.1894/rje-44.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Li Q, Liu Y, Zhou J, Gong Q, Li H, Lai J, Li L. The complete mitochondrial genome of Gobiobotia filifer (Teleostei, Cypriniformes: Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3325-6. [PMID: 25806579 DOI: 10.3109/19401736.2015.1018205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Gobiobotia filifer is a small economic fish which distributes in the upstream of Yangtze River and its distributaries. For the environmental pollution and overfishing, its population declined drastically in recent decades, so it is essential to protect its resource. In this study, the complete mitochondrial genome sequence of G. filifer was determined with PCR technology, which contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a non-coding control region with the total length of 16,613 bp. The order and composition of genes were similar to most of the other teleost fish. Most of the genes were encoded on heavy strand, except for ND6 genes and eight tRNAs. Just like most other vertebrates, the bias of G and C has been found in different genes/regions. The complete mitochondrial genome sequence of G. filifer would contribute to better understand evolution of this lineage, population genetics, and will help administrative department to make rules and laws to protect this lineage.
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Affiliation(s)
- Qiang Li
- a The Fishery Institute of The Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , People's Republic of China
| | - Ya Liu
- a The Fishery Institute of The Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , People's Republic of China
| | - Jian Zhou
- a The Fishery Institute of The Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , People's Republic of China
| | - Quan Gong
- a The Fishery Institute of The Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , People's Republic of China
| | - Hua Li
- a The Fishery Institute of The Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , People's Republic of China
| | - Jiansheng Lai
- a The Fishery Institute of The Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , People's Republic of China
| | - Lianman Li
- a The Fishery Institute of The Sichuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , People's Republic of China
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14
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Zhou C, Zhao H, Li H. The complete mitogenome of Acrossocheilus kreyenbergii (Cypriniformes; Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1068-9. [PMID: 24963772 DOI: 10.3109/19401736.2014.928871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Acrossocheilus kreyenbergii is a small fish and widely distributed in China, for example, Guangxi, Jiangxi, Zhejiang, Anhui, and also found in Henan province. The complete mitochondrial genome sequence of Acrossocheilus kreyenbergii has been obtained with PCR by using the conservative fragment primers of its closely relative species. Just like most of fishes, the gene composition and arrangement of mitochondrial genome sequence of this species are similar to most of other vertebrates', which including 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and a non-coding control region with total length of 16,849 bp. There is a 270 bp non-coding fragment (from 15,768 to 16,037) in its control region compared with other fish of genus Acrossocheilus. Most of genes are encoded on Heavy-Strand (H-strand), exclude eight tRNA and ND6 genes, which are encoded on Light-Strand (L-strand). The complete mitochondrial genome sequence of Acrossocheilus kreyenbergii would contribute to better understand population genetics, conservation, and diversity of genus Acrossocheilus.
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Affiliation(s)
- Chuanjiang Zhou
- a College of Fisheries, Henan Normal University , Xinxiang , China
| | - Haipeng Zhao
- b School of Life Science, Henan University , Kaifeng , China , and
| | - Haitao Li
- c Pingdingshan Aquatic Product Technique Promoting Station , Pingdingshan , China
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15
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Zhou C, Wang X, Wang D, He S. The complete mitochondrial genome ofLeiocassis crassilabris(Teleostei, Siluriformes: Bagridae). ACTA ACUST UNITED AC 2014; 25:183-4. [DOI: 10.3109/19401736.2013.792067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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16
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Zhou C, Wang X, Guan L, He S. The complete mitochondrial genome of Clarias fuscus (Teleostei, Siluriformes: Clariidae). MITOCHONDRIAL DNA 2014; 26:270-1. [PMID: 24460162 DOI: 10.3109/19401736.2013.823177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Clarias fuscus is an important economic fish in China and distributed widely in south China, e.g. Yangtze river, Pearl River, and Min River, even Hainan island. It is also distributed in Southeast Asia and Africa, so it is a good model for study population genetics and geological changes of these region. In this study, the complete mitochondrial genome sequence of C. fuscus has been obtained with PCR. The gene composition and arrangement of mitochondrial genome sequence of C. fuscus are similar to most of other vertebrates, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region with total length of 16,518 bp. Most of genes are encoded on Heavy-Strand (H-strand), except for eight tRNA and ND6 genes. Like most vertebrates, the bias of G and C has universality in different region (genes). The complete mitochondrial genome sequence of C. fuscus would contribute for better understanding of population genetics, conservation, biogeography, evolution of this species.
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Affiliation(s)
- Chuanjiang Zhou
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , People's Republic of China
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Padhi A. Genetic evidence of multiple matrilineal lineages of the channel catfish, Ictalurus punctatus in North America. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0479-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zhao H, Kong X, Zhou C. The mitogenome of Pangasius sutchi (Teleostei, Siluriformes: Pangasiidae). ACTA ACUST UNITED AC 2013; 25:342-4. [PMID: 23795847 DOI: 10.3109/19401736.2013.800492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Pangasius sutchi is an important ornamental and economic fish in Southeast Asia e.g. Thailand, Malaysia and China. The complete mitochondrial genome sequence of P. sutchi has been sequenced, which contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and a non-coding control region with the total length of 16,522 bp. The gene order and composition are similar to most of other vertebrates. Just like most other vertebrates, the bias of G and C was found in different region/genes statistics results. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The mitogenome sequence of P. sutchi would contribute to better understand population genetics, evolution of this lineage.
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Affiliation(s)
- Haipeng Zhao
- School of Life Science, Henan University , Kaifeng , People's Republic of China
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Li Q, Du J, Liu Y, Zhou J, Ke H, Liu C, Liu G. The complete mitochondrial genome of Liobagrus marginatus (Teleostei, Siluriformes: Amblycipitidae). ACTA ACUST UNITED AC 2013; 25:120-1. [PMID: 23795826 DOI: 10.3109/19401736.2013.792057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Liobagrus marginatus is an economic fish which distribute in the upstream of Yangtze river and its distributary. For its taste fresh, environmental pollution and overfishing, its population declined drastically and body miniaturization in recent decades, so it is essential to protect its resource. In this study, the complete mitochondrial genome sequence of Liobagrus marginatus was sequenced, which contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes, and a non-coding control region with the total length of 16,497 bp. The gene arrangement and composition are similar to most of other fish. Most of the genes are encoded on heavy-strand, except for eight tRNA and ND6 genes. Just like most other vertebrates, the bias of G and C has been found in statistics results of different genes/regions. The complete mitochondrial genome sequence of Liobagrus marginatus would contribute to better understand population genetics, evolution of this lineage, and will help administrative departments to make rules and laws to protect it.
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Affiliation(s)
- Qiang Li
- The Fishery Institute of the SiChuan Academy of Agricultural Sciences, Sichuan Provincial Laboratory for Natural Resources Protection and Sustainable Utilization , Chengdu , People's Republic of China
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Zhou C, Wang D, Yu M, He S. The complete mitochondrial genome of Glyptothorax fukiensis fukiensis (Teleostei, Siluriformes: Sisoridae). ACTA ACUST UNITED AC 2012; 23:414-6. [PMID: 22943285 DOI: 10.3109/19401736.2012.710211] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Glyptothorax fukiensis fukiensis is distributed widely in South China, e.g., Yangtze River, Pearl River, even Hainan Province, so it is a good model to study population genetics and historical biogeography. In this study, the complete mitochondrial genome sequence of G. fukiensis fukiensis has been obtained with PCR, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region with the total length of 16,530 bp. The gene arrangement and composition are similar to most of other vertebrates. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. Just like most other vertebrates, the bias of G and C has a universality in different statistics results. The complete mitochondrial genome sequence of G. fukiensis fukiensis is the first report for Sisoridae, it would contribute to better understand population genetics, biogeography, and evolution of this lineage.
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Affiliation(s)
- Chuanjiang Zhou
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
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Karinthanyakit W, Jondeung A. Molecular phylogenetic relationships of pangasiid and schilbid catfishes in Thailand. JOURNAL OF FISH BIOLOGY 2012; 80:2549-2570. [PMID: 22650433 DOI: 10.1111/j.1095-8649.2012.03303.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this study, the phylogenetic relationships among 13 pangasiids and six schilbids of Thailand were reconstructed based on the almost complete mitochondrial cytochrome b (cyt b), 12S rRNA, tRNA-Val and 16S rRNA, as well as the partial nuclear recombination-activating gene 1 (rag1) sequences by using the maximum likelihood and the Bayesian inference methods of phylogenetic reconstruction. The reconstructed phylogeny based on the concatenated sequence data set recovered Pangasiidae and Schilbidae as reciprocally monophyletic groups. Within Pangasiidae, four major clades were recovered, which according to the cyt b genetic distances can be categorized into four genera: Pangasius, Pseudolais, Helicophagus and Pangasianodon. The genus Pangasianodon was strongly supported as the most basal taxon within pangasiids, whereas Pseudolais + Helicophagus were recovered as a sister group of Pangasius. Within the latter, the giant pangasius Pangasius sanitwongsei was recovered as a sister group of the spot pangasius Pangasius larnaudii, Pangasius krempfi as a sister group of Pangasius nasutus + Pangasius conchophilus and Pangasius polyuranodon as a sister species of Pangasius macronema. Other internal phylogenetic relationships, however, were unresolved. Within Schilbidae, Pseudeutropius was supported as the most basal lineage. Eutropiichthys was recovered as a sister group of Clupisoma. The enigmatic Clupisoma sinense was recognized as more closely related to Laides longibarbis than to Clupisoma prateri. Thus, based on the cyt b genetic distances, a recategorization of C. sinense to the genus Laides is suggested. On the basis of a relaxed clock fossil calibration, the divergence of pangasiids and schilbids was estimated to have occurred 14·93 million years before present (b.p.) during the Miocene epoch. The separation between Pangasiidae and Schilbidae took place c. 13·12 Mb.p. during the early middle Miocene. The estimated divergence time of pangasiids is similar to the age of the calibrated fossil, Cetopangasius chaetobranchus, which was discovered in north-central Thailand. This suggests that the oldest pangasiid ancestor diverged into diverse genera in the area.
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Affiliation(s)
- W Karinthanyakit
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Paholyothin Road, Bangkok 10900, Thailand
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Cheng Y, Xu T, Jin X, Shi G, Wang R. The complete mitochondrial genome of silver croaker Argyrosomus argentatus (Perciforems; Sciaenidae): Genome characterization and phylogenetic consideration. Mol Biol 2012. [DOI: 10.1134/s0026893312020215] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Salcedo NJ, Rodriguez D, Strauss RE, Baker RJ. The Fitzcarrald Arch: A Vicariant Event for Chaetostoma (Siluriformes: Loricariidae) Speciation? COPEIA 2011. [DOI: 10.1643/ci-10-062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Liu Z. A review of catfish genomics: progress and perspectives. Comp Funct Genomics 2011; 4:259-65. [PMID: 18629126 PMCID: PMC2447413 DOI: 10.1002/cfg.265] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2003] [Revised: 01/31/2003] [Accepted: 01/31/2003] [Indexed: 01/18/2023] Open
Abstract
Catfish is one of the lower teleosts whose genome research is important for
evolutionary genomics. As the major aquaculture species in the USA, its genome
research also has practical and economical implications. Much progress has been
made in recent years, including the development of large numbers of molecular
markers, the construction of framework genetic linkage maps, the identification of
putative markers involved in performance traits, and the development of genomic
resources. Repetitive elements have been identified and characterized in the catfish
genome that should facilitate physical analysis of the catfish genome. A large
number of genes or full-length cDNAs have been analysed using genomic approaches,
providing information on gene structure, gene evolution and gene expression in
relation to functions. Catfish genome research has come to a stage when physical
mapping through BAC contig construction is greatly demanded, in order to develop
regional markers for QTL analysis and for large-scale comparative mapping. The
current effort in large-scale EST analysis and type I marker mapping should
further enhance research efficiency through comparative mapping. Candidate gene
identification is being accelerated through the use of cDNA microarrays.
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Affiliation(s)
- Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, 203 Swingle Hall Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences Aquatic Genomics Unit Auburn University Auburn AL 36849 USA
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Prosdocimi F, de Carvalho DC, de Almeida RN, Beheregaray LB. The complete mitochondrial genome of two recently derived species of the fish genus Nannoperca (Perciformes, Percichthyidae). Mol Biol Rep 2011; 39:2767-72. [PMID: 21681429 DOI: 10.1007/s11033-011-1034-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 06/03/2011] [Indexed: 11/29/2022]
Abstract
Here we report the complete sequence of mitochondrial genomes for two sister taxa of freshwater teleosts, the recently derived Yarra pigmy perch Nannoperca obscura and the southern pigmy perch Nannoperca australis. These represent the first complete mitochondrial genomes for Percichthyidae (Perciformes), a family mostly distributed in Australia. The de novo genome assembly of 316,430 pyrosequencing reads from 454 libraries has produced the entire mitochondria for N. obscura and a nearly complete version for N. australis. The mtDNA genome from the latter was completed through the design of one primer set and standard Sanger sequencing for genome finishing, followed by the hybrid assembly of reads with MIRA software using N. obscura sequence as reference genome. The complete mitogenomes of N. obscura and N. australis are 16,496 and 16,494 bp in size, respectively. Both genomes contain 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a control region. Several characteristics of mitochondria typically found in teleost fishes were detected, such as: (i) most genes found in the heavy strand, with the exception of ND6 and eight tRNA genes; (ii) avoidance of G as the third base of codons; (iii) presence of gene overlapping; (iv) percentage of bases usage. We found only eight indels and 197 nucleotide substitutions between these Nannoperca mitogenomes, consistent with a previous hypothesis of recent speciation. The data reported here provide a resource for comparative analysis of recent evolution of mitochondrial genomes.
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Affiliation(s)
- Francisco Prosdocimi
- Bioinformatics and Genome Biology Laboratory, Universidade Católica de Brasília, Brasília, Brazil
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26
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Bean PT, Jackson JT, McHenry DJ, Bonner TH, Forstner MRJ. Rediscovery of the Headwater Catfish Ictalurus lupus (Ictaluridae) in a Western Gulf-Slope Drainage. SOUTHWEST NAT 2011. [DOI: 10.1894/n10-rje-08.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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The complete mitochondrial genome of bighead croaker, Collichthys niveatus (Perciformes, Sciaenidae): structure of control region and phylogenetic considerations. Mol Biol Rep 2010; 38:4673-85. [DOI: 10.1007/s11033-010-0602-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Accepted: 11/22/2010] [Indexed: 11/26/2022]
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Wang J, Shen T, Ju J, Yang G. The complete mitochondrial genome of the Chinese longsnout catfish Leiocassis longirostris (Siluriformes: Bagridae) and a time-calibrated phylogeny of ostariophysan fishes. Mol Biol Rep 2010; 38:2507-16. [PMID: 21104148 DOI: 10.1007/s11033-010-0388-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
Abstract
The complete mitogenome sequence of the Chinese longsnout catfish Leiocassis longirostris was determined using long-polymerase chain reaction (long-PCR) and directly sequenced with primer walking method. The complete mtDNA was 16,534 bp in length and contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region (D-loop), the gene composition/order of which was identical to that observed in most other vertebrates. Phylogenetic relationship of 15 ostariophysan fishes was reconstructed using Bayesian inference and maximum likelihood methods based on a total of 15,658 nucleotides from all the 13 protein-coding, two rRNA, and 22 tRNA genes, using recently developed models of rate autocorrelation, which resolved the phylogenetic relationship of the major ostariophysan lineages with a high statistical support. The present result was consistent with some previous molecular cladistic work which supported the grouping of (((((Characiformes, Gymnotiformes), Siluriformes), Cypriniformes), Gonorynchiformes), outgroup). The Chinese longsnout catfish together with the Bagrid catfish (both from the same family Bagridae) had a closer affinity with Amblycipitidae than with other four analyzed catfish families. The relaxed molecular clock method incorporated into the program BEAST vl.5.3 was used to estimate divergence dates among ostariophysan lineages, which revealed that the major ostariophysan lineages diversified in the middle Jurassic (around 164.5 million years ago (Mya)) and the split of Leiocassis/Pseudobagrus occurred in the Oligocene to Miocene (8.9-25.1 Mya). The time-calibrated tree generated in this study would provide a powerful evolutionary tool for broad-scale comparative studies of the catfishes and the ostariophysan fishes.
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Affiliation(s)
- Jialian Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
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29
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Cheng Y, Xu T, Shi G, Wang R. Complete mitochondrial genome of the miiuy croaker Miichthys miiuy (Perciformes, Sciaenidae) with phylogenetic consideration. Mar Genomics 2010; 3:201-9. [DOI: 10.1016/j.margen.2010.10.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 10/13/2010] [Accepted: 10/15/2010] [Indexed: 11/26/2022]
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Jondeung A, Karinthanyakit W. The complete mitochondrial DNA sequence of the short mackerel (Rastrelliger brachysoma), and its phylogenetic position within Scombroidei, Perciformes. ACTA ACUST UNITED AC 2010; 21:36-47. [PMID: 20331328 DOI: 10.3109/19401731003622529] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In order to support studies of short mackerel population genetic structure in the Gulf of Thailand and phylogenetic relationships, the mitochondrial genome of the short mackerel, Rastrelliger brachysoma, has recently been determined by a partial cloning technique, long PCR with three pairs of newly designed primers and primer walking sequencing. The complete mitochondrial genome is 16,539 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) and a control region (CR) as in other bony fishes. Within the 845-bp CR, we identified several conserved motifs. The phylogeny obtained by Bayesian analyses based on two nucleotide datasets corresponding to the cytb and nd2 mitochondrial genes strongly support the inclusion of R. brachysoma within the monophyletic tribe of Scombrini in the family Scombridae. The obtained phylogeny also reveals high-statistical support for the existence of two distinct groups indicating that Scombroidei and Xiphioidei are two separate suborders.
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Affiliation(s)
- Amnuay Jondeung
- Department of Genetics, Kasetsart University, Bangkok, Thailand.
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POULSEN JANY, MØLLER PETERR, LAVOUÉ SÉBASTIEN, KNUDSEN STEENW, NISHIDA MUTSUMI, MIYA MASAKI. Higher and lower-level relationships of the deep-sea fish order Alepocephaliformes (Teleostei: Otocephala) inferred from whole mitogenome sequences. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01323.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kim KY, Lee SY, Bang IC, Nam YK. Complete mitogenome sequence of an endangered freshwater fish, Iksookimia choii (Teleostei; Cypriniformes; Cobitidae). ACTA ACUST UNITED AC 2009; 19:438-45. [PMID: 19489137 DOI: 10.1080/19401730802449188] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Iksookimia choii (Teleostei; Cypriniformes; Cobitidae) is an endangered freshwater fish species because of anthropogenic pressures around its natural habitats. We present the complete mitogenome sequence of L. choii to provide baseline data for use in the development of conservation plans and captive breeding programs. The total size, gene content and arrangement, and cloverleaf secondary structures of transfer RNA genes of I. choii mitogenome were highly homogeneous to previously known vertebrate mitogenomes. Phylogenetic analysis using nucleotide sequences of protein-coding and transfer RNA genes reflected the taxonomic clustering in the familial levels among species of the superfamily Cobitoidea. I. choii, which was recently transferred to the newly erected genus Iksookimia from Cobitis, was phylogenetically affiliated to one of two Cobitis species with strong statistical supports, indicating its taxonomically unstable status.
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Affiliation(s)
- Keun-Yong Kim
- Department of Aquaculture, Pukyong National University, Busan, South Korea
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Hardman M, Hardman LM. The Relative Importance of Body Size and Paleoclimatic Change as Explanatory Variables Influencing Lineage Diversification Rate: An Evolutionary Analysis of Bullhead Catfishes (Siluriformes: Ictaluridae). Syst Biol 2008; 57:116-30. [DOI: 10.1080/10635150801902193] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Michael Hardman
- Laboratory of Molecular Systematics, Finnish Forest Research Institute Jokiniemenkuja 1, 01301, Vantaa, Finland; E-mail: (M.H.)
| | - Lotta M. Hardman
- Laboratory of Molecular Systematics, Finnish Forest Research Institute Jokiniemenkuja 1, 01301, Vantaa, Finland; E-mail: (M.H.)
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Kartavtsev YP, Jung SO, Lee YM, Byeon HK, Lee JS. Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipididae): Genome description and phylogenetic considerations inferred from the Cyt b and 16S rRNA genes. Gene 2007; 396:13-27. [PMID: 17434693 DOI: 10.1016/j.gene.2007.01.027] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2006] [Revised: 01/27/2007] [Accepted: 01/31/2007] [Indexed: 10/23/2022]
Abstract
Mitochondrial DNA (mtDNA) from the bullhead torrent catfish, Liobagrus obesus, was isolated by long-polymerase chain reaction (Long-PCR) with universal primers and was fully sequenced by primer working using flanking sequences. The complete mtDNA from L. obesus was 16,531 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region, demonstrating a structure very similar to that of other bony fish. An analysis of the protein-coding genes revealed a statistically substantiated bias in (T+C): (A+G) content, supporting earlier findings regarding this peculiarity. As indicated by a chi-square test, the observed scores for pyrimidine and purine content were different from those expected assuming a 50:50 ratio: chi(2)=41.63, d.f.=5, p<0.000001 for three categories, including the 1st, 2nd, and 3rd codon positions. Further, there was a difference in nucleotide content between ND6 and the other 12 protein-coding genes in L. obesus. The values of p-distances, as summarized for different scales of evolutionary history at the Cyt b gene, revealed a clear pattern of increased nucleotide diversity at four levels: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intraorder. Scores of average p-distances of the four categories in catfish were (1) 1.59+/-0.54%, (2) 5.28+/-1.72% (3) 16.37+/-1.26%, and (4) 19.81+/-0.14%, respectively. These data support the hypothesis that speciation in the order Siluriformes, in most cases, follows a geographic mode through the accumulation of a numerous small genetic changes over a long time period. A phylogenetic tree for the bullhead torrent catfish and several other fish species belonging to the order Siluriformes was developed on the basis of respective Cyt b sequences (1138 bp); the analysis revealed a monophyletic origin for the five examined families. A species-specific clustering of sequences from single species was obtained, supporting additionally basic phylogenetic information for the catfish and the barcoding suitability of Cyt b sequence data. Lastly, one of the well-supported properties of our phylogenetic tree (99% repetition level in our analysis) was the monophyletic placement of all catfish (order Siluriformes) among other ray-finned fish of the class Actinopterigii. Also discussed herein are the aspects of phylogeny based on the 16S rRNA gene.
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Affiliation(s)
- Yuri P Kartavtsev
- Department of Chemistry, and the National Research Lab of Marine Molecular and Environmental Bioscience, College of Natural Sciences, Hanyang University, Seoul 133-791, South Korea
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Kim BC, Kang TW, Kim MS, Kim CB. The complete mitogenome of Rhodeus uyekii (Cypriniformes, Cyprinidae). ACTA ACUST UNITED AC 2007; 17:181-6. [PMID: 17286045 DOI: 10.1080/10425170600806928] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The complete nucleotide sequence of the mitochondrial genome from the R. uyekii with a total size of 16,817 bp has been determined by long PCR technology. Mitogenome of R. uyekii encoding 13 putative proteins, two ribosomal RNAs and 22 tRNAs shows typical teleost mitogenome structure. Nucleotide composition, amino acid composition and codon usage are in the range of values estimated from other teleost mitogenomes. In the AT rich region of R. uyekii, several conserved blocks which are identified from vertebrates are observed in the genome. R. uyekii, the Korean endemic species, belongs to cyprinid fish from which the information of nine mitogenomes is available. To understand the phylogenetic relationships of Cypriniformes from the known mitogenome information, we analysed Cypriniformes mitogenome based on protein coding gene sequences. In spite of more resolved picture of phylogenetic interrelationships in cyprinid fish in this study, the further study with comprehensive taxon sampling for mitogenome information is strongly needed.
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Affiliation(s)
- Byong-Chul Kim
- National Genome Information Centre, 52 Eoun-dong, Yusong-gu, Daejeon, South Korea
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Peng Z, Wang J, He S. The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 2006; 376:290-7. [PMID: 16737786 DOI: 10.1016/j.gene.2006.04.014] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Revised: 04/17/2006] [Accepted: 04/19/2006] [Indexed: 10/24/2022]
Abstract
The complete sequence of the 16,539 nucleotide mitochondrial genome from the single species of the catfish family Cranoglanididae, the helmet catfish Cranoglanis bouderius, was determined using the long and accurate polymerase chain reaction (LA PCR) method. The nucleotide sequences of C. bouderius mitochondrial DNA have been compared with those of three other catfish species in the same order. The contents of the C. bouderius mitochondrial genome are 13 protein-coding genes, two ribosomal RNA and 22 transfer RNA genes, and a non-coding control region, the gene order of which is identical to that observed in most other vertebrates. Phylogenetic analyses for 13 otophysan fishes were performed using Bayesian method based on the concatenated mtDNA protein-coding gene sequence and the individual protein-coding gene sequence data set. The competing otophysan topologies were then tested by using the approximately unbiased test, the Kishino-Hasegawa test, and the Shimodaira-Hasegawa test. The results show that the grouping ((((Characiformes, Gymnotiformes), Siluriformes), Cypriniformes), outgroup) is the most likely but there is no significant difference between this one and the other alternative hypotheses. In addition, the phylogenetic placement of the family Cranoglanididae among siluriform families was also discussed.
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Affiliation(s)
- Zuogang Peng
- Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, 7th Donghu South Road, Wuhan 430072, China
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Peng Z, He S, Wang J, Wang W, Diogo R. Mitochondrial molecular clocks and the origin of the major Otocephalan clades (Pisces: Teleostei): A new insight. Gene 2006; 370:113-24. [PMID: 16476526 DOI: 10.1016/j.gene.2005.11.024] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2005] [Revised: 11/24/2005] [Accepted: 11/25/2005] [Indexed: 11/20/2022]
Abstract
The Otocephala, a clade including ostariophysan and clupeomorph teleosts, represents about a quarter of total fish species diversity, with about 1000 genera and more than 7000 species. A series of recent papers have defended that the origin of this clade and of its major groups may be significantly older than the oldest fossils of each of these groups suggest. Some of these recent papers explicitly defend a Pangean origin for some otocephalan groups such as the Siluriformes or Cypriniformes. To know whether or not the otocephalans as a whole, and particularly the mainly freshwater, cosmopolitan otophysans could have originated before the splitting of the Pangean supercontinent is of extreme importance, since otophysan fishes are among the most useful animal groups for the determination of historical continental relationships. In the present work we examined divergence times for each major otocephalan group by an analysis of complete mtDNA sequences, in order to investigate if these divergence times support the hypotheses advanced in recent studies. The complete mtDNA sequences of nine representative non-otocephalan fish species and of twenty-one representative otocephalan species was compared. The present study is thus, among the studies dealing with molecular divergence times of teleosts, the one in which a greater number of otocephalan species are included. The divergence times obtained support that the major otocephalan groups had a much older origin than the oldest fossil records available for these groups suggest. The origin of the Otocephala is estimated as having occurred about 282 Mya, with the origin of the Otophysi being estimated at about 251 Mya.
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Affiliation(s)
- Zuogang Peng
- Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, 7# Donghu South Road, Wuhan 430072, China
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Affiliation(s)
- A Karsi
- USDA-ARS Catfish Genetics Research Unit, Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS, USA.
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Karsi A, Waldbieser GC, Small BC, Liu Z, Wolters WR. Molecular cloning of proopiomelanocortin cDNA and multi-tissue mRNA expression in channel catfish. Gen Comp Endocrinol 2004; 137:312-21. [PMID: 15201069 DOI: 10.1016/j.ygcen.2004.03.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Revised: 03/17/2004] [Accepted: 03/22/2004] [Indexed: 11/24/2022]
Abstract
Channel catfish (Ictalurus punctatus) proopiomelanocortin (POMC) cDNA was cloned to investigate its structure, evolution, and expression in different tissues. POMC is an important gene in the hypothalamus-pituitary-adrenal axis, the main mediator of the stress response. POMC gene was isolated from a pituitary cDNA library and nucleotide sequence was determined. POMC cDNA is composed of 1164 nucleotides with a 639 nucleotide open reading frame encoding a protein of 212 amino acids. Catfish POMC protein contains a signal peptide (SP, Met(1)-Ala(28)), N-terminal peptide (Gln(29)-Glu(101)), adrenocorticotropic hormone (ACTH, Ser(104)-Met(142)), alpha-melanocyte stimulating hormone (alpha-MSH, Ser(104)-Val(116)), corticotropin-like intermediate lobe peptide (CLIP, Arg(121)-Met(142)), beta-lipotropin (beta-LPH, Glu(145)-His(212)), gamma-lipotropin (gamma-LPH, Glu(145)- Ser(177)), beta-MSH (Asp(161)-Ser(177)), and beta-endorphin (beta-EP, Tyr(180)-His(212)). Catfish POMC protein does not contain a gamma-MSH region and most of the joining peptide and part of the gamma-LPH are deleted. Protein sequence alignment showed the highest similarity with the carp (Cyprinus carpio) POMC I (66.5%) and POMC II (67%), while the sea lamprey (Petromyzon marinus) POC (17.9%) and POM (18.8%) were the most divergent. The average similarity was 46.95% among the 44 POMC proteins from 36 different species analyzed. Compared to the POMC mRNA levels in the pituitary, the concentration of the POMC mRNA was 0.0594% in the anterior kidney and 0.0012-0.0045% in all the other tissues except in the skin where the lowest expression (0.0005%) was observed. Overall architecture of channel catfish POMC is highly similar to those from other teleosts.
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Affiliation(s)
- Attila Karsi
- USDA-ARS Catfish Genetics Research Unit, Thad Cochran National Warmwater Aquaculture Center, P.O. Box 38, Stoneville, MS 38776, USA.
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5 Genetics and breeding. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-9309(04)80007-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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