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Singh V, Itoh Y, Del'Olio S, Hassan A, Naschberger A, Flygaard RK, Nobe Y, Izumikawa K, Aibara S, Andréll J, Whitford PC, Barrientos A, Taoka M, Amunts A. Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk. Nat Commun 2024; 15:4272. [PMID: 38769321 PMCID: PMC11106087 DOI: 10.1038/s41467-024-48163-x] [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: 08/07/2022] [Accepted: 04/19/2024] [Indexed: 05/22/2024] Open
Abstract
The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNAVal. The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed us to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transitions in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide a description of the structure and function of the human mitoribosome.
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Affiliation(s)
- Vivek Singh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
| | - Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 113-0033, Tokyo, Japan
| | - Samuel Del'Olio
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Asem Hassan
- Department of Physics, Northeastern University, Boston, MA, 02115, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, 02115, USA
| | - Andreas Naschberger
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
- King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Rasmus Kock Flygaard
- Department of Molecular Biology and Genetics, Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Keiichi Izumikawa
- Department of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Shintaro Aibara
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
| | - Juni Andréll
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Paul C Whitford
- Department of Physics, Northeastern University, Boston, MA, 02115, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, 02115, USA
| | - Antoni Barrientos
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden.
- Westlake University, Hangzhou, China.
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2
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Dadkhah K, Mianji GR, Barzegar A, Farhadi A. Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA. BMC Ecol Evol 2023; 23:55. [PMID: 37749487 PMCID: PMC10521412 DOI: 10.1186/s12862-023-02166-2] [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: 10/18/2022] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND The sturgeon group has been economically significant worldwide due to caviar production. Sturgeons consist of 27 species in the world. Mitogenome data could be used to infer genetic diversity and investigate the evolutionary history of sturgeons. A limited number of complete mitogenomes in this family were sequenced. Here, we annotated the mitochondrial Huso huso genome, which revealed new aspects of this species. RESULTS In this species, the mitochondrial genome consisted of 13 genes encoding proteins, 22tRNA and 2rRNA, and two non-coding regions that followed other vertebrates. In addition, H. huso had a pseudo-tRNA-Glu between ND6 and Cytb and a 52-nucleotide tandem repeat with two replications in 12S rRNA. This duplication event is probably related to the slipped strand during replication, which could remain in the strand due to mispairing during replication. Furthermore, an 82 bp repeat sequence with three replications was observed in the D-loop control region, which is usually visible in different species. Regulatory elements were also seen in the control region of the mitochondrial genome, which included termination sequences and conserved regulatory blocks. Genomic compounds showed the highest conservation in rRNA and tRNA, while protein-encoded genes and nonencoded regions had the highest divergence. The mitochondrial genome was phylogenetically assayed using 12 protein-encoding genes. CONCLUSIONS In H. huso sequencing, we identified a distinct genome organization relative to other species that have never been reported. In recent years, along with the advancement in sequencing identified more genome rearrangements. However, it is an essential aspect of researching the evolution of the mitochondrial genome that needs to be recognized.
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Affiliation(s)
- Khadijeh Dadkhah
- Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.
| | - Ghodrat Rahimi Mianji
- Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ali Barzegar
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ayoub Farhadi
- Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
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Gutiérrez EG, Ortega J, Savoie A, Baeza JA. The mitochondrial genome of the mountain wooly tapir, Tapirus pinchaque and a formal test of the effect of altitude on the adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates. BMC Genomics 2023; 24:527. [PMID: 37674108 PMCID: PMC10481570 DOI: 10.1186/s12864-023-09596-8] [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: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND The harsh conditions of high-altitude environments are known to drive the evolution of physiological and morphological traits in endothermic animals. These conditions are expected to result in the adaptive evolution of protein coding genes encoded in mitochondrial genomes that are vital for the oxidative phosphorylation pathway. In this study, we formally tested for signatures of adaptive evolution on mitochondrial protein coding genes in Tapirus pinchaque and other odd-toed ungulates inhabiting high-elevation environments. RESULTS The AT-rich mitochondrial genome of T. pinchaque is 16,750 bp long. A phylomitogenomic analysis supports the monophyly of the genus Tapirus and families in the Perissodactyla. The ratio of non-synonymous to synonymous substitutions demonstrated that all mitochondrial genes undergo purifying selection in T. pinchaque and other odd ungulates living at high elevations. Over this negative background selection, Branch Models suggested that cox3 and nad6 might be undergoing stronger purifying selection than other mitochondrial protein coding genes. Furthermore, Site Models suggested that one and four sites in nad2 and nad5, respectively, could be experiencing positive selection. However, these results were supported by Likelihood Ratio Tests but not Bayesian Empirical Bayes posterior probabilities. Additional analyses (in DataMonkey) indicated a relaxation of selection strength in nad6, evidence of episodic diversifying selection in cob, and revealed episodic positive/diversifying selection signatures for two sites in nad1, and one site each in nad2 and nad4. CONCLUSION The mitochondrial genome of T. pinchaque is an important genomic resource for conservation of this species and this study contributes to the understanding of adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates inhabiting high-altitude environments.
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Affiliation(s)
- Edgar G Gutiérrez
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Químicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala S/N, Col. Santo Tomás, Ciudad de México, C.P. 11340, Mexico
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Químicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala S/N, Col. Santo Tomás, Ciudad de México, C.P. 11340, Mexico
| | - Avery Savoie
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA.
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL, 34949, USA.
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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4
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Singh V, Itoh Y, Del'Olio S, Hassan A, Naschberger A, Flygaard RK, Nobe Y, Izumikawa K, Aibara S, Andréll J, Whitford PC, Barrientos A, Taoka M, Amunts A. Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542018. [PMID: 37503168 PMCID: PMC10369894 DOI: 10.1101/2023.05.24.542018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNA Val . The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transition in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide the most complete description so far of the structure and function of the human mitoribosome.
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5
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Yang T, Liu Y, Ning Z. Comparative Mitogenomic Analysis of Two Snake Eels Reveals Irregular Gene Rearrangement and Phylogenetic Implications of Ophichthidae. Animals (Basel) 2023; 13:ani13030362. [PMID: 36766251 PMCID: PMC9913227 DOI: 10.3390/ani13030362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
The family Ophichthidae has the largest number and the most various species (about 359 valid species) in the order Anguilliformes worldwide. Both morphological and molecular characteristics have been used to assess their taxonomic status. However, due to the ambiguous morphological features, molecular data such as mitochondrial DNA sequences have been implemented for the correct identification and classification of these fishes. In this study, the gene arrangement and structure characteristics of two Ophichthidae mitochondrial genomes were investigated for the first time. The total mitogenome lengths of O. evermanni and O. erabo were 17,759 bp and 17,856 bp, respectively. Comparing with the ancestral mitochondrial gene order, the irregular gene rearrangement happened between ND6 and tRNA-Pro (P) genes with another similar control region emerging between tRNA-Thr (T) and ND6 genes, which could be explained by the tandem duplication and random loss (TDRL) model appropriately. ML phylogenetic tree demonstrated that the family Ophichthidae was monophyletic origin, but genus Ophichthus might be polyphyletic because of the confused cluster relationships among different species.
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6
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Complete Mitogenomes of Polypedates Tree Frogs Unveil Gene Rearrangement and Concerted Evolution within Rhacophoridae. Animals (Basel) 2022; 12:ani12182449. [PMID: 36139309 PMCID: PMC9494961 DOI: 10.3390/ani12182449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary Duplicated control regions have been reported several times in the tree frog family Rhacophoridae, and previous studies have mostly relied on sequence analysis to reconstruct their evolution. This is the first study to employ a phylogenetic method to demonstrate the existence of concerted and parallel evolution succinctly and intuitively in the duplicated control regions of the family Rhacophoridae. Phylogenetic relationships were also used to illustrate the parallel evolution of ATP8 loss of function in the genus Polypedates. In general, this study elucidated the evolutionary patterns and pathways of mitochondrial gene rearrangement of the family Rhacophoridae from a phylogenetic perspective, which aids in understanding the evolutionary history of this fascinating tree frog taxon from a molecular evolution standpoint. Abstract New developments in sequencing technology and nucleotide analysis have allowed us to make great advances in reconstructing anuran phylogeny. As a clade of representative amphibians that have radiated from aquatic to arboreal habitats, our understanding of the systematic status and molecular biology of rhacophorid tree frogs is still limited. We determined two new mitogenomes for the genus Polypedates (Rhacophoridae): P. impresus and P. mutus. We conducted comparative and phylogenetic analyses using our data and seven other rhacophorid mitogenomes. The mitogenomes of the genera Polypedates, Buergeria, and Zhangixalus were almost identical, except that the ATP8 gene in Polypedates had become a non-coding region; Buergeria maintained the legacy “LTPF” tRNA gene cluster compared to the novel “TLPF” order in the other two genera; and B. buergeri and Z. dennysi had no control region (CR) duplication. The resulting phylogenetic relationship supporting the above gene rearrangement pathway suggested parallel evolution of ATP8 gene loss of function (LoF) in Polypedates and CR duplication with concerted evolution of paralogous CRs in rhacophorids. Finally, conflicting topologies in the phylograms of 185 species reflected the advantages of phylogenetic analyses using multiple loci.
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7
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Patel S, Evans CW, Stuckey A, Matzke NJ, Millar CD. A Unique Mitochondrial Gene Block Inversion in Antarctic Trematomin Fishes: A Cautionary Tale. J Hered 2022; 113:414-420. [PMID: 35657776 PMCID: PMC9308043 DOI: 10.1093/jhered/esac028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/29/2022] [Indexed: 11/29/2022] Open
Abstract
Many Antarctic notothenioid fishes have major rearrangements in their mitochondrial (mt) genomes. Here, we report the complete mt genomes of 3 trematomin notothenioids: the bald notothen (Trematomus (Pagothenia) borchgrevinki), the spotted notothen (T. nicolai), and the emerald notothen (T. bernacchii). The 3 mt genomes were sequenced using next-generation Illumina technology, and the assemblies verified by Sanger sequencing. When compared with the canonical mt gene order of the Antarctic silverfish (Pleuragramma antarctica), we found a large gene inversion in the 3 trematomin mt genomes that included tRNAIle, ND1, tRNALeu2, 16S, tRNAVal, 12S, tRNAPhe, and the control region. The trematomin mt genomes contained 3 intergenic spacers, which are thought to be the remnants of previous gene and control region duplications. All control regions included the characteristic conserved regulatory sequence motifs. Although short-read next-generation DNA sequencing technology has allowed the rapid and cost-effective sequencing of a large number of complete mt genomes, it is essential in all cases to verify the assembly in order to prevent the publication and use of erroneous data.
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Affiliation(s)
- Selina Patel
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Clive W Evans
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Alex Stuckey
- Genomics England, Queen Mary University of London, Dawson Hall, London EC1M 6BQ, United Kingdom
| | - Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Craig D Millar
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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8
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Montaña-Lozano P, Moreno-Carmona M, Ochoa-Capera M, Medina NS, Boore JL, Prada CF. Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class. Sci Rep 2022; 12:5479. [PMID: 35361853 PMCID: PMC8971445 DOI: 10.1038/s41598-022-09512-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/21/2022] [Indexed: 11/09/2022] Open
Abstract
Vertebrate mitochondrial genomes have been extensively studied for genetic and evolutionary purposes, these are normally believed to be extremely conserved, however, different cases of gene rearrangements have been reported. To verify the level of rearrangement and the mitogenome evolution, we performed a comparative genomic analysis of the 2831 vertebrate mitochondrial genomes representing 12 classes available in the NCBI database. Using a combination of bioinformatics methods, we determined there is a high number of errors in the annotation of mitochondrial genes, especially in tRNAs. We determined there is a large variation in the proportion of rearrangements per gene and per taxonomic class, with higher values observed in Actinopteri, Amphibia and Reptilia. We highlight that these are results for currently available vertebrate sequences, so an increase in sequence representativeness in some groups may alter the rearrangement rates, so in a few years it would be interesting to see if these rates are maintained or altered with the new mitogenome sequences. In addition, within each vertebrate class, different patterns in rearrangement proportion with distinct hotspots in the mitochondrial genome were found. We also determined that there are eleven convergence events in gene rearrangement, nine of which are new reports to the scientific community.
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Affiliation(s)
- Paula Montaña-Lozano
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Manuela Moreno-Carmona
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Mauricio Ochoa-Capera
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Natalia S Medina
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia
| | - Jeffrey L Boore
- Providence St. Joseph Health and Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA, 98109, USA
| | - Carlos F Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Ibague, Colombia.
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9
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Li J, Singh U, Bhandary P, Campbell J, Arendsee Z, Seetharam AS, Wurtele ES. Foster thy young: enhanced prediction of orphan genes in assembled genomes. Nucleic Acids Res 2021; 50:e37. [PMID: 34928390 PMCID: PMC9023268 DOI: 10.1093/nar/gkab1238] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/22/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023] Open
Abstract
Proteins encoded by newly-emerged genes ('orphan genes') share no sequence similarity with proteins in any other species. They provide organisms with a reservoir of genetic elements to quickly respond to changing selection pressures. Here, we systematically assess the ability of five gene prediction pipelines to accurately predict genes in genomes according to phylostratal origin. BRAKER and MAKER are existing, popular ab initio tools that infer gene structures by machine learning. Direct Inference is an evidence-based pipeline we developed to predict gene structures from alignments of RNA-Seq data. The BIND pipeline integrates ab initio predictions of BRAKER and Direct inference; MIND combines Direct Inference and MAKER predictions. We use highly-curated Arabidopsis and yeast annotations as gold-standard benchmarks, and cross-validate in rice. Each pipeline under-predicts orphan genes (as few as 11 percent, under one prediction scenario). Increasing RNA-Seq diversity greatly improves prediction efficacy. The combined methods (BIND and MIND) yield best predictions overall, BIND identifying 68% of annotated orphan genes, 99% of ancient genes, and give the highest sensitivity score regardless dataset in Arabidopsis. We provide a light weight, flexible, reproducible, and well-documented solution to improve gene prediction.
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Affiliation(s)
- Jing Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50014, USA
| | - Urminder Singh
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Priyanka Bhandary
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Jacqueline Campbell
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture Agriculture Research Service, Ames, IA 50014, USA
| | - Zebulun Arendsee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA 50014, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
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10
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Different gene rearrangements of the genus Dardanus (Anomura: Diogenidae) and insights into the phylogeny of Paguroidea. Sci Rep 2021; 11:21833. [PMID: 34750431 PMCID: PMC8576005 DOI: 10.1038/s41598-021-01338-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/11/2021] [Indexed: 11/27/2022] Open
Abstract
Complete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and molecular evolution. In this study, the complete mitogenomes of two hermit crabs, Dardanus arrosor and Dardanus aspersus, were sequenced for the first time and compared with other published mitogenomes of Paguroidea. Each of the two mitogenomes contains an entire set of 37 genes and a putative control region, but they display different gene arrangements. The different arrangements of the two mitogenomes might be the result of transposition, reversal, and tandem duplication/random loss events from the ancestral pancrustacean pattern. Genome sequence similarity analysis reveals the gene rearrangement in 15 Paguroidea mitogenomes. After synteny analysis between the 15 Paguroidea mitogenomes, an obvious rearranged region is found in D. aspersus mitogenome. Across the 13 protein-coding genes (PCGs) tested, COI has the least and ND6 has the largest genetic distances among the 15 hermit crabs, indicating varied evolution rates of PCGs. In addition, the dN/dS ratio analysis shows that all PCGs are evolving under purifying selection. The phylogenetic analyses based on both gene order and sequence data present the monophyly of three families (Paguridae, Coenobitidae, and Pylochelidae) and the paraphyly of the family Diogenidae. Meanwhile, the phylogenetic tree based on the nucleotide sequences of 13 PCGs shows that two Dardanus species formed a sister group with five Coenobitidae species. These findings help to better understand the gene rearrangement and phylogeny of Paguroidea, as well as provide new insights into the usefulness of mitochondrial gene order as a phylogenetic marker.
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11
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Papetti C, Babbucci M, Dettai A, Basso A, Lucassen M, Harms L, Bonillo C, Heindler FM, Patarnello T, Negrisolo E. Not Frozen in the Ice: Large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish. Genome Biol Evol 2021; 13:6133229. [PMID: 33570582 PMCID: PMC7936035 DOI: 10.1093/gbe/evab017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2021] [Indexed: 12/21/2022] Open
Abstract
The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analyzed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications, and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5,300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analyzing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesized that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.
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Affiliation(s)
- Chiara Papetti
- Department of Biology, University of Padova, Padova 35121,Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma 00196, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Agnes Dettai
- Institut de Systematique, Evolution, Biodiversité (ISYEB) Muséum national d'Histoire naturelle-CNRS-Sorbonne Université-EPHE, MNHN, Paris 75005, France
| | - Andrea Basso
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Magnus Lucassen
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, Bremerhaven 27570, Germany
| | - Lars Harms
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, Bremerhaven 27570, Germany.,Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg (HIFMB), Ammerlsity of Oldenburg (HIFMOldenburg 26129, Germany
| | - Celine Bonillo
- Service de Systématique Moléculaire, UMS2700 Acquisition et Analyse de Données (2AD), MNHN, Paris 75005, France
| | | | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Enrico Negrisolo
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy.,CRIBI Interdepartmental Research Centre for Innovative Biotechnologies, University of Padova, viale G. Colombo 3, Padova 35121, Italy
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12
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Zhang Y, Gong L, Lu X, Jiang L, Liu B, Liu L, Lü Z, Li P, Zhang X. Gene rearrangements in the mitochondrial genome of Chiromantes eulimene (Brachyura: Sesarmidae) and phylogenetic implications for Brachyura. Int J Biol Macromol 2020; 162:704-714. [DOI: 10.1016/j.ijbiomac.2020.06.196] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 11/25/2022]
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13
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Cai YT, Li Q, Zhang JY, Storey KB, Yu DN. Characterization of the mitochondrial genomes of two toads, Anaxyrus americanus (Anura: Bufonidae) and Bufotes pewzowi (Anura: Bufonidae), with phylogenetic and selection pressure analyses. PeerJ 2020; 8:e8901. [PMID: 32328346 PMCID: PMC7164433 DOI: 10.7717/peerj.8901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 03/12/2020] [Indexed: 12/31/2022] Open
Abstract
Mitogenomes are useful in analyzing phylogenetic relationships and also appear to influence energy metabolism, thermoregulation and osmoregulation. Much evidence has accumulated for positive selection acting on mitochondrial genes associated with environmental adaptation. Hence, the mitogenome is a likely target for environmental selection. The family Bufonidae (true toads) has only nine complete and four partial mitogenomes published compared to the 610 known species of this family. More mitogenomes are needed in order to obtain a clearer understanding of the phylogenetic relationships within Bufonidae that are currently controversial. To date, no mitogenomes have been reported from the genera Anaxyrus and Bufotes. Anaxyrus americanus can live in low temperature environments and Bufotes pewzowi can live in high salinity environments. We sequenced the mitogenomes of these two species to discuss the phylogenetic relationships within Bufonidae and the selection pressures experienced by specimens living in low temperature or saline environments. Like other toads, the circular mitogenomes of both species contained the typical 37 genes. Anaxyrus americanus had the highest A+T content of the complete mitogenome among the Bufonidae. In addition, A. americanus showed a negative AT-skew in the control region, whereas Bufotes pewzowi showed a positive AT-skew. Additionally, both toad species had unique molecular features in common: an ND1 gene that uses TTG as the start codon, an extra unpaired adenine (A) in the anticodon arm of trnS (AGY), and the loss of the DHU loop in trnC. The monophyly of Bufonidae was corroborated by both BI and ML trees. An analysis of selective pressure based on the 13 protein coding genes was conducted using the EasyCodeML program. In the branch model analysis, we found two branches of A. americanus and Bufotes pewzowi that were under negative selection. Additionally, we found two positively selected sites (at positions 115 and 119, BEB value > 0.90) in the ND6 protein in the site model analysis. The residue D (119) was located only in A. americanus and may be related to adaptive evolution in low temperature environments. However, there was no evidence of a positively selected site in Bufotes pewzowi in this study.
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Affiliation(s)
- Yu-Ting Cai
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Qin Li
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Jia-Yong Zhang
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
| | | | - Dan-Na Yu
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
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14
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Tabassum N, Alam MJ, Kim JH, Lee SR, Lee JH, Park H, Kim HW. Characterization of complete mitochondrial genome of Pogonophryne albipinna (Perciformes: Artedidraconidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 5:156-157. [PMID: 33366465 PMCID: PMC7720972 DOI: 10.1080/23802359.2019.1698361] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The complete mitochondrial genome of Pogonophryne albipinna was determined by the MiSeq platform, which was the first report in the family Artedidraconidae. The circular form of its mitochondrial genome was 17,086 bp, which contained the canonical eukaryotic 37 genes. The gene orders of P. albipinna was identical to the other icefish species, in which there was additional non-coding region and translocation of ND6 gene. Except for ATP6 gene and COI (GTG), 11 genes begin with the typical start codon, while incomplete stop codons (T– –) were identified in COII, ND4, and CytB. Phylogenetic tree with the currently known mitogenomes in suborder Notothenioidei showed that P. albipinna was located distinctly from those in Bathydraconidae and Nototheniidae forming a unique cluster as Artedidraconidae. The first complete mitochondrial genome of P. albipinna would be the fundamental data to understand the evolutional relationship of icefish species in the Antarctic Oceans.
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Affiliation(s)
- Nazia Tabassum
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea
| | - Md Jobaidul Alam
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea
| | - Jeong-Hoon Kim
- Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, Republic of Korea
| | - Soo Rin Lee
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea
| | - Ji-Hyun Lee
- Department of Marine Biology, Pukyong National University, Busan, Republic of Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Hyun-Woo Kim
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea.,Department of Marine Biology, Pukyong National University, Busan, Republic of Korea
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15
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Luo H, Kong X, Chen S, Shi W. Mechanisms of gene rearrangement in 13 bothids based on comparison with a newly completed mitogenome of the threespot flounder, Grammatobothus polyophthalmus (Pleuronectiformes: Bothidae). BMC Genomics 2019; 20:792. [PMID: 31666003 PMCID: PMC6821024 DOI: 10.1186/s12864-019-6128-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 09/23/2019] [Indexed: 12/03/2022] Open
Abstract
Background The mitogenomes of 12 teleost fish of the bothid family (order Pleuronectiformes) indicated that the genomic-scale rearrangements characterized in previous work. A novel mechanism of genomic rearrangement called the Dimer-Mitogenome and Non-Random Loss (DMNL) model was used to account for the rearrangement found in one of these bothids, Crossorhombus azureus. Results The 18,170 bp mitogenome of G. polyophthalmus contains 37 genes, two control regions (CRs), and the origin of replication of the L-strand (OL). This mitogenome is characterized by genomic-scale rearrangements: genes located on the L-strand are grouped in an 8-gene cluster (Q-A-C-Y-S1-ND6-E-P) that does not include tRNA-N; genes found on the H-strand are grouped together (F-12S … CytB-T) except for tRNA-D that was translocated inside the 8-gene L-strand cluster. Compared to non-rearranged mitogenomes of teleost fishes, gene organization in the mitogenome of G. polyophthalmus and in that of the other 12 bothids characterized thus far is very similar. These rearrangements could be sorted into four types (Type I, II, III and IV), differing in the particular combination of the CR, tRNA-D gene and 8-gene cluster and the shuffling of tRNA-V. The DMNL model was used to account for all but one gene rearrangement found in all 13 bothid mitogenomes. Translocation of tRNA-D most likely occurred after the DMNL process in 10 bothid mitogenomes and could have occurred either before or after DMNL in the three other species. During the DMNL process, the tRNA-N gene was retained rather than the expected tRNA-N′ gene. tRNA-N appears to assist in or act as OL function when the OL secondary structure could not be formed from intergenic sequences. A striking finding was that each of the non-transcribed genes has degenerated to a shorter intergenic spacer during the DMNL process. These findings highlight a rare phenomenon in teleost fish. Conclusions This result provides significant evidence to support the existence of dynamic dimeric mitogenomes and the DMNL model as the mechanism of gene rearrangement in bothid mitogenomes, which not only promotes the understanding of mitogenome structural diversity, but also sheds light on mechanisms of mitochondrial genome rearrangement and replication.
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Affiliation(s)
- Hairong Luo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyu Kong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou, 510301, China.
| | - Shixi Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou, 510301, China
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16
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Huang A, Liu S, Li H, Luo H, Ni Q, Yao Y, Xu H, Zeng B, Li Y, Wei Z, Li S, Zhang M. The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis. PeerJ 2019; 7:e7415. [PMID: 31396450 PMCID: PMC6679912 DOI: 10.7717/peerj.7415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 07/04/2019] [Indexed: 11/30/2022] Open
Abstract
The mitochondrial genome (mitogenome) sequence of the tree frog Polypedates megacephalus (16,473 bp) was previously reported as having the unusual characteristic of lacking the ND5 gene. In this study, a new mitogenome of P. megacephalus (19,952 bp) was resequenced using the next-generation sequencing (NGS) and standard Sanger sequencing technologies. It was discovered that the ND5 gene was not lost but translocated to the control region (CR) from its canonical location between the ND4 and ND6 genes. In addition, a duplicated control region was found in the new mitogenome of this species. Conservative region identification of the ND5 gene and phylogenetic analysis confirmed that the ND5 gene was located between two control regions. The phylogenetic relationship among 20 related species of anura revealed a rearrangement of the ND5 gene during the evolutionary process. These results also highlighted the advantages of next-generation sequencing. It will not only decrease the time and cost of sequencing, but also will eliminate the errors in published mitogenome databases.
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Affiliation(s)
- An Huang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shuo Liu
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, China
| | - Haijun Li
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hongdi Luo
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Bo Zeng
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ying Li
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhimin Wei
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Song Li
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, China
| | - Mingwang Zhang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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17
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Balakirev ES. Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins. Genes (Basel) 2019; 10:E592. [PMID: 31387337 PMCID: PMC6723515 DOI: 10.3390/genes10080592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/30/2019] [Accepted: 08/02/2019] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial (mt) genomes of the sea urchins Strongylocentrotus intermedius and Mesocentrotus nudus demonstrate the identical patterns of intraspecific length variability of the ND6 gene, consisting of 489 bp (S variant) and 498 bp (L variant), respectively. For both species, the ND6 length difference is due to the 488A>G substitution, which changes the stop codon TAG in S variant for a tryptophan codon TGG in L variant and elongates the corresponding ND6 protein by three additional amino acids, Trp-Leu-Trp. The phylogenetic analysis based on mt genomes of sea urchins and related echinoderm groups from GenBank has shown the S and L ND6 variants as shared among the camarodont sea urchins; the rest of the echinoderms demonstrate the S variant only. The data suggest that the ND6 488A>G substitution can be the first example of the trans-species polymorphism in sea urchins, persisting at least since the time of the Odontophora diversification at the Eocene/Oligocene boundary (approximately 34 million years ago), which was characterized by an abrupt climate change and significant global ocean cooling. Alternative hypotheses, including the convergent RNA editing and/or codon reassignment, are not supported by direct comparisons of the ND6 gene sequences with the corresponding transcripts using the basic local alignment search tool (BLAST) of full sea urchin transcriptomes.
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Affiliation(s)
- Evgeniy S Balakirev
- National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 17 Palchevsky Street, 690041 Vladivostok, Russia.
- School of Biomedicine, Far Eastern Federal University, 8 Sukhanov Street, 690950 Vladivostok, Russia.
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18
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Tan MH, Gan HM, Lee YP, Bracken-Grissom H, Chan TY, Miller AD, Austin CM. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci Rep 2019; 9:10756. [PMID: 31341205 PMCID: PMC6656734 DOI: 10.1038/s41598-019-47145-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/05/2019] [Indexed: 01/21/2023] Open
Abstract
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
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Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia.
- Deakin Genomics Centre, Deakin University, Geelong, Australia.
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Heather Bracken-Grissom
- Department of Biological Sciences, Florida International University, North Miami, Florida, 33181, USA
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 20224, Taiwan
| | - Adam D Miller
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
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19
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Huang W, Luo H, Luo S, Huang A, Ni Q, Yao Y, Xu H, Zeng B, Li Y, Wei Z, Zhang M. The complete mitogenome of the splendid japalure Japalura splendida (Squamata, Agamidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2641-2642. [PMID: 33365662 PMCID: PMC7706609 DOI: 10.1080/23802359.2019.1643797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The complete mitogenome of Japalura splendida (16,673 bp in length) is determined and analyzed in this study. It contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and one non-coding regions. All the genes in J. splendida are distributed on the H-strand, except for the ND6 gene and seven tRNA genes which are encoded on the L-strand. The phylogenetic tree suggests that J. splendida and Japalura flaviceps formed a sister group and reveals the order ((((Acanthosaura lepidogaster, Acanthosaura armata), ((J. splendida, J. flaviceps), Pseudocalotes microlepis))), Calotes versicolor) with substantial support for the monophyly.
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Affiliation(s)
- Weiyi Huang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hongdi Luo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Sangdawa Luo
- Forestry and Grassland Administration of Qushui County, Lhasa, China
| | - An Huang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhimin Wei
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Mingwang Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
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20
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Gong L, Jiang H, Zhu K, Lu X, Liu L, Liu B, Jiang L, Ye Y, Lü Z. Large-scale mitochondrial gene rearrangements in the hermit crab Pagurus nigrofascia and phylogenetic analysis of the Anomura. Gene 2019; 695:75-83. [PMID: 30738095 DOI: 10.1016/j.gene.2019.01.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
Abstract
Complete mitochondrial genome (mitogenome) provides important information for better understanding of gene rearrangement, molecular evolution and phylogenetic analysis. Currently, only a few Paguridae mitogenomes have been reported. Herein, we described the complete mitogenome of hermit crab Pagurus nigrofascia. The total length was 15,423 bp, containing 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNA genes, as well as an AT-rich region. The genome composition was highly A + T biased (71.4%), and exhibited a negative AT-skew (-0.006) and GC-skew (-0.138). Eight tRNA genes, two PCGs and an AT-rich region found to be rearranged with respect to the pancrustacean ground pattern gene order. Duplication-random loss and recombination model were adopted to explain the large-scale gene rearrangement events. Two phylogenetic trees of Anomura involving 12 families were constructed. The results showed that all Paguridae species were clustered into one clade except Pagurus longicarpus, which for the first time imposed raises doubt about the morphological taxonomy of this species. Furthermore, the present study found that higher- level phylogenetic relationships within Anomura were controversial, compared with the previous studies. Our results help to better understand gene rearrangements and the evolutionary status of P. nigrofascia and lay foundation for further phylogenetic study of Anomura.
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Affiliation(s)
- Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China.
| | - Hui Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Kehua Zhu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Xinting Lu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Lihua Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Yingying Ye
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022 Zhoushan, China; National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
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21
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Urantówka AD, Kroczak A, Silva T, Padrón RZ, Gallardo NF, Blanch J, Blanch B, Mackiewicz P. New Insight into Parrots' Mitogenomes Indicates That Their Ancestor Contained a Duplicated Region. Mol Biol Evol 2018; 35:2989-3009. [PMID: 30304531 PMCID: PMC6278868 DOI: 10.1093/molbev/msy189] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial genomes of vertebrates are generally thought to evolve under strong selection for size reduction and gene order conservation. Therefore, a growing number of mitogenomes with duplicated regions changes our view on the genome evolution. Among Aves, order Psittaciformes (parrots) is especially noteworthy because of its large morphological, ecological, and taxonomical diversity, which offers an opportunity to study genome evolution in various aspects. Former analyses showed that tandem duplications comprising the control region with adjacent genes are restricted to several lineages in which the duplication occurred independently. However, using an appropriate polymerase chain reaction strategy, we demonstrate that early diverged parrot groups contain mitogenomes with the duplicated region. These findings together with mapping duplication data from other mitogenomes onto parrot phylogeny indicate that the duplication was an ancestral state for Psittaciformes. The state was inherited by main parrot groups and was lost several times in some lineages. The duplicated regions were subjected to concerted evolution with a frequency higher than the rate of speciation. The duplicated control regions may provide a selective advantage due to a more efficient initiation of replication or transcription and a larger number of replicating genomes per organelle, which may lead to a more effective energy production by mitochondria. The mitogenomic duplications were associated with phenotypic features and parrots with the duplicated region can live longer, show larger body mass as well as predispositions to a more active flight. The results have wider implications on the presence of duplications and their evolution in mitogenomes of other avian groups.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Aleksandra Kroczak
- Department of Genomics, Faculty of Biotechnology, Wrocław University, Wrocław, Poland
| | | | | | | | - Julie Blanch
- Rosewood Bird Gardens & Breeding Farm, Rosewood, QLD, Australia
| | - Barry Blanch
- Rosewood Bird Gardens & Breeding Farm, Rosewood, QLD, Australia
| | - Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, Wrocław University, Wrocław, Poland
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22
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ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements. Mol Phylogenet Evol 2018; 127:320-331. [DOI: 10.1016/j.ympev.2018.05.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/03/2018] [Accepted: 05/13/2018] [Indexed: 01/08/2023]
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23
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Bhandary P, Seetharam AS, Arendsee ZW, Hur M, Wurtele ES. Raising orphans from a metadata morass: A researcher's guide to re-use of public 'omics data. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 267:32-47. [PMID: 29362097 DOI: 10.1016/j.plantsci.2017.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/07/2017] [Accepted: 10/15/2017] [Indexed: 05/19/2023]
Abstract
More than 15 petabases of raw RNAseq data is now accessible through public repositories. Acquisition of other 'omics data types is expanding, though most lack a centralized archival repository. Data-reuse provides tremendous opportunity to extract new knowledge from existing experiments, and offers a unique opportunity for robust, multi-'omics analyses by merging metadata (information about experimental design, biological samples, protocols) and data from multiple experiments. We illustrate how predictive research can be accelerated by meta-analysis with a study of orphan (species-specific) genes. Computational predictions are critical to infer orphan function because their coding sequences provide very few clues. The metadata in public databases is often confusing; a test case with Zea mays mRNA seq data reveals a high proportion of missing, misleading or incomplete metadata. This metadata morass significantly diminishes the insight that can be extracted from these data. We provide tips for data submitters and users, including specific recommendations to improve metadata quality by more use of controlled vocabulary and by metadata reviews. Finally, we advocate for a unified, straightforward metadata submission and retrieval system.
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Affiliation(s)
- Priyanka Bhandary
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA 50011, USA
| | - Zebulun W Arendsee
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Manhoi Hur
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA.
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24
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Ramos B, González-Acuña D, Loyola DE, Johnson WE, Parker PG, Massaro M, Dantas GPM, Miranda MD, Vianna JA. Landscape genomics: natural selection drives the evolution of mitogenome in penguins. BMC Genomics 2018; 19:53. [PMID: 29338715 PMCID: PMC5771141 DOI: 10.1186/s12864-017-4424-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 12/28/2017] [Indexed: 12/21/2022] Open
Abstract
Background Mitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation can generate more efficient coupling of energy production. However, selection over mitochondrial DNA (mtDNA) genes has usually been evaluated at the population level. We sequenced by NGS 12 mitogenomes and with four published genomes, assessed genetic variation in ten penguin species distributed from the equator to Antarctica. Signatures of selection of 13 mitochondrial protein-coding genes were evaluated by comparing among species within and among genera (Spheniscus, Pygoscelis, Eudyptula, Eudyptes and Aptenodytes). The genetic data were correlated with environmental data obtained through remote sensing (sea surface temperature [SST], chlorophyll levels [Chl] and a combination of SST and Chl [COM]) through the distribution of these species. Results We identified the complete mtDNA genomes of several penguin species, including ND6 and 8 tRNAs on the light strand and 12 protein coding genes, 14 tRNAs and two rRNAs positioned on the heavy strand. The highest diversity was found in NADH dehydrogenase genes and the lowest in COX genes. The lowest evolutionary divergence among species was between Humboldt (Spheniscus humboldti) and Galapagos (S. mendiculus) penguins (0.004), while the highest was observed between little penguin (Eudyptula minor) and Adélie penguin (Pygoscelis adeliae) (0.097). We identified a signature of purifying selection (Ka/Ks < 1) across the mitochondrial genome, which is consistent with the hypothesis that purifying selection is constraining mitogenome evolution to maintain Oxidative phosphorylation (OXPHOS) proteins and functionality. Pairwise species maximum-likelihood analyses of selection at codon sites suggest positive selection has occurred on ATP8 (Fixed-Effects Likelihood, FEL) and ND4 (Single Likelihood Ancestral Counting, SLAC) in all penguins. In contrast, COX1 had a signature of strong negative selection. ND4 Ka/Ks ratios were highly correlated with SST (Mantel, p-value: 0.0001; GLM, p-value: 0.00001) and thus may be related to climate adaptation throughout penguin speciation. Conclusions These results identify mtDNA candidate genes under selection which could be involved in broad-scale adaptations of penguins to their environment. Such knowledge may be particularly useful for developing predictive models of how these species may respond to severe climatic changes in the future. Electronic supplementary material The online version of this article (10.1186/s12864-017-4424-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Barbara Ramos
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna, 4860, Santiago, Chile.,Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Republica 252, Santiago, Chile
| | - Daniel González-Acuña
- Departamento de Ciencias Pecuarias, Facultad de Ciencias Veterinarias, Universidad de Concepción, Av. Vicente Méndez 595, 3780000, Chillán, CP, Chile
| | - David E Loyola
- Centro Nacional de Genómica y Bioinformática, Portugal 49, Santiago, Chile.,I+DEA Biotech, Av. Central 3413, Padre Hurtado, Santiago, Chile
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - Patricia G Parker
- University of Missouri St Louis and Saint Louis Zoo, One University Blvd., St. Louis, MO, 63121-4400, USA
| | - Melanie Massaro
- School of Environmental Sciences and Institute for Land, Water and Society, Charles Sturt University, PO Box 789, Albury, NSW, Australia
| | - Gisele P M Dantas
- Pontifícia Universidade Católica de Minas Gerais, Av. Dom José Gaspar 500, Coração Eucarístico, Belo Horizonte, MG, Brazil
| | - Marcelo D Miranda
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna, 4860, Santiago, Chile
| | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna, 4860, Santiago, Chile. .,Centro de Cambio Global UC, Santiago, Chile.
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25
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Lee-Estevez M, Larama G, Figueroa E, Ulloa-Rodríguez P, Díaz R, Valdebenito I, Farías JG. Complete mitochondrial genome sequence of Patagonian blenny, Eleginops maclovinus (Perciformes: Eleginopidae) with phylogenetic consideration. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0954-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Song W, Li L, Huang H, Chen F, Zhao M, Jiang K, Zhang F, Ma C, Chen X, Ma L. Isolation and characterization of the mitochondrial genome of Gymnodraco acuticeps (Perciformes: Bathydraconidae) with phylogenetic consideration. Mitochondrial DNA B Resour 2017; 2:526-527. [PMID: 33473885 PMCID: PMC7799673 DOI: 10.1080/23802359.2017.1361361] [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: 07/11/2017] [Accepted: 07/26/2017] [Indexed: 12/03/2022] Open
Abstract
Gymnodraco acuticepsis is an Antarctic fish living in the Southern Ocean. Until now, studies on G. acuticeps are still limited. As an Antarctic fish, obtaining and characterization of the mitochondrial genome of G. acuticeps will be important for elucidation of the mechanism of cold-adapting evolution in mitochondrion. In this study, we first isolated and characterized the mitochondrial genome sequence of G. acuticeps with 15,987 bp in length. It contained of 34 genes (12 protein-coding genes, 20 transfer RNA genes, 2 ribosomal RNA genes) and a partial putative control region. Gene organization and nucleotide composition of obtained mito-genome were similar to those of other Antarctic fish. Twenty-eight genes were encoded by heavy strand, while six genes were encoded by light strand. Further, the phylogenetic tree, which based on 12 protein-coding genes, revealed that the G. acuticeps was genetically closest to species Parachaenichthys charcoti among 18 species. We hope this work would be helpful for the population genetics and molecular evolution studies.
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Affiliation(s)
- Wei Song
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingzhi Li
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Hongliang Huang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Fenfang Chen
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Ming Zhao
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Keji Jiang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Fengying Zhang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Chunyan Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Xuezhong Chen
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingbo Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
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27
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Satoh TP, Miya M, Mabuchi K, Nishida M. Structure and variation of the mitochondrial genome of fishes. BMC Genomics 2016; 17:719. [PMID: 27604148 PMCID: PMC5015259 DOI: 10.1186/s12864-016-3054-y] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/27/2016] [Indexed: 11/10/2022] Open
Abstract
Background The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data. The aim of this study was to characterize the structure and variability of the fish mt genome through comparative analysis of large datasets. Results An analysis of the secondary structure of proteins for 250 fish species (248 ray-finned and 2 cartilaginous fishes) illustrated that cytochrome c oxidase subunits (COI, COII, and COIII) and a cytochrome bc1 complex subunit (Cyt b) had substantial amino acid conservation. Among the four proteins, COI was the most conserved, as more than half of all amino acid sites were invariable among the 250 species. Our models identified 43 and 58 stems within 12S rRNA and 16S rRNA, respectively, with larger numbers than proposed previously for vertebrates. The models also identified 149 and 319 invariable sites in 12S rRNA and 16S rRNA, respectively, in all fishes. In particular, the present result verified that a region corresponding to the peptidyl transferase center in prokaryotic 23S rRNA, which is homologous to mt 16S rRNA, is also conserved in fish mt 16S rRNA. Concerning the gene order, we found 35 variations (in 32 families) that deviated from the common gene order in vertebrates. These gene rearrangements were mostly observed in the area spanning the ND5 gene to the control region as well as two tRNA gene cluster regions (IQM and WANCY regions). Although many of such gene rearrangements were unique to a specific taxon, some were shared polyphyletically between distantly related species. Conclusions Through a large-scale comparative analysis of 250 fish species mt genomes, we elucidated various structural aspects of the fish mt genome and the encoded genes. The present results will be important for understanding functions of the mt genome and developing programs for nucleotide sequence analysis. This study demonstrated the significance of extensive comparisons for understanding the structure of the mt genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3054-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Takashi P Satoh
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8654, Japan. .,Collection Center, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba City, Ibaraki, 305-0005, Japan. .,Present address: Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, 459 Shirahama, Nishimuro, Wakayama, 649-2211, Japan.
| | - Masaki Miya
- Natural History Museum and Institute, 955-2 Aoba-cho, Chuo-ku, Chiba City, Chiba, 260-8682, Japan
| | - Kohji Mabuchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8654, Japan
| | - Mutsumi Nishida
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8654, Japan. .,Present address: University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa, 908-0213, Japan.
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28
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Papetti C, Lucassen M, Pörtner HO. Integrated studies of organismal plasticity through physiological and transcriptomic approaches: examples from marine polar regions. Brief Funct Genomics 2016; 15:365-72. [PMID: 27345433 DOI: 10.1093/bfgp/elw024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transcriptomic methods are now widely used in functional genomic research. The vast amount of information received from these studies comes along with the challenge of developing a precise picture of the functional consequences and the characteristic regulatory mechanisms. Here we assess recent studies in marine species and their adaptation to polar (and seasonal) cold and explore how they have been able to draw reliable conclusions from transcriptomic patterns on functional consequences in the organisms. Our analysis indicates that the interpretation of transcriptomic data suffers from insufficient understanding of the consequences for whole organism performance and fitness and comes with the risk of supporting only preliminary and superficial statements.We propose that the functional understanding of transcriptomic data may be improved by their tighter integration into overarching physiological concepts that support the more specific interpretation of the 'omics' data and, at the same time, can be developed further through embedding the transcriptomic phenomena observed. Such possibilities have not been fully exploited.In the context of thermal adaptation and limitation, we explore preliminary evidence that the concept of oxygen and capacity limited thermal tolerance (OCLTT) may provide sufficient complexity to guide the integration of such data and the development of associated functional hypotheses. At the same time, we identify a lack of methodological approaches linking genes and function to higher levels of integration, in terms of organism and ecosystem functioning, at temporal and geographical scales, to support more reliable conclusions and be predictive with respect to the effects of global changes.
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29
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Beers JM, Jayasundara N. Antarctic notothenioid fish: what are the future consequences of 'losses' and 'gains' acquired during long-term evolution at cold and stable temperatures? ACTA ACUST UNITED AC 2016; 218:1834-45. [PMID: 26085661 DOI: 10.1242/jeb.116129] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Antarctic notothenioids dominate the fish fauna of the Southern Ocean. Evolution for millions of years at cold and stable temperatures has led to the acquisition of numerous biochemical traits that allow these fishes to thrive in sub-zero waters. The gain of antifreeze glycoproteins has afforded notothenioids the ability to avert freezing and survive at temperatures often hovering near the freezing point of seawater. Additionally, possession of cold-adapted proteins and membranes permits them to sustain appropriate metabolic rates at exceptionally low body temperatures. The notothenioid genome is also distinguished by the disappearance of traits in some species, losses that might prove costly in a warmer environment. Perhaps the best-illustrated example is the lack of expression of hemoglobin in white-blooded icefishes from the family Channichthyidae. Loss of key elements of the cellular stress response, notably the heat shock response, has also been observed. Along with their attainment of cold tolerance, notothenioids have developed an extreme stenothermy and many species perish at temperatures only a few degrees above their habitat temperatures. Thus, in light of today's rapidly changing climate, it is critical to evaluate how these extreme stenotherms will respond to rising ocean temperatures. It is conceivable that the remarkable cold specialization of notothenioids may ultimately leave them vulnerable to future thermal increases and threaten their fitness and survival. Within this context, our review provides a current summary of the biochemical losses and gains that are known for notothenioids and examines these cold-adapted traits with a focus on processes underlying thermal tolerance and acclimation capacity.
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Affiliation(s)
- Jody M Beers
- Hopkins Marine Station, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA 93950, USA
| | - Nishad Jayasundara
- Nicholas School of the Environment, Duke University, 450 Research Drive, Durham, NC 27708, USA
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30
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Song W, Li L, Huang H, Zhao M, Jiang K, Zhang F, Zhao M, Chen X, Ma L. The complete mitochondrial genome sequence and gene organization of Trematomus bernacchii (Perciformes: Nototheniidae) with phylogenetic consideration. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:50-51. [PMID: 33473404 PMCID: PMC7800238 DOI: 10.1080/23802359.2015.1137818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In this study, the complete mitochondrial DNA sequence was obtained from Trematomus bernacchii. The full length of mitogenome was 16 018 bp, including 20 transfer RNA genes, a 16S ribosomal RNA genes and an incomplete 12S rRNA, 12 protein-coding genes and an incomplete ND6 protein-coding gene, and 2 non-coding regions: control region (D-loop) and origin of light-strand (L-strand) replication (OL). Most genes were located on the heavy-strand (H-strand), while ND6 and seven tRNA genes were located on the L-strand. T. bernacchii’s mitogenome was comprised of 24.52% for A, 25.44% for C, 20.38% for G and 29.66% for T, with a higher A + T content (54.18%). From the NJ phylogenetic tree, it revealed that T. bernacchii’s was genetically closest to species Dissostichus eleginoides among seven species within suborder Notothenioidei. This study could lay the foundation for the future studies in species identification, taxonomic status, molecular systematics, stock evaluation and conservation genetics for T. bernacchii’s.
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Affiliation(s)
- Wei Song
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingzhi Li
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Hongliang Huang
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Mengdi Zhao
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Keji Jiang
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Fengying Zhang
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Ming Zhao
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Xuezhong Chen
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingbo Ma
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
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31
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Gong L, Shi W, Yang M, Li D, Kong X. Novel gene arrangement in the mitochondrial genome of Bothus myriaster (Pleuronectiformes: Bothidae): evidence for the Dimer-Mitogenome and Non-random Loss model. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3089-92. [DOI: 10.3109/19401736.2014.1003922] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Li Gong
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China and
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Wei Shi
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China and
| | - Min Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China and
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Donghe Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China and
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyu Kong
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China and
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Low level of genetic divergence between Harpagifer fish species (Perciformes: Notothenioidei) suggests a Quaternary colonization of Patagonia from the Antarctic Peninsula. Polar Biol 2014. [DOI: 10.1007/s00300-014-1623-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Lee J, Lee H, Lee J, Jo J, Choi J, Park H. Complete mitochondrial genome of the Antarctic icefish, Chaenocephalus aceratus (Perciforms, Channichthyidae). ACTA ACUST UNITED AC 2014; 26:887-8. [PMID: 24409864 DOI: 10.3109/19401736.2013.861444] [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 complete sequence of the mitochondrial genome of the Antarctic icefish Chaenocephalus aceratus was determined to be 17311 bp in length, and to contain 13 protein coding genes (PCGs), 22 tRNA genes and 2 rRNA genes. The total A+T content is 52.8%. The notothenioid-exclusive ND6/tRNAGlu translocation was observed in the mitogenome of C. aceratus. Generally, the order and contents of the other genes are identical with those of other fishes. Antarctic icefishes, the only vertebrates which do not have hemoglobins, have evolved to survive sub-freezing temperature. Therefore, the whole mitogenome sequences of C. aceratus will provide the insights into resolving the evolutionary history of icefish.
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Affiliation(s)
- Jungeun Lee
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
| | - Hyoungseok Lee
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
| | - Jongkyu Lee
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
| | - Jin Jo
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
| | - Jungeun Choi
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
| | - Hyun Park
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
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Lee J, Lee H, Lee J, Choi J, Park H. Complete mitochondrial genome of the Antarctic silverfish, Pleuragramma antarcticum (Perciformes, Nototheniidae). ACTA ACUST UNITED AC 2014; 26:885-6. [PMID: 24409863 DOI: 10.3109/19401736.2013.861443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete sequence of the mitochondrial genome of Pleuragramma antarcticum was obtained from the assembled genome data. The complete sequence was determined to be 18,460 bp in length, containing 13 protein coding genes, 22 tRNA genes, 2 rRNA genes, 2 control regions and a repeat. The general order and contents of the genes are identical with those of other fishes. The Antarctic notothenioid-specific translocation of ND6/tRNA(Glu) exists in the mitogenome. Pleuragramma antarcticum is the only pelagic species which dominates Antarctic fish fauna by more than 90%. Thus, the whole mitogenome sequences of P. antarcticum will provide the basis to understand the deep phylogeny of the Antarctic species.
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Affiliation(s)
- Jungeun Lee
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
| | - Hyoungseok Lee
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
| | - Jongkyu Lee
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
| | - Jungeun Choi
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
| | - Hyun Park
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
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35
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Zheng C, Nie L, Wang J, Zhou H, Hou H, Wang H, Liu J. Recombination and evolution of duplicate control regions in the mitochondrial genome of the Asian big-headed turtle, Platysternon megacephalum. PLoS One 2013; 8:e82854. [PMID: 24367563 PMCID: PMC3867392 DOI: 10.1371/journal.pone.0082854] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 10/29/2013] [Indexed: 01/24/2023] Open
Abstract
Complete mitochondrial (mt) genome sequences with duplicate control regions (CRs) have been detected in various animal species. In Testudines, duplicate mtCRs have been reported in the mtDNA of the Asian big-headed turtle, Platysternon megacephalum, which has three living subspecies. However, the evolutionary pattern of these CRs remains unclear. In this study, we report the completed sequences of duplicate CRs from 20 individuals belonging to three subspecies of this turtle and discuss the micro-evolutionary analysis of the evolution of duplicate CRs. Genetic distances calculated with MEGA 4.1 using the complete duplicate CR sequences revealed that within turtle subspecies, genetic distances between orthologous copies from different individuals were 0.63% for CR1 and 1.2% for CR2app:addword:respectively, and the average distance between paralogous copies of CR1 and CR2 was 4.8%. Phylogenetic relationships were reconstructed from the CR sequences, excluding the variable number of tandem repeats (VNTRs) at the 3' end using three methods: neighbor-joining, maximum likelihood algorithm, and Bayesian inference. These data show that any two CRs within individuals were more genetically distant from orthologous genes in different individuals within the same subspecies. This suggests independent evolution of the two mtCRs within each P. megacephalum subspecies. Reconstruction of separate phylogenetic trees using different CR components (TAS, CD, CSB, and VNTRs) suggested the role of recombination in the evolution of duplicate CRs. Consequently, recombination events were detected using RDP software with break points at ≈290 bp and ≈1,080 bp. Based on these results, we hypothesize that duplicate CRs in P. megacephalum originated from heterological ancestral recombination of mtDNA. Subsequent recombination could have resulted in homogenization during independent evolutionary events, thus maintaining the functions of duplicate CRs in the mtDNA of P. megacephalum.
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Affiliation(s)
- Chenfei Zheng
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Liuwang Nie
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Jue Wang
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Huaxing Zhou
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Huazhen Hou
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Hao Wang
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Juanjuan Liu
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
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Zhuang X, Qu M, Zhang X, Ding S. A comprehensive description and evolutionary analysis of 22 grouper (perciformes, epinephelidae) mitochondrial genomes with emphasis on two novel genome organizations. PLoS One 2013; 8:e73561. [PMID: 23951357 PMCID: PMC3739747 DOI: 10.1371/journal.pone.0073561] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 07/29/2013] [Indexed: 11/19/2022] Open
Abstract
Groupers of the family Epinephelidae are a diverse and economically valuable group of reef fishes. To investigate the evolution of their mitochondrial genomes we characterized and compared these genomes among 22 species, 17 newly sequenced. Among these fishes we identified three distinct genome organizations, two of them never previously reported in vertebrates. In 19 of these species, mitochondrial genomes followed the typical vertebrate canonical organization with 13 protein-coding genes, 22 tRNAs, two rRNAs, and a non-coding control region. Differing from this, members of genus Variola have an extra tRNA-Ile between tRNA-Val and 16S rRNA. Evidence suggests that this evolved from tRNA-Val via a duplication event due to slipped strand mispairing during replication. Additionally, Cephalopholisargus has an extra tRNA-Asp in the midst of the control region, likely resulting from long-range duplication of the canonical tRNA-Asp through illicit priming of mitochondrial replication by tRNAs. Along with their gene contents, we characterized the regulatory elements of these mitochondrial genomes' control regions, including putative termination-associated sequences and conserved sequence blocks. Looking at the mitochondrial genomic constituents, rRNA and tRNA are the most conserved, followed by protein-coding genes, and non-coding regions are the most divergent. Divergence rates vary among the protein-coding genes, and the three cytochrome oxidase subunits (COI, II, III) are the most conserved, while NADH dehydrogenase subunit 6 (ND6) and the ATP synthase subunit 8 (ATP8) are the most divergent. We then tested the phylogenetic utility of this new mt genome data using 12 protein-coding genes of 48 species from the suborder Percoidei. From this, we provide further support for the elevation of the subfamily Epinephelinae to family Epinephelidae, the resurrection of the genus Hyporthodus, and the combination of the monotypic genera Anyperodon and Cromileptes to genus Epinephelus, and Aethaloperca to genus Cephalopholis.
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Affiliation(s)
- Xuan Zhuang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Meng Qu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- The Laboratory of Marine Biodiversity and Global Change, Xiamen University, Xiamen, China
| | - Xiang Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- The Laboratory of Marine Biodiversity and Global Change, Xiamen University, Xiamen, China
| | - Shaoxiong Ding
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- The Laboratory of Marine Biodiversity and Global Change, Xiamen University, Xiamen, China
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Strobel A, Graeve M, Poertner HO, Mark FC. Mitochondrial acclimation capacities to ocean warming and acidification are limited in the antarctic Nototheniid Fish, Notothenia rossii and Lepidonotothen squamifrons. PLoS One 2013; 8:e68865. [PMID: 23874794 PMCID: PMC3707867 DOI: 10.1371/journal.pone.0068865] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 06/06/2013] [Indexed: 11/25/2022] Open
Abstract
Antarctic notothenioid fish are characterized by their evolutionary adaptation to the cold, thermostable Southern Ocean, which is associated with unique physiological adaptations to withstand the cold and reduce energetic requirements but also entails limited compensation capacities to environmental change. This study compares the capacities of mitochondrial acclimation to ocean warming and acidification between the Antarctic nototheniid Notothenia rossii and the sub-Antarctic Lepidonotothen squamifrons, which share a similar ecology, but different habitat temperatures. After acclimation of L. squamifrons to 9°C and N. rossii to 7°C (normocapnic/hypercapnic, 0.2 kPa CO2/2000 ppm CO2) for 4-6 weeks, we compared the capacities of their mitochondrial respiratory complexes I (CI) and II (CII), their P/O ratios (phosphorylation efficiency), proton leak capacities and mitochondrial membrane fatty acid compositions. Our results reveal reduced CII respiration rates in warm-acclimated L. squamifrons and cold hypercapnia-acclimated N. rossii. Generally, L. squamifrons displayed a greater ability to increase CI contribution during acute warming and after warm-acclimation than N. rossii. Membrane unsaturation was not altered by warm or hypercapnia-acclimation in both species, but membrane fatty acids of warm-acclimated L. squamifrons were less saturated than in warm normocapnia-/hypercapnia-acclimated N. rossii. Proton leak capacities were not affected by warm or hypercapnia-acclimation of N. rossii. We conclude that an acclimatory response of mitochondrial capacities may include higher thermal plasticity of CI supported by enhanced utilization of anaplerotic substrates (via oxidative decarboxylation reactions) feeding into the citrate cycle. L. squamifrons possesses higher relative CI plasticities than N. rossii, which may facilitate the usage of energy efficient NADH-related substrates under conditions of elevated energy demand, possibly induced by ocean warming and acidification. The observed adjustments of electron transport system complexes with a higher flux through CI under warming and acidification suggest a metabolic acclimation potential of the sub-Antarctic L. squamifrons, but only limited acclimation capacities for N. rossii.
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Affiliation(s)
- Anneli Strobel
- Integrative Ecophysiology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
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Cloning and characterization of a Δ9-desaturase gene of the Antarctic fish Chionodraco hamatus and Trematomus bernacchii. J Comp Physiol B 2012; 183:379-92. [PMID: 23007833 DOI: 10.1007/s00360-012-0702-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 07/30/2012] [Accepted: 08/04/2012] [Indexed: 11/27/2022]
Abstract
Chionodraco hamatus and Trematomus bernacchii are perciforms, members of the fish suborder Notothenioidei that live in the Antarctic Ocean and experience very cold and persistent environmental temperature. These fish have biochemical and molecular features that allow them to live at these extreme cold temperatures. Fine tuning of the level of unsaturated fatty acids content in membrane is a key mechanism of living organisms to adapt to cold and high temperatures. Desaturases are key enzymes that synthesize unsaturated fatty acyl-CoAs from saturated fatty acids. We cloned and sequenced a Δ(9)-desaturase gene and its cDNA of C. hamatus, and the cDNA of T. bernacchii. The coded proteins are virtually identical and share homology to other Δ(9)-desaturase fish sequences. These proteins contain, in the first trans-membrane domain, two cysteine residues that may form a disulfur bond present in the corresponding membrane region of Δ(9)-desaturase proteins of other Antarctic fish but not in Eleginops maclovinus that experiences higher environmental temperatures and in all other Δ(9)-desaturase genes of mammals present in data bases. C. hamatus Δ(9)-desaturase gene complements a Saccharomyces cerevisiae mutant lacking Δ(9)-desaturase (Ole1) gene. Analysis of sequence homology of the trans-membrane domains of Δ(9)-desaturase and the cytoplasmic region of the same proteins of Antarctic fish, non-Antarctic fish and mammals suggest that the significant differences found in the homologous sequences of the first trans-membrane domain may be due to the specific lipid content of their membrane.
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Lin Q, Cui P, Ding F, Hu S, Yu J. Replication-Associated Mutational Pressure (RMP) Governs Strand-Biased Compositional Asymmetry (SCA) and Gene Organization in Animal Mitochondrial Genomes. Curr Genomics 2012; 13:28-36. [PMID: 22942673 PMCID: PMC3269014 DOI: 10.2174/138920212799034811] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 10/01/2011] [Accepted: 10/04/2011] [Indexed: 11/30/2022] Open
Abstract
The nucleotide composition of the light (L-) and heavy (H-) strands of animal mitochondrial genomes is known to exhibit strand-biased compositional asymmetry (SCA). One of the possibilities is the existence of a replication-associated mutational pressure (RMP) that may introduce characteristic nucleotide changes among mitochondrial genomes of different animal lineages. Here, we discuss the influence of RMP on nucleotide and amino acid compositions as well as gene organization. Among animal mitochondrial genomes, RMP may represent the major force that compels the evolution of mitochondrial protein-coding genes, coupled with other process-based selective pressures, such as on components of translation machinery— tRNAs and their anticodons. Through comparative analyses of sequenced mitochondrial genomes among diverse animal lineages and literature reviews, we suggest a strong RMP effect, observed among invertebrate mitochondrial genes as compared to those of vertebrates, that is either a result of positive selection on the invertebrate or a relaxed selective pressure on the vertebrate mitochondrial genes.
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Affiliation(s)
- Qiang Lin
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100029 Beijing, China
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LIN CHUYIN, LIN WENWEN, KAO HSIAOWEI. The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids. Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2012.00820.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Schirtzinger EE, Tavares ES, Gonzales LA, Eberhard JR, Miyaki CY, Sanchez JJ, Hernandez A, Müeller H, Graves GR, Fleischer RC, Wright TF. Multiple independent origins of mitochondrial control region duplications in the order Psittaciformes. Mol Phylogenet Evol 2012; 64:342-56. [PMID: 22543055 DOI: 10.1016/j.ympev.2012.04.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 04/08/2012] [Accepted: 04/10/2012] [Indexed: 01/06/2023]
Abstract
Mitochondrial genomes are generally thought to be under selection for compactness, due to their small size, consistent gene content, and a lack of introns or intergenic spacers. As more animal mitochondrial genomes are fully sequenced, rearrangements and partial duplications are being identified with increasing frequency, particularly in birds (Class Aves). In this study, we investigate the evolutionary history of mitochondrial control region states within the avian order Psittaciformes (parrots and cockatoos). To this aim, we reconstructed a comprehensive multi-locus phylogeny of parrots, used PCR of three diagnostic fragments to classify the mitochondrial control region state as single or duplicated, and mapped these states onto the phylogeny. We further sequenced 44 selected species to validate these inferences of control region state. Ancestral state reconstruction using a range of weighting schemes identified six independent origins of mitochondrial control region duplications within Psittaciformes. Analysis of sequence data showed that varying levels of mitochondrial gene and tRNA homology and degradation were present within a given clade exhibiting duplications. Levels of divergence between control regions within an individual varied from 0-10.9% with the differences occurring mainly between 51 and 225 nucleotides 3' of the goose hairpin in domain I. Further investigations into the fates of duplicated mitochondrial genes, the potential costs and benefits of having a second control region, and the complex relationship between evolutionary rates, selection, and time since duplication are needed to fully explain these patterns in the mitochondrial genome.
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Affiliation(s)
- Erin E Schirtzinger
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA.
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Mark FC, Lucassen M, Strobel A, Barrera-Oro E, Koschnick N, Zane L, Patarnello T, Pörtner HO, Papetti C. Mitochondrial function in Antarctic nototheniids with ND6 translocation. PLoS One 2012; 7:e31860. [PMID: 22363756 PMCID: PMC3283701 DOI: 10.1371/journal.pone.0031860] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/13/2012] [Indexed: 12/02/2022] Open
Abstract
Fish of the suborder Notothenioidei have successfully radiated into the Southern Ocean and today comprise the dominant fish sub-order in Antarctic waters in terms of biomass and species abundance. During evolution in the cold and stable Antarctic climate, the Antarctic lineage of notothenioids developed several unique physiological adaptations, which make them extremely vulnerable to the rapid warming of Antarctic waters currently observed. Only recently, a further phenomenon exclusive to notothenioid fish was reported: the translocation of the mitochondrial gene encoding the NADH Dehydrogenase subunit 6 (ND6), an indispensable part of complex I in the mitochondrial electron transport system.This study investigated the potential physiological consequences of ND6 translocation for the function and thermal sensitivity of the electron transport system in isolated liver mitochondria of the two nototheniid species Notothenia coriiceps and Notothenia rossii, with special attention to the contributions of complex I (NADH DH) and complex II (Succinate DH) to oxidative phosphorylation. Furthermore, enzymatic activities of NADH:Cytochrome c Oxidoreductase and Cytochrome C Oxidase were measured in membrane-enriched tissue extracts.During acute thermal challenge (0-15°C), capacities of mitochondrial respiration and enzymatic function in the liver could only be increased until 9°C. Mitochondrial complex I (NADH Dehydrogenase) was fully functional but displayed a higher thermal sensitivity than the other complexes of the electron transport system, which may specifically result from its unique amino acid composition, revealing a lower degree of stability in notothenioids in general. We interpret the translocation of ND6 as functionally neutral but the change in amino acid sequence as adaptive and supportive of cold stenothermy in Antarctic nototheniids. From these findings, an enhanced sensitivity to ocean warming can be deduced for Antarctic notothenioid fish.
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Affiliation(s)
- Felix C Mark
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
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Williams EP, Peer AC, Miller TJ, Secor DH, Place AR. A phylogeny of the temperate seabasses (Moronidae) characterized by a translocation of the mt-nd6 gene. JOURNAL OF FISH BIOLOGY 2012; 80:110-130. [PMID: 22220893 DOI: 10.1111/j.1095-8649.2011.03158.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The entire mitochondrial genome of the striped bass Morone saxatilis was sequenced together with the mitochondrial (mt) control regions of the white bass Morone chrysops, white perch Morone americana, yellow bass Morone mississippiensis, spotted seabass Dicentrarchus punctatus, European seabass Dicentrarchus labrax and the Japanese seabass Lateolabrax japonicus. The resultant 17 580 base pair circular genome of M. saxatilis contains 38 genes (13 proteins, 23 transfer RNAs and two ribosomal RNAs) and a control region bordered by the proline and phenylalanine mitochondrial tRNAs. Gene arrangement was similar to other vertebrates, except that the mt-nd6 gene was found within the control region rather than the canonical position between the mt-nd5 and mt-cyb genes. This translocation was found in all the Morone and Dicentrarchus species studied without functional copies or pseudogenes in the ancestral position. In L. japonicus, the mt-nd6 gene was found in the canonical position without evidence of an mt-nd6 gene in the control region. A Bayesian analysis of these and published mt-nd6 sequences from 45 other Perciformes grouped the Morone and Dicentrarchus species monophyletically with a probability of 1·00 with respect to L. japonicus and all other perciforms, and placed the Dicentrarchus species in the basal position. These data reinforce current placement of L. japonicus outside the Moronidae and provide a clear evolutionary character to define this family. The phylogeny of the Moronidae presented here also supports the hypothesis of an anadromous common ancestor to this family that gave rise to the North American estuarine and freshwater species. A series of tandem repeats previously reported in M. saxatilis was found in the control region of all Morone species between the mt-nd6 and mt-rnr1 genes, but not in either Dicentrarchus species, which reinforces the continued use of these two separate genera.
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Affiliation(s)
- E P Williams
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
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