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Davison A, Chowdhury M, Johansen M, Uliano-Silva M, Blaxter M. High heteroplasmy is associated with low mitochondrial copy number and selection against non-synonymous mutations in the snail Cepaea nemoralis. BMC Genomics 2024; 25:596. [PMID: 38872121 DOI: 10.1186/s12864-024-10505-w] [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: 03/01/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
Molluscan mitochondrial genomes are unusual because they show wide variation in size, radical genome rearrangements and frequently show high variation (> 10%) within species. As progress in understanding this variation has been limited, we used whole genome sequencing of a six-generation matriline of the terrestrial snail Cepaea nemoralis, as well as whole genome sequences from wild-collected C. nemoralis, the sister species C. hortensis, and multiple other snail species to explore the origins of mitochondrial DNA (mtDNA) variation. The main finding is that a high rate of SNP heteroplasmy in somatic tissue was negatively correlated with mtDNA copy number in both Cepaea species. In individuals with under ten mtDNA copies per nuclear genome, more than 10% of all positions were heteroplasmic, with evidence for transmission of this heteroplasmy through the germline. Further analyses showed evidence for purifying selection acting on non-synonymous mutations, even at low frequency of the rare allele, especially in cytochrome oxidase subunit 1 and cytochrome b. The mtDNA of some individuals of Cepaea nemoralis contained a length heteroplasmy, including up to 12 direct repeat copies of tRNA-Val, with 24 copies in another snail, Candidula rugosiuscula, and repeats of tRNA-Thr in C. hortensis. These repeats likely arise due to error prone replication but are not correlated with mitochondrial copy number in C. nemoralis. Overall, the findings provide key insights into mechanisms of replication, mutation and evolution in molluscan mtDNA, and so will inform wider studies on the biology and evolution of mtDNA across animal phyla.
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Affiliation(s)
- Angus Davison
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Mehrab Chowdhury
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Margrethe Johansen
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Marcela Uliano-Silva
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
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Ferrari RR, Ricardo PC, Dias FC, de Souza Araujo N, Soares DO, Zhou QS, Zhu CD, Coutinho LL, Arias MC, Batista TM. The nuclear and mitochondrial genome assemblies of Tetragonisca angustula (Apidae: Meliponini), a tiny yet remarkable pollinator in the Neotropics. BMC Genomics 2024; 25:587. [PMID: 38862915 PMCID: PMC11167848 DOI: 10.1186/s12864-024-10502-z] [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: 01/04/2024] [Accepted: 06/05/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND The field of bee genomics has considerably advanced in recent years, however, the most diverse group of honey producers on the planet, the stingless bees, are still largely neglected. In fact, only eleven of the ~ 600 described stingless bee species have been sequenced, and only three using a long-read (LR) sequencing technology. Here, we sequenced the nuclear and mitochondrial genomes of the most common, widespread and broadly reared stingless bee in Brazil and other neotropical countries-Tetragonisca angustula (popularly known in Brazil as jataí). RESULTS A total of 48.01 Gb of DNA data were generated, including 2.31 Gb of Pacific Bioscience HiFi reads and 45.70 Gb of Illumina short reads (SRs). Our preferred assembly comprised 683 contigs encompassing 284.49 Mb, 62.84 Mb of which (22.09%) corresponded to 445,793 repetitive elements. N50, L50 and complete BUSCOs reached 1.02 Mb, 91 contigs and 97.1%, respectively. We predicted that the genome of T. angustula comprises 17,459 protein-coding genes and 4,108 non-coding RNAs. The mitogenome consisted of 17,410 bp, and all 37 genes were found to be on the positive strand, an unusual feature among bees. A phylogenomic analysis of 26 hymenopteran species revealed that six odorant receptor orthogroups of T. angustula were found to be experiencing rapid evolution, four of them undergoing significant contractions. CONCLUSIONS Here, we provided the first nuclear and mitochondrial genome assemblies for the ecologically and economically important T. angustula, the fourth stingless bee species to be sequenced with LR technology thus far. We demonstrated that even relatively small amounts of LR data in combination with sufficient SR data can yield high-quality genome assemblies for bees.
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Affiliation(s)
- Rafael Rodrigues Ferrari
- Centro de Formação em Ciências Ambientais, Universidade Federal do Sul da Bahia, Porto Seguro, Brazil
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Paulo Cseri Ricardo
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Felipe Cordeiro Dias
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Dalliane Oliveira Soares
- Centro de Formação em Ciências Ambientais, Universidade Federal do Sul da Bahia, Porto Seguro, Brazil
| | - Qing-Song Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Sate Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Luiz Lehmann Coutinho
- Departamento de Ciências Animais, Universidade de São Paulo/ESALQ, Piracicaba, Brazil
| | - Maria Cristina Arias
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| | - Thiago Mafra Batista
- Centro de Formação em Ciências Ambientais, Universidade Federal do Sul da Bahia, Porto Seguro, Brazil.
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Li K, Yu SW, Hu H, Feng YF, Storey KB, Ma Y, Zhang JY, Yu DN. The Phylogenetic Relationship of Lamiinae (Coleoptera: Cerambycidae) Using Mitochondrial Genomes. Genes (Basel) 2023; 15:13. [PMID: 38275595 PMCID: PMC10815127 DOI: 10.3390/genes15010013] [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: 11/05/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Lamiinae is the largest subfamily of the Cerambycidae (longhorn beetles), with approximately 21,863 described species. Previous phylogenetic studies of Lamiinae showed that this subfamily was monophyletic, but the relationship between the tribes of Lamiinae is still controversial. Partial molecular data and species morphological characteristics are not sufficient to resolve species phylogenetic studies perfectly. At the same time, the full mitochondrial genome contains more comprehensive genetic data. Benefiting from the development of next-generation sequencing (NGS), mitochondrial genomes can be easily acquired and used as reliable molecular markers to investigate phylogenetic relationships within Cerambycidae. Using NGS technology, we obtained 11 mitochondrial genome sequences of Lamiinae species. Based on this newly generated mitochondrial genome dataset matrix, we reconstructed the phylogeny of Lamiinae. The Bayesian Inference and Maximum Likelihood analyses strongly support the monophyly of four tribes (Lamiini, Batocerini, Mesosini, and Saperdini), whereas the tribe Acanthocinini was identified as paraphyletic. Other mitochondrial structural features were also observed: the start codon in the nad1 gene of all 11 mitochondrial genomes is TTG; 17-22 bp intergenic spacers (IGS) with a 'TACTA' motif were found between trnS2 and nad1. Moreover, two long IGS were found in Mesosa myops and Batocera sp. Tandem repeats were found in the IGS of Batocera sp.
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Affiliation(s)
- Ke Li
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Sheng-Wu Yu
- Longquan Protection Center of Qianjiangyuan-Baishanzu National Park, Lishui 323700, China
| | - Hao Hu
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Yu-Feng Feng
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Yue Ma
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Yong Zhang
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Dan-Na Yu
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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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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Gorobeyko UV, Sheremetyeva IN, Kazakov DV, Guskov VY. A new type of tandem repeats in Myotis petax (Chiroptera, Vespertilionidae) mitochondrial control region. Mol Biol Rep 2023; 50:5137-5146. [PMID: 37115485 DOI: 10.1007/s11033-023-08468-4] [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: 12/31/2022] [Accepted: 04/18/2023] [Indexed: 04/29/2023]
Abstract
BACKGROUND Tandem repeats in mitochondrial DNA control region are known to different animal taxa, including bat species of the family Vespertilionidae. The long R1-repeats in the bat ETAS-domain are often presented in a variable copy number and may exhibit both inter-individual and intra-individual sequence diversity. The function of repeats in the control region is still unclear, but it has been shown that repetitive sequences in some animal groups (shrews, cats and sheep) may include parts of ETAS1 and ETAS2 conservative blocks of mitochondrial DNA. METHODS AND RESULTS Analysis of the control region sequences for 31 Myotis petax specimens allowed the identification of the inter-individual variability and clarification of the composition of the R1-repeats. The copy number of the R1-repeats varies from 4 to 7 in individuals. The specimens examined do not exhibit a size heteroplasmy previously described for Myotis species. The unusual short 30 bp R1-repeats have been detected in M. petax for the first time. The ten specimens from Amur Region and Primorsky Territory have one or two copies of these additional repeats. CONCLUSIONS It was determined that the R1-repeats in M. petax control region consist of parts of the ETAS1 and ETAS2 blocks. The origin of the additional repeats seems to be related to the 51 bp deletion in the central part of the R1-repeat unit and subsequent duplication. Comparison of repetitive sequences in the control region of closely-related Myotis species identified the occurrence of incomplete repeats also resulting from the short deletions, but distinct from additional repeats of M. petax.
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Affiliation(s)
- Uliana Vasilievna Gorobeyko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of Sciences, 159 Prospect Stoletiya St., Vladivostok, 690022, Russia.
| | - Irina Nikolaevna Sheremetyeva
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of Sciences, 159 Prospect Stoletiya St., Vladivostok, 690022, Russia
| | - Denis Vasilievich Kazakov
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 6 Volodarskogo St., Tyumen, 625003, Russia
| | - Valentin Yurievich Guskov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of Sciences, 159 Prospect Stoletiya St., Vladivostok, 690022, Russia
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Xu W, Lin S, Liu H. Mitochondrial genomes of five Hyphessobrycon tetras and their phylogenetic implications. Ecol Evol 2021; 11:12754-12764. [PMID: 34594536 PMCID: PMC8462149 DOI: 10.1002/ece3.8019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 11/10/2022] Open
Abstract
To date, the taxonomic status and phylogenetic affinities within Hyphessobrycon, even among other genera in Characidae, remain unclear. Here, we determined five new mitochondrial genomes (mitogenomes) of Hyphessobrycon species (H. elachys, H. flammeus, H. pulchripinnis, H. roseus, and H. sweglesi). The mitogenomes were all classical circular structures, with lengths ranging from 16,008 to 17,224 bp. The type of constitutive genes and direction of the coding strand that appeared in the mitogenomes were identical to those of other species in Characidae. The highest value of the Ka/Ks ratio within 13 protein-coding genes (PCGs) was found in ND2 with 0.83, suggesting that they were subject to purifying selection in the Hyphessobrycon genus. Comparison of the control region sequences among seven Hyphessobrycon fish revealed that repeat units differ in length and copy number across different species, which led to sharp differences in mitogenome sizes. Phylogenetic trees based on the 13 PCGs did not support taxonomic relationships, as the Hyphessobrycon fish mixed with those from other genera. These data were combined to explore higher level relationships within Characidae and could aid in the understanding of the evolution of this group.
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Affiliation(s)
- Wei Xu
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Shupeng Lin
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Hongyi Liu
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
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mtDNA Heteroplasmy: Origin, Detection, Significance, and Evolutionary Consequences. Life (Basel) 2021; 11:life11070633. [PMID: 34209862 PMCID: PMC8307225 DOI: 10.3390/life11070633] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is predominately uniparentally transmitted. This results in organisms with a single type of mtDNA (homoplasmy), but two or more mtDNA haplotypes have been observed in low frequency in several species (heteroplasmy). In this review, we aim to highlight several aspects of heteroplasmy regarding its origin and its significance on mtDNA function and evolution, which has been progressively recognized in the last several years. Heteroplasmic organisms commonly occur through somatic mutations during an individual’s lifetime. They also occur due to leakage of paternal mtDNA, which rarely happens during fertilization. Alternatively, heteroplasmy can be potentially inherited maternally if an egg is already heteroplasmic. Recent advances in sequencing techniques have increased the ability to detect and quantify heteroplasmy and have revealed that mitochondrial DNA copies in the nucleus (NUMTs) can imitate true heteroplasmy. Heteroplasmy can have significant evolutionary consequences on the survival of mtDNA from the accumulation of deleterious mutations and for its coevolution with the nuclear genome. Particularly in humans, heteroplasmy plays an important role in the emergence of mitochondrial diseases and determines the success of the mitochondrial replacement therapy, a recent method that has been developed to cure mitochondrial diseases.
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Lin ZJ, Wang X, Wang J, Tan Y, Tang X, Werren JH, Zhang D, Wang X. Comparative analysis reveals the expansion of mitochondrial DNA control region containing unusually high G-C tandem repeat arrays in Nasonia vitripennis. Int J Biol Macromol 2020; 166:1246-1257. [PMID: 33159940 DOI: 10.1016/j.ijbiomac.2020.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/01/2020] [Accepted: 11/02/2020] [Indexed: 11/25/2022]
Abstract
Insect mitochondrial DNA (mtDNA) ranges from 14 to 19 kbp, and the size difference is attributed to the AT-rich control region. Jewel wasps have a parasitoid lifestyle, which may affect mitochondria function and evolution. We sequenced, assembled, and annotated mitochondrial genomes in Nasonia and outgroup species. Gene composition and order are conserved within Nasonia, but they differ from other parasitoids by two large inversion events that were not reported before. We observed a much higher substitution rate relative to the nuclear genome and mitochondrial introgression between N. giraulti and N. oneida, which is consistent with previous studies. Most strikingly, N. vitripennis mtDNA has an extremely long control region (7665 bp), containing twenty-nine 217 bp tandem repeats and can fold into a super-cruciform structure. In contrast to tandem repeats commonly found in other mitochondria, these high-copy repeats are highly conserved (98.7% sequence identity), much longer in length (approximately 8 Kb), extremely GC-rich (50.7%), and CpG-rich (percent CpG 19.4% vs. 1.1% in coding region), resulting in a 23 kbp mtDNA beyond the typical size range in insects. These N. vitripennis-specific mitochondrial repeats are not related to any known sequences in insect mitochondria. Their evolutionary origin and functional consequences warrant further investigations.
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Affiliation(s)
- Zi Jie Lin
- Department of Chemistry, Columbus State University, Columbus, GA 31909, United States of America
| | - Xiaozhu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, United States of America
| | - Jinbin Wang
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yongjun Tan
- Department of Biology, College of Arts & Sciences, Saint Louis University, St. Louis, MO 63103, United States of America
| | - Xueming Tang
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY 14627, United States of America
| | - Dapeng Zhang
- Department of Biology, College of Arts & Sciences, Saint Louis University, St. Louis, MO 63103, United States of America
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, United States of America; HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States of America; Alabama Agricultural Experiment Station, Auburn University, Auburn, AL 36849, United States of America; Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, United States of America.
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Kornienko IV, Chebotarev DA, Makhotkin MA, Grigoriev VA, Ponomareva EN, Matishov GG. Termination of Replication and Mechanisms of Heteroplasmy in Sturgeon Mitochondrial DNA. Mol Biol 2019. [DOI: 10.1134/s0026893319010060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Turanov SV, Lee YH, Kartavtsev YP. Structure, evolution and phylogenetic informativeness of eelpouts (Cottoidei: Zoarcales) mitochondrial control region sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:264-272. [PMID: 29991298 DOI: 10.1080/24701394.2018.1484117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Control region (CR) is a major non-coding domain of mitochondrial DNA in vertebrates which contains the promoters for replication and transcription of mitochondrial genome along with the binding sites for metabolic machinery and, hence, is a vital element for the integrity of mitochondrial genome as a biological replicator. The origin and diversity of structural elements within CR have been intensively studied in recent years with the involvement of new diverse taxa. In this paper, we provide new data on the nucleotide and structural patterns of CR evolution and phylogenetic suitability among eelpouts (Cottoidei: Zoarcales). To achieve this, we carried out a comparative phylogenetic and structural analysis of 29 CR sequences belonging to the long shanny Stichaeus grigorjewi together with nine sequences of other eelpouts taxa representing four families in contrast to mitochondrial protein-coding fragments. The CR organization within S. grigorjewi, as well as in all other eelpouts, is consistent with the common three-domain structure known from most vertebrates. We found a hidden CR variation constrains on the landscape level and a lack of nucleotide saturation. Finally, our results demonstrate the advantage of the length variation in CR sequences for phylogenetic reconstructions among eelpouts.
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Affiliation(s)
- Sergei V Turanov
- a Laboratory of Molecular Systematic, A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch , Russian Academy of Sciences , Vladivostok , Russia.,b Chair of Water Biological Resources and Aquaculture, Far Eastern State Technical Fisheries University , Vladivostok , Russia
| | - Youn-Ho Lee
- c Laboratory of Marine Genomics, Korean Institute of Ocean Science and Technology , Ansan , Republic of Korea
| | - Yuri Ph Kartavtsev
- a Laboratory of Molecular Systematic, A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch , Russian Academy of Sciences , Vladivostok , Russia.,d Chair of Biodiversity and Marine Bioresources, Far Eastern Federal University , Vladivostok , Russia
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Qian L, Wang H, Yan J, Pan T, Jiang S, Rao D, Zhang B. Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes. BMC Genomics 2018; 19:354. [PMID: 29747572 PMCID: PMC5946542 DOI: 10.1186/s12864-018-4717-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 04/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake's mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes. RESULTS In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the OL was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNALeu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome. CONCLUSIONS The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.
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Affiliation(s)
- Lifu Qian
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Shanqun Jiang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.
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du Toit Z, du Plessis M, Dalton DL, Jansen R, Paul Grobler J, Kotzé A. Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae. BMC Genomics 2017; 18:746. [PMID: 28934931 PMCID: PMC5609056 DOI: 10.1186/s12864-017-4140-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 09/14/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck's ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). RESULTS The results indicate that the mitogenomes of the African pangolins are 16,558 bp for S. temminckii, 16,540 bp for S. gigantea, 16,649 bp for P. tetradactyla and 16,565 bp for P. tricuspis. Phylogenetic comparisons of the African pangolins indicated two lineages with high posterior probabilities providing evidence to support the classification of two genera; Smutsia and Phataginus. The total GC content between African pangolins was observed to be similar between species (36.5% - 37.3%). The most frequent codon was found to be A or C at the 3rd codon position. Significant variations in GC-content and codon usage were observed for several regions between African and Asian pangolin species which may be attributed to mutation pressure and/or natural selection. Lastly, a total of two insertions of 80 bp and 28 bp in size respectively was observed in the control region of the black-bellied pangolin which were absent in the other African pangolin species. CONCLUSIONS The current study presents reference mitogenomes of all four African pangolin species and thus expands on the current set of reference genomes available for six of the eight extant pangolin species globally and represents the first phylogenetic analysis with six pangolin species using full mitochondrial genomes. Knowledge of full mitochondrial DNA genomes will assist in providing a better understanding on the evolution of pangolins which will be essential for conservation genetic studies.
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Affiliation(s)
- Zelda du Toit
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
- Centre for Conservation Science, National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa
| | - Morné du Plessis
- Centre for Conservation Science, National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa
| | - Desiré L Dalton
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa.
- Centre for Conservation Science, National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa.
- Department of Zoology, University of Venda, Thohoyandou, South Africa.
| | - Raymond Jansen
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Antoinette Kotzé
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
- Centre for Conservation Science, National Zoological Gardens of South Africa, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
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13
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Ghiselli F, Milani L, Iannello M, Procopio E, Chang PL, Nuzhdin SV, Passamonti M. The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae). PeerJ 2017; 5:e3692. [PMID: 28848689 PMCID: PMC5571815 DOI: 10.7717/peerj.3692] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/25/2017] [Indexed: 12/30/2022] Open
Abstract
Despite the large number of animal complete mitochondrial genomes currently available in public databases, knowledge about mitochondrial genomics in invertebrates is uneven. This paper reports, for the first time, the complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus, also known as the European clam. Ruditapes decussatus is morphologically and ecologically similar to the Manila clam Ruditapes philippinarum, which has been recently introduced for aquaculture in the very same habitats of Ruditapes decussatus, and that is replacing the native species. Currently the production of the European clam is almost insignificant, nonetheless it is considered a high value product, and therefore it is an economically important species, especially in Portugal, Spain and Italy. In this work we: (i) assembled Ruditapes decussatus mitochondrial genome from RNA-Seq data, and validated it by Sanger sequencing; (ii) analyzed and characterized the Ruditapes decussatus mitochondrial genome, comparing its features with those of other venerid bivalves; (iii) assessed mitochondrial sequence polymorphism (SP) and copy number variation (CNV) of tandem repeats across 26 samples. Despite using high-throughput approaches we did not find evidence for the presence of two sex-linked mitochondrial genomes, typical of the doubly uniparental inheritance of mitochondria, a phenomenon known in ∼100 bivalve species. According to our analyses, Ruditapes decussatus is more genetically similar to species of the Genus Paphia than to the congeneric Ruditapes philippinarum, a finding that bolsters the already-proposed need of a taxonomic revision. We also found a quite low genetic variability across the examined samples, with few SPs and little variability of the sequences flanking the control region (Largest Unassigned Regions (LURs). Strikingly, although we found low nucleotide variability along the entire mitochondrial genome, we observed high levels of length polymorphism in the LUR due to CNV of tandem repeats, and even a LUR length heteroplasmy in two samples. It is not clear if the lack of genetic variability in the mitochondrial genome of Ruditapes decussatus is a cause or an effect of the ongoing replacement of Ruditapes decussatus with the invasive Ruditapes philippinarum, and more analyses, especially on nuclear sequences, are required to assess this point.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
| | - Emanuele Procopio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
| | - Peter L Chang
- Department of Biological Sciences, Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Sergey V Nuzhdin
- Department of Biological Sciences, Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy, Bologna, Italy
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14
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Zouros E, Pogson GH, Cook DI, Dadswell MJ. APPARENT SELECTIVE NEUTRALITY OF MITOCHONDRIAL DNA SIZE VARIATION: A TEST IN THE DEEP-SEA SCALLOP PLACOPECTEN MAGELLANICUS. Evolution 2017; 46:1466-1476. [PMID: 28568984 DOI: 10.1111/j.1558-5646.1992.tb01137.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/1991] [Accepted: 02/14/1992] [Indexed: 11/28/2022]
Abstract
Animal mitochondrial DNA (mtDNA) is believed to have evolved under intense selection for economy of the size of the molecule. Among scallop species mtDNA size may vary by a factor of two and among conspecific individuals by as much as 25%. We have examined the possibility that large mtDNA size differences may be associated with fitness in the deep sea scallop Placopecten magellanicus by comparing shell lengths of individuals with different copy numbers of a large mtDNA repeated sequence. Among juvenile cohorts of same age, shell length is known to be a good index of overall fitness in marine bivalves and it is shown here to be affected by differences in nuclear genotype, expressed as the degree of enzyme heterozygosity. We have observed no correlation between shell length and mtDNA length and interpreted this to mean that variation in the size of animal mtDNA is effectively neutral to the forces of natural selection acting on the individual. This type of mtDNA variation must, therefore, be explained in terms of biases in the molecular mechanisms causing expansion or contraction of the molecule, differential replication rates of mtDNA molecules of different size, and the stochastic assortment of mtDNA size classes among individuals.
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Affiliation(s)
- E Zouros
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, CANADA.,Department of Biology, University of Crete and Institute of Marine Biology of Crete, Iraklion, Crete, GREECE
| | - G H Pogson
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, CANADA
| | - D I Cook
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, CANADA
| | - M J Dadswell
- Department of Biology, Acadia University, Wolfville, Nova Scotia, BOP 1X0, CANADA
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15
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Turner TF, Trexler JC, Kuhn DN, Robison HW. LIFE-HISTORY VARIATION AND COMPARATIVE PHYLOGEOGRAPHY OF DARTERS (PISCES: PERCIDAE) FROM THE NORTH AMERICAN CENTRAL HIGHLANDS. Evolution 2017; 50:2023-2036. [DOI: 10.1111/j.1558-5646.1996.tb03589.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/1995] [Accepted: 11/30/1995] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas F. Turner
- Department of Biological Sciences; Florida International University; Miami Florida 33199
| | - Joel C. Trexler
- Department of Biological Sciences; Florida International University; Miami Florida 33199
| | - David N. Kuhn
- Department of Biological Sciences; Florida International University; Miami Florida 33199
| | - Henry W. Robison
- Department of Biology; Southern Arkansas University; Magnolia Arkansas 71753
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16
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Zhang HL, Ye F. Comparative Mitogenomic Analyses of Praying Mantises (Dictyoptera, Mantodea): Origin and Evolution of Unusual Intergenic Gaps. Int J Biol Sci 2017; 13:367-382. [PMID: 28367101 PMCID: PMC5370444 DOI: 10.7150/ijbs.17035] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/20/2016] [Indexed: 11/23/2022] Open
Abstract
Praying mantises are a diverse group of predatory insects. Although some Mantodea mitogenomes have been reported, a comprehensive comparative and evolutionary genomic study is lacking for this group. In the present study, four new mitogenomes were sequenced, annotated, and compared to the previously published mitogenomes of other Mantodea species. Most Mantodea mitogenomes share a typical set of mitochondrial genes and a putative control region (CR). Additionally, and most intriguingly, another large non-coding region (LNC) was detected between trnM and ND2 in all six Paramantini mitogenomes examined. The main section in this common region of Paramantini may have initially originated from the corresponding control region for each species, whereas sequence differences between the LNCs and CRs and phylogenetic analyses indicate that LNC and CR are largely independently evolving. Namely, the LNC (the duplicated CR) may have subsequently degenerated during evolution. Furthermore, evidence suggests that special intergenic gaps have been introduced in some species through gene rearrangement and duplication. These gaps are actually the original abutting sequences of migrated or duplicated genes. Some gaps (G5 and G6) are homologous to the 5' and 3' surrounding regions of the duplicated gene in the original gene order, and another specific gap (G7) has tandem repeats. We analysed the phylogenetic relationships of fifteen Mantodea species using 37 concatenated mitochondrial genes and detected several synapomorphies unique to species in some clades.
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Affiliation(s)
- Hong-Li Zhang
- School of Life Sciences, Datong University, Datong 037009, China
| | - Fei Ye
- College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
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17
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Tokishita SI, Shibuya H, Kobayashi T, Sakamoto M, Ha JY, Yokobori SI, Yamagata H, Hanazato T. Diversification of mitochondrial genome of Daphnia galeata (Cladocera, Crustacea): Comparison with phylogenetic consideration of the complete sequences of clones isolated from five lakes in Japan. Gene 2017; 611:38-46. [PMID: 28219780 DOI: 10.1016/j.gene.2017.02.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 01/20/2017] [Accepted: 02/13/2017] [Indexed: 02/02/2023]
Abstract
To characterize genetic diversity and gene flow among Daphnia galeata populations, the complete nucleotide (nt) sequences of the mitochondrial (mt) DNAs of D. galeata clones isolated from five lakes in Japan (Lakes Shirakaba, Suwa, Kizaki, Kasumigaura, and Biwa) were determined. Comparison of non-synonymous (amino acid altering) substitution rates with synonymous substitution rates of D. galeata mt protein-coding genes demonstrated that ATPase8 and COI genes were the most and least susceptible, respectively, to the evolutional forces selecting the aa substitutions. Several non-synonymous substitutions were found in ATPase8 and ATPase6 even in the comparison that no synonymous substitution was found. Comparison of the total number of nt variations among the mt DNAs suggested the phylogenetic relationship ((((Shirakaba/Suwa, Kizaki), Kasumigaura), Biwa), D. pulex). Maximum-likelihood analysis using the total nt sequences of mt protein-coding genes confirmed this relationship with bootstrap values higher than 98%. All the mtDNAs of the analyzed Japanese D. galeata clones contained a control region of essentially the same structure that is distinct from those of the previously reported European Daphnia species of the D. longispina complex. The two control regions of different structures spread among mtDNAs of the Japanese and European Daphnia species, respectively, probably after the divergence of the Japanese D. galeata under different selection pressures associated with their habitats.
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Affiliation(s)
- Shin-Ichi Tokishita
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
| | - Hiroyuki Shibuya
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Taku Kobayashi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Masaki Sakamoto
- Department of Environmental Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Jin-Yong Ha
- Department of Environmental Sciences, Faculty of Science, Shinshu University, Matsumoto Asahi 3-1-1, Nagano 390-8621, Japan
| | - Shin-Ichi Yokobori
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Hideo Yamagata
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Takayuki Hanazato
- Suwa Hydrobiological Station, Shinshu University, 5-2-4 Kogandori, Suwa, Nagano 392-0027, Japan
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18
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Zhang HL, Liu BB, Wang XY, Han ZP, Zhang DX, Su CN. Comparative Mitogenomic Analysis of Species Representing Six Subfamilies in the Family Tenebrionidae. Int J Mol Sci 2016; 17:ijms17060841. [PMID: 27258256 PMCID: PMC4926375 DOI: 10.3390/ijms17060841] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/22/2016] [Accepted: 05/24/2016] [Indexed: 11/16/2022] Open
Abstract
To better understand the architecture and evolution of the mitochondrial genome (mitogenome), mitogenomes of ten specimens representing six subfamilies in Tenebrionidae were selected, and comparative analysis of these mitogenomes was carried out in this study. Ten mitogenomes in this family share a similar gene composition, gene order, nucleotide composition, and codon usage. In addition, our results show that nucleotide bias was strongly influenced by the preference of codon usage for A/T rich codons which significantly correlated with the G + C content of protein coding genes (PCGs). Evolutionary rate analyses reveal that all PCGs have been subjected to a purifying selection, whereas 13 PCGs displayed different evolution rates, among which ATPase subunit 8 (ATP8) showed the highest evolutionary rate. We inferred the secondary structure for all RNA genes of Tenebrio molitor (Te2) and used this as the basis for comparison with the same genes from other Tenebrionidae mitogenomes. Some conserved helices (stems) and loops of RNA structures were found in different domains of ribosomal RNAs (rRNAs) and the cloverleaf structure of transfer RNAs (tRNAs). With regard to the AT-rich region, we analyzed tandem repeat sequences located in this region and identified some essential elements including T stretches, the consensus motif at the flanking regions of T stretch, and the secondary structure formed by the motif at the 3′ end of T stretch in major strand, which are highly conserved in these species. Furthermore, phylogenetic analyses using mitogenomic data strongly support the relationships among six subfamilies: ((Tenebrionidae incertae sedis + (Diaperinae + Tenebrioninae)) + (Pimeliinae + Lagriinae)), which is consistent with phylogenetic results based on morphological traits.
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Affiliation(s)
- Hong-Li Zhang
- School of Life Sciences, Datong University, Datong 037009, China.
| | - Bing-Bing Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi 030006, China.
| | - Xiao-Yang Wang
- College of Life Science, Shaanxi Normal University, Xi'an 710062, China.
| | - Zhi-Ping Han
- School of Life Sciences, Datong University, Datong 037009, China.
| | - Dong-Xu Zhang
- School of Life Sciences, Datong University, Datong 037009, China.
| | - Cai-Na Su
- School of Life Sciences, Datong University, Datong 037009, China.
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19
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Comparative Mitogenomics of the Genus Odontobutis (Perciformes: Gobioidei: Odontobutidae) Revealed Conserved Gene Rearrangement and High Sequence Variations. Int J Mol Sci 2015; 16:25031-49. [PMID: 26492246 PMCID: PMC4632788 DOI: 10.3390/ijms161025031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/09/2015] [Accepted: 10/14/2015] [Indexed: 01/01/2023] Open
Abstract
To understand the molecular evolution of mitochondrial genomes (mitogenomes) in the genus Odontobutis, the mitogenome of Odontobutis yaluensis was sequenced and compared with those of another four Odontobutis species. Our results displayed similar mitogenome features among species in genome organization, base composition, codon usage, and gene rearrangement. The identical gene rearrangement of trnS-trnL-trnH tRNA cluster observed in mitogenomes of these five closely related freshwater sleepers suggests that this unique gene order is conserved within Odontobutis. Additionally, the present gene order and the positions of associated intergenic spacers of these Odontobutis mitogenomes indicate that this unusual gene rearrangement results from tandem duplication and random loss of large-scale gene regions. Moreover, these mitogenomes exhibit a high level of sequence variation, mainly due to the differences of corresponding intergenic sequences in gene rearrangement regions and the heterogeneity of tandem repeats in the control regions. Phylogenetic analyses support Odontobutis species with shared gene rearrangement forming a monophyletic group, and the interspecific phylogenetic relationships are associated with structural differences among their mitogenomes. The present study contributes to understanding the evolutionary patterns of Odontobutidae species.
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20
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Wang X, Liu N, Zhang H, Yang XJ, Huang Y, Lei F. Extreme variation in patterns of tandem repeats in mitochondrial control region of yellow-browed tits (Sylviparus modestus, Paridae). Sci Rep 2015; 5:13227. [PMID: 26288099 PMCID: PMC4541255 DOI: 10.1038/srep13227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 07/21/2015] [Indexed: 11/09/2022] Open
Abstract
To investigate the evolutionary pattern and origins of tandem repeats in the mitochondrial control region of the yellow-browed tit (Sylviparus modestus), the control region and another four mitochondrial loci from fifteen individuals were analyzed. A 117-bp tandem repeat unit that repeated once, twice or three times in different individuals was found, and a rarely reported arrangement for this tandem repeats region that a 5' imperfect copy at its downstream and a 3' imperfect copy at its upstream was observed. The haplotype network, phylogenetic trees, and ancestral state reconstruction of the combined dataset of five loci suggested multiple origins of the same repeat number. The turnover model via slipped-strand mispairing was introduced to interpret the results, because mispairing occurred so frequently that multiple origins of certain repeat number were observed. Insertion via recombination should be a better explanation for the origin of this tandem repeat unit, considering characteristics of the combined sequence of the 3' and 5' imperfect copy, including identification of its homolog in other passerines and its predicted secondary structure.
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Affiliation(s)
- Xiaoyang Wang
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Sciences, Shaanxi Normal University, No. 199, South Chang'an Road, Xi'an 710062, China
| | - Nian Liu
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Sciences, Shaanxi Normal University, No. 199, South Chang'an Road, Xi'an 710062, China
| | - Hongli Zhang
- College of Life Science, Datong University, Xingyun Street, Datong 037009, China
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32, Jiaochang East Road, Kunming 650223, China
| | - Yuan Huang
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Sciences, Shaanxi Normal University, No. 199, South Chang'an Road, Xi'an 710062, China
| | - Fumin Lei
- 1] Co-Innovation Center for Qinba regions' sustainable development, College of Life Sciences, Shaanxi Normal University, No. 199, South Chang'an Road, Xi'an 710062, China [2] Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
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21
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Mu X, Wang X, Liu Y, Song H, Liu C, Gu D, Wei H, Luo J, Hu Y. An unusual mitochondrial genome structure of the tonguefish, Cynoglossus trigrammus: Control region translocation and a long additional non-coding region inversion. Gene 2015; 573:216-24. [PMID: 26187073 DOI: 10.1016/j.gene.2015.07.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 10/23/2022]
Abstract
Flatfishes (Pleuronectiformes) exhibit different types of large-scale gene rearrangements. In the present study, the mitochondrial (mt) genome (18,369bp) of a tonguefish, Cynoglossus trigrammus, was determined using de novo mitochondrion genome sequencing. Compared with other flatfishes, the mt genome of C. trigrammus revealed distinct mitogenome architectures that primarily included two striking findings: 1) insertion of an additional long non-coding region (1647bp) making it the second largest genome length among Pleuronectiformes and 2) the translocation of the control region. The reconstructed phylogenetic tree based on 13 mt protein-coding gene sequences recovered the monophyletic suborder Pleuronectoidei and the family Cynoglossidae. These data provide useful information for a better understanding of the mitogenomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.
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Affiliation(s)
- Xidong Mu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xuejie Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yi Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Hongmei Song
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Chao Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Dangen Gu
- Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Hui Wei
- Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Jianren Luo
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yinchang Hu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
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22
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Hu QX, Fan Y, Xu L, Pang W, Wang S, Zheng YT, Lv LB, Yao YG. Analysis of the complete mitochondrial genome and characterization of diverse NUMTs of Macaca leonina. Gene 2015; 571:279-85. [PMID: 26151895 DOI: 10.1016/j.gene.2015.06.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 06/08/2015] [Accepted: 06/26/2015] [Indexed: 11/19/2022]
Abstract
As a non-human primate, the pig-tailed macaque has received wide attention because it can be infected by HIV-1. In this study, we determined the complete mtDNA sequence of the northern pig-tailed macaque (Macaca leonina). Unexpectedly, during the amplification of the mtDNA control region (D-loop region) we observed several D-loop-like sequences, which were NUMTs (nuclear mitochondrial sequences) and a total of 14 D-loop-like NUMT haplotypes were later identified in five individuals. The neighbor-joining tree and estimated divergence time based on these D-loop-like NUMT sequences of M. leonina provide some insights into the understanding of the evolutionary history of NUMTs. D-loop-like haplotypes G and H, which also exist in the nuclear genome of mulatta, appear to have been translocated into the nuclear genome before the divergence of M. mulatta and M. leonina. The other D-loop-like NUMT haplotypes were translocated into the nuclear genome of M. leonina after the divergence of the two species. Later sequence conversion was predicted to occur among these 14 D-loop-like NUMT haplotypes. The overall structure of the mtDNA of M. leonina was found to be similar to that seen in other mammalian mitochondrial genomes. Phylogenetic analysis based on the maximum likelihood method shows M. leonina clustered with Macaca silenus among the analyzed mammalian species.
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Affiliation(s)
- Qiu-Xiang Hu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yu Fan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ling Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Shuang Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Long-Bao Lv
- Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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Gong L, Shi W, Si LZ, Wang ZM, Kong XY. The complete mitochondrial genome of peacock sole Pardachirus pavoninus (Pleuronectiformes: Soleidae) and comparative analysis of the control region among 13 soles. Mol Biol 2015. [DOI: 10.1134/s0026893315030061] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ma Q, Wu B, Li J, Song Z. Complete mitochondrial genome of Ptychobarbus kaznakovi (Teleostei: Cypriniformes: Cyprinidae), and repetitive sequences in the D-loop. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1683-4. [PMID: 25238112 DOI: 10.3109/19401736.2014.958727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial DNA genome of Ptychobarbus kaznakovi was sequenced and characterized. The genome is 16,842 bp in length. Similar with most teleosts, it has two ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and one displacement loop (D-loop) region. Conserved sequence blocks, including ETAS, CSB-B, D, E, F, and CSB1-3, were identified in the D-loop, which is similar to other species in Cypriniformes. Nevertheless, a 55 bp tandem repeat array was also identified at 3' end of the D-loop, which is the first finding in Schizothoracinae. Phylogenetic analysis showed that the species of Ptychobarbus (P. dipogon and P. kaznakovi) formed a monophyletic group and represented close relationship to the species without scales in Schizothoracinae.
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Affiliation(s)
- Qingzhan Ma
- a Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife , College of Life Sciences, Sichuan University , Chengdu , China and
| | - Bo Wu
- a Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife , College of Life Sciences, Sichuan University , Chengdu , China and
| | - Jiuxuan Li
- a Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife , College of Life Sciences, Sichuan University , Chengdu , China and
| | - Zhaobin Song
- a Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife , College of Life Sciences, Sichuan University , Chengdu , China and.,b Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education , College of Life Sciences, Sichuan University , Chengdu , China
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Merker S, Thomas S, Völker E, Perwitasari-Farajallah D, Feldmeyer B, Streit B, Pfenninger M. Control region length dynamics potentially drives amino acid evolution in tarsier mitochondrial genomes. J Mol Evol 2014; 79:40-51. [PMID: 25008552 DOI: 10.1007/s00239-014-9631-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/19/2014] [Indexed: 11/25/2022]
Abstract
Patterns and processes of molecular evolution critically influence inferences in phylogeny and phylogeography. Within primates, a shift in evolutionary rates has been identified as the rationale for contrasting findings from mitochondrial and nuclear DNA studies as to the position of Tarsius. While the latter now seems settled, we sequenced complete mitochondrial genomes of three Sulawesi tarsiers (Tarsius dentatus, T. lariang, and T. wallacei) and analyzed substitution rates among tarsiers and other primates to infer driving processes of molecular evolution. We found substantial length polymorphism of the D-loop within tarsier individuals, but little variation of predominant lengths among them, regardless of species. Length variation was due to repetitive elements in the CSB domain-minisatellite motifs of 35 bp length and microsatellite motifs of 6 bp length. Amino acid evolutionary rates were second highest among major primate taxa relative to nucleotide substitution rates. We observed many radical possibly function-altering amino acid changes that were rarely driven by positive selection and thus potentially slightly deleterious or neutral. We hypothesize that the observed pattern of an increased amino acid evolutionary rate in tarsier mitochondrial genomes may be caused by hitchhiking of slightly deleterious mutations with favored D-loop length variants selected for maximizing replication success within the cell or the mitochondrion.
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Affiliation(s)
- Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Rosenstein 1, 70191, Stuttgart, Germany,
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Padhi A. Geographic variation within a tandemly repeated mitochondrial DNA D-loop region of a North American freshwater fish, Pylodictis olivaris. Gene 2014; 538:63-8. [PMID: 24440244 DOI: 10.1016/j.gene.2014.01.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 01/04/2014] [Accepted: 01/08/2014] [Indexed: 10/25/2022]
Abstract
The present study reports the distribution of a 35-bp mitochondrial DNA (mtDNA) D-loop tandemly repeated sequence in the populations of a North American freshwater catfish, Pylodictis olivaris, and the important role of a past geological event in the phylogeographic pattern of this species. A total of 330 individuals of flathead catfish, representing 34 drainages throughout the species' native range in the United States, were collected. While more than 70% of individuals sampled from the Southeastern Gulf Coast drainages were characterized by the presence of a 35-bp mtDNA D-loop tandem repeat proximal to the 5' end, more than 95% of samples from the Mississippi River and its tributaries, as well as from the drainages of the Southwest Gulf Coast region, lack this tandem repeat. Concomitantly, phylogenetic analyses revealed the existence of two distinct matrilineal lineages (lineage I and II) of P. olivaris, which were estimated to have diverged from a common ancestor sometime between 0.70 and 2.05myr ago. While one lineage is comprised of samples from the Mississippi River and its tributaries and rivers draining to the Southwest Gulf Coast, the other lineage is comprised of samples from the Southeastern Gulf Coast drainages. Each lineage also has two sub-lineages, which also showed geographic specificity.
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Affiliation(s)
- Abinash Padhi
- Department of Biological Sciences, University of Tulsa, 800 S. Tucker Dr., OK 74104, USA.
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27
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Ba H, Wu L, Liu Z, Li C. An examination of the origin and evolution of additional tandem repeats in the mitochondrial DNA control region of Japanese sika deer (Cervus Nippon). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:276-81. [PMID: 24621225 DOI: 10.3109/19401736.2014.892077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Tandem repeat units are only detected in the left domain of the mitochondrial DNA control region in sika deer. Previous studies showed that Japanese sika deer have more tandem repeat units than its cousins from the Asian continent and Taiwan, which often have only three repeat units. To determine the origin and evolution of these additional repeat units in Japanese sika deer, we obtained the sequence of repeat units from an expanded dataset of the control region from all sika deer lineages. The functional constraint is inferred to act on the first repeat unit because this repeat has the least sequence divergence in comparison to the other units. Based on slipped-strand mispairing mechanisms, the illegitimate elongation model could account for the addition or deletion of these additional repeat units in the Japanese sika deer population. We also report that these additional repeat units could be occurring in the internal positions of tandem repeat regions, possibly via coupling with a homogenization mechanism within and among these lineages. Moreover, the increased number of repeat units in the Japanese sika deer population could reflect a balance between mutation and selection, as well as genetic drift.
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Affiliation(s)
- Hengxing Ba
- a Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China .,b State Key Laboratory for Molecular Biology of Special Economical Animals , Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China , and
| | - Lang Wu
- c Center for Clinical and Translational Science, Mayo Clinic , Rochester , MN , USA
| | - Zongyue Liu
- a Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China .,b State Key Laboratory for Molecular Biology of Special Economical Animals , Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China , and
| | - Chunyi Li
- a Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China .,b State Key Laboratory for Molecular Biology of Special Economical Animals , Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China , and
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Liu W, Yao YF, Yu Q, Ni QY, Zhang MW, Yang JD, Mai MM, Xu HL. Genetic variation and phylogenetic relationship between three serow species of the genus Capricornis based on the complete mitochondrial DNA control region sequences. Mol Biol Rep 2013; 40:6793-802. [PMID: 24057256 DOI: 10.1007/s11033-013-2796-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 09/14/2013] [Indexed: 11/24/2022]
Abstract
The molecular evidence of phylogenetic status regarding the Formosan serow (Capricornis swinhoei) is not robust and little is known about the genetic diversity of the Sumatran serow (Capricornis sumatraensis), which partly is due to the hardness in sample collection. Here we determined the sequences of the complete mitochondrial DNA control region (1,014 bp) of 19 Sumatran-serow individuals. Nine new haplotypes were defined based on 78 variable sites. Combined analysis with other 32 haplotypes downloaded from the public database, including 1 Sumatran-serow, 11 Formosan-serow and 20 Japanese-serow (Capricornis crispus) haplotypes, a relatively high level of nucleotide diversity was first observed in Sumatran serow (π = 0.0249). By comparative analysis with structural consensus sequences from other mammals, we have identified central, left and right domains and depicted the putative functional structure, including extend termination associated sequences and conserve sequence blocks, in mtDNA control region. The alignment of mtDNA control region revealed that both Sumatran and Japanese serow have two tandem repeats (TRs), but three TRs in Formosan serow. Phylogenetic analyses revealed that the Formosan serow is distinct species with the Japanese serow, but a sister group with the Sumatran serow. The divergence time estimated among three serow species revealed that Pleistocene climate changes and the uplift of Qinghai-Tibetan plateau might play an important role in the genetic differentiation of the serows. These results mainly provide the convinced evidence on the genetic relationship between three serow species.
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Affiliation(s)
- Wei Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, 625014, People's Republic of 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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He XL, Ding CQ, Han JL. Lack of Structural Variation but Extensive Length Polymorphisms and Heteroplasmic Length Variations in the Mitochondrial DNA Control Region of Highly Inbred Crested Ibis, Nipponia nippon. PLoS One 2013; 8:e66324. [PMID: 23805212 PMCID: PMC3689774 DOI: 10.1371/journal.pone.0066324] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 05/03/2013] [Indexed: 01/21/2023] Open
Abstract
The animal mitochondrial DNA (mtDNA) length polymorphism and heteroplasmy are accepted to be universal. Here we report the lack of structural variation but the presence of length polymorphism as well as heteroplasmy in mtDNA control region of an endangered avian species - the Crested Ibis (Nipponia nippon). The complete control region was directly sequenced while the distribution pattern and inheritance of the length variations were examined using both direct sequencing and genotyping of the PCR fragments from captive birds with pedigrees, wild birds and a historical specimen. Our results demonstrated that there was no structural variation in the control region, however, different numbers of short tandem repeats with an identical motif of CA3CA2CA3 at the 3'-end of the control region determined the length polymorphisms among and heteroplasmy within individual birds. There were one to three predominant fragments in every bird; nevertheless multiple minor fragments coexist in all birds. These extremely high polymorphisms were suggested to have derived from the 'replication slippage' of a perfect microsatellite evolution following the step-wise mutational model. The patterns of heteroplasmy were found to be shifted between generations and among siblings but rather stable between blood and feather samples. This study provides the first evidence of a very extensive mtDNA length polymorphism and heteroplasmy in the highly inbred Crested Ibis which carries an mtDNA genome lack of structural genetic diversity. The analysis of pedigreed samples also sheds light on the transmission of mtDNA length heteroplasmy in birds following the genetic bottleneck theory. Further research focusing on the generation and transmission of particular mtDNA heteroplasmy patterns in single germ line of Crested Ibis is encouraged by this study.
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Affiliation(s)
- Xue-Lian He
- College of Nature Conservation, Beijing Forestry University, Beijing, China
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chang-Qing Ding
- College of Nature Conservation, Beijing Forestry University, Beijing, China
- * E-mail: (CQD); (JLH)
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- * E-mail: (CQD); (JLH)
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Pause-melting misalignment: a novel model for the birth and motif indel of tandem repeats in the mitochondrial genome. BMC Genomics 2013; 14:103. [PMID: 23414101 PMCID: PMC3599147 DOI: 10.1186/1471-2164-14-103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 02/11/2013] [Indexed: 01/11/2023] Open
Abstract
Background Tandem repeats (TRs) in the mitochondrial (mt) genome control region have been documented in a wide variety of vertebrate species. The mechanism by which repeated tracts originate and undergo duplication and deletion, however, remains unclear. Results We analyzed DNA sequences of mt genome TRs (mtTRs) in the ridged-eye flounder (Pleuronichthys cornutus), and characterized DNA sequences of mtTRs from other vertebrates using the data available in GenBank. Tandem repeats are concentrated in the control regions; however, we found approximately 16.6% of the TRs elsewhere in the mt genome. The flounder mtTRs possess three motif types with hypervariable characteristics at the 3′ end of the control region (CR). Conclusion Based on our analysis of this larger dataset of mtTR sequences, we propose a novel model of Pause Melting Misalignment (PMM) to describe the birth and motif indel of tandem repeats. PMM is activated during a pause event in mitochondrial replication in which a dynamic competition between the nascent (N) heavy strand and the displaced (D) heavy strand may lead to the melting of the N-strand from the template (T) light strand. When mispairing occurs during rebinding of the N-strand, one or several motifs can be inserted or deleted in both strands during the next round of mt-replication or repair. This model can explain the characteristics of TRs in available vertebrate mt genomes.
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Limited phylogenetic distribution of a long tandem-repeat cluster in the mitochondrial control region in Bubo (Aves, Strigidae) and cluster variation in Blakiston's fish owl (Bubo blakistoni). Mol Phylogenet Evol 2012; 66:889-97. [PMID: 23211719 DOI: 10.1016/j.ympev.2012.11.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 11/15/2012] [Accepted: 11/20/2012] [Indexed: 11/23/2022]
Abstract
To investigate the phylogenetic position of Blakiston's fish owl (Bubo blakistoni), we sequenced the mitochondrial (mt) DNA control region and cytochrome b (cyt b) for nine Bubo species. Maximum-likelihood analyses of combined control region and cyt b sequences, and cyt b sequences alone, showed that species formerly placed in genus Ketupa comprise a monophyletic group. Unexpectedly, we discovered a long cluster of 20-25 tandem repeat units 77 or 78bp long in the third control region domain in four of the nine Bubo species for which the control region was sequenced (B. blakistoni, B. flavipes, and B. ketupu in the Ketupa clade; B. lacteus), leading to overall control region lengths of 3.0-3.8kpb estimated from agarose gel electrophoresis. The control region in B. lacteus is the longest (3.8kbp) reported to date in vertebrates. Sequencing of eight repeat units at each end of the cluster in 20 B. blakistoni individuals detected several types of repeat units 77 or 78bp long, and six patterns in the order of unit types. The occurrence of a repeat cluster in all three species examined in the Ketupa clade suggests their common ancestor also had a cluster, whereas a maximum parsimony tree showed repeat-unit types grouping by species, rather than by paralog groups, suggesting independent origins of the clusters. We reconcile these results with a turnover model, in which the range in cluster-length variation and unit types at the 5' end are hypothetically functionally constrained by the protein-binding function of the control region, but otherwise there is a continual turnover of units in evolutionary time, with new unit types arising through mutations, proliferating by duplication of single and double repeat blocks, and being lost through deletion. Estimated free energies for reconstructed secondary structures of single and especially pairs of repeat units were higher than for homologous single-unit blocks in species lacking a repeat cluster, supporting slipped-strand mispairing as the mechanism of cluster turnover.
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Abstract
The hallmarks of animal mitochondrial DNA (mtDNA) are a rapid rate of sequence evolution, a small genome carrying the same set of homologous genes, maternal inheritance and lack of recombination. Over the past few years, a variety of different observations has challenged these accepted notions of mitochondrial biology. Notable examples include evidence for variable rates of mtDNA sequence evolution among taxa, evidence for large and variable mitochondrial genome sizes in certain groups, and a growing number of cases in metazoans of 'paternal leakage' in the inheritance of mtDNA. Several recent studies have uncovered different lines of evidence suggesting that an organism's thermal habit, or metabolic rate, can influence the evolution of mtDNA.
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Affiliation(s)
- D M Rand
- David Rand is at the Dept of Ecology and Evolutionary Biology, Box G-W, Brown University, Providence, RI 02912, USA
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34
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Poortvliet M, Hoarau G. The complete mitochondrial genome of the Spinetail Devilray,Mobula japanica. ACTA ACUST UNITED AC 2012; 24:28-30. [DOI: 10.3109/19401736.2012.716051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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35
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Terencio ML, Schneider CH, Gross MC, Feldberg E, Porto JIR. Structure and organization of the mitochondrial DNA control region with tandemly repeated sequence in the Amazon ornamental fish. ACTA ACUST UNITED AC 2012; 24:74-82. [PMID: 22954310 DOI: 10.3109/19401736.2012.717934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Tandemly repeated sequences are a common feature of vertebrate mitochondrial DNA control regions. However, questions still remain about their mode of evolution and function. To better understand patterns of variation in length and to explore the existence of previously described domain, we have characterized the control region structure of the Amazonian ornamental fish Nannostomus eques and Nannostomus unifasciatus. The control region ranged from 1121 to 1142 bp in length and could be separated into three domains: the domain associated with the extended terminal associated sequences, the central conserved domain, and the conserved sequence blocks domain. In the first domain, we encountered a sequence repeated 10 times in tandem (variable number tandem repeat (VNTR)) that could adopt an "inverted repetitions" type structural conformation. The results suggest that the VNTR pattern encountered in both N. eques and N. unifasciatus is consistent with the prerequisites of the illegitimate elongation model in which the unequal pairing of the chains near the 5'-end of the control region favors the formation of repetitions.
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Affiliation(s)
- Maria Leandra Terencio
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Pesquisas em Biologia Aquática, Av. André Araújo, 2936, Petrópolis, 69011-970 Manaus, AM, Brazil.
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Chen M, Yao R, Su JF, Wang H, Li YP, Liu YQ, Jiang XF, Qin L, Wang ZD, Lu C. Length polymorphism and structural organization of the A+T-rich region of mitochondrial DNA in Antheraea pernyi (Lepidoptera: Saturniidae). BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Terencio ML, Schneider CH, Porto JIR. Molecular signature of the D-loop in the brown pencilfish Nannostomus eques (Characiformes, Lebiasinidae) reveals at least two evolutionary units in the Rio Negro basin, Brazil. JOURNAL OF FISH BIOLOGY 2012; 81:110-124. [PMID: 22747807 DOI: 10.1111/j.1095-8649.2012.03320.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The genetic variability of the brown pencilfish Nannostomus eques was studied, based on an analysis of sequences from the control region (1084 bp) of mitochondrial (mt)DNA in 125 individuals collected from eight tributaries along the upper (Açaituba, Miuá, Jaradi and Arixanã), middle (Demini), and lower (Jacundá, Maguari and Catalão) Rio Negro (Brazil). Phylogenetic inferences using mtDNA data from N. eques revealed two evolutionary units. Genetic distance between them ranged from 5.5 to 8.3% and differed by 8.5-11.8% from the sister species pencilfish Nannostomus unifasciatus. The time of divergence between the two evolutionary units was estimated to be the Middle Pliocene (c. 2.99 million years before present). Population genetic analysis (DNA polymorphism, AMOVA and Mantel test) showed high haplotype diversity (HD, >0.90) in each evolutionary unit, a strong population genetic structure in the Demini River that formed a monophyletic group and a correlation between genetic divergence and geographical distance in only one of these units (evolutionary unit 1). On the basis of molecular data, the rapids and waterfalls near São Gabriel da Cachoeira (Upper Rio Negro) were the main barriers to gene flow within evolutionary unit 1 in some localities. The emergences of the Branco River and the Anavilhanas Archipelago were apparently responsible for the discrepancy in distribution of the two evolutionary units, except at Jacundá, where the evolutionary units were sympatric. In view of the differences between the evolutionary units, N. eques cannot be treated as a single stock in the Rio Negro basin. These results may have important implications for the fishery management of this ornamental fish.
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Affiliation(s)
- M L Terencio
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Pesquisas em Biologia Aquática, Av. André Araújo, 2936, Petrópolis, Manaus, Amazonas 69011-970, Brasil.
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The mitogenome of Gammarus duebeni (Crustacea Amphipoda): A new gene order and non-neutral sequence evolution of tandem repeats in the control region. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2012; 7:201-11. [DOI: 10.1016/j.cbd.2012.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/21/2012] [Accepted: 02/27/2012] [Indexed: 11/23/2022]
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Damas J, Carneiro J, Gonçalves J, Stewart JB, Samuels DC, Amorim A, Pereira F. Mitochondrial DNA deletions are associated with non-B DNA conformations. Nucleic Acids Res 2012; 40:7606-21. [PMID: 22661583 PMCID: PMC3439893 DOI: 10.1093/nar/gks500] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial DNA (mtDNA) deletions are a primary cause of mitochondrial disease and are believed to contribute to the aging process and to various neurodegenerative diseases. Despite strong observational and experimental evidence, the molecular basis of the deletion process remains obscure. In this study, we test the hypothesis that the primary cause of mtDNA vulnerability to breakage resides in the formation of non-B DNA conformations, namely hairpin, cruciform and cloverleaf-like elements. Using the largest database of human mtDNA deletions built thus far (753 different cases), we show that site-specific breakage hotspots exist in the mtDNA. Furthermore, we discover that the most frequent deletion breakpoints occur within or near predicted structures, a result that is supported by data from transgenic mice with mitochondrial disease. There is also a significant association between the folding energy of an mtDNA region and the number of breakpoints that it harbours. In particular, two clusters of hairpins (near the D-loop 3′-terminus and the L-strand origin of replication) are hotspots for mtDNA breakage. Consistent with our hypothesis, the highest number of 5′- and 3′-breakpoints per base is found in the highly structured tRNA genes. Overall, the data presented in this study suggest that non-B DNA conformations are a key element of the mtDNA deletion process.
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Affiliation(s)
- Joana Damas
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Rua Dr Roberto Frias s/n, 4200-465 Porto, Portugal
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40
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Sindičić M, Gomerčić T, Galov A, Polanc P, Huber Đ, Slavica A. Repetitive sequences in Eurasian lynx (Lynx lynx L.) mitochondrial DNA control region. ACTA ACUST UNITED AC 2012; 23:201-7. [DOI: 10.3109/19401736.2012.668894] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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41
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Wang Y, Guo R, Li H, Zhang X, Du J, Song Z. The complete mitochondrial genome of the Sichuan taimen (Hucho bleekeri): Repetitive sequences in the control region and phylogenetic implications for Salmonidae. Mar Genomics 2011; 4:221-8. [DOI: 10.1016/j.margen.2011.06.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/04/2011] [Accepted: 06/11/2011] [Indexed: 11/17/2022]
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42
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Wang H, Zhang S, Xiao G, Liu B. Complete mtDNA of the Meretrix lamarckii (Bivalvia: Veneridae) and molecular identification of suspected M. lamarckii based on the whole mitochondrial genome. Mar Genomics 2011; 4:263-71. [PMID: 22118638 DOI: 10.1016/j.margen.2011.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 06/23/2011] [Accepted: 06/28/2011] [Indexed: 10/17/2022]
Abstract
The complete nucleotide sequence of the mitochondrial genome of the clam Meretrix lamarckii (Bivalvia: Veneridae) was determined. It contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a non-coding region. We also sequenced the mitochondrial genome of the sample collected from Zhejiang province, which showed morphologic discrepancy compared with classic M. lamarckii. Comparison of two complete mitochondrial DNA data demonstrated that the two sequences have a similarity as high as 99%. The complete mitochondrial genome of M. lamarckii from Hainan is 20,965nts in length and the sample from Zhejiang is 21,209nts in length. We therefore record one new locality for the M. lamarckii and thus the geographic distribution of M. lamarckii stretches from the south coast of Guangdong China to more north, arriving at the south coast of Zhejiang China.
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Affiliation(s)
- Hongxia Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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43
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Comparison research and phylogenetic implications of mitochondrial control regions in four soft-shelled turtles of Trionychia (Reptilia, Testudinata). Genes Genomics 2010. [DOI: 10.1007/s13258-010-0015-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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44
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Okada K, Yamazaki Y, Yokobori S, Wada H. Repetitive sequences in the lamprey mitochondrial DNA control region and speciation of Lethenteron. Gene 2010; 465:45-52. [PMID: 20599597 DOI: 10.1016/j.gene.2010.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2010] [Revised: 06/11/2010] [Accepted: 06/18/2010] [Indexed: 11/16/2022]
Abstract
The sequence of the mitochondrial DNA control region was examined in four species of lamprey in the genus Lethenteron. The 3' half of the control region contains highly variable repeat sequences, showing variation in both copy number and nucleotide sequence, even within local populations. Detailed analyses of the sequences of the repeats allowed us to deduce that slipped-strand mispairing during DNA replication, accompanied by a high rate of substitutions and indels, was primarily responsible for the variation in the repeats. We also found that some cases might be better explained by gene conversion, due to intermolecular recombination. Based on the observed variable nature of the mitochondrial control region, we searched for molecular markers in mitochondrial DNA, because there are few fixed genetic markers for distinguishing between Lethenteron japonicum and Lethenteron kessleri. However, we found no reliable markers in the control region. No fixed substitution was observed in intron sequences of the nuclear gene SoxD. Thus, these two species likely diverged quite recently and may possess only a limited number of fixed genetic loci.
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Affiliation(s)
- Kazunori Okada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
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45
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Species delineation in Pampus (Perciformes) and the phylogenetic status of the Stromateoidei based on mitogenomics. Mol Biol Rep 2010; 38:1103-14. [DOI: 10.1007/s11033-010-0207-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 06/11/2010] [Indexed: 11/26/2022]
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46
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Yan J, Liu L, Liu S, Guo X, Liu Y. Comparative analysis of mitochondrial control region in polyploid hybrids of red crucian carp (Carassius auratus) x blunt snout bream (Megalobrama amblycephala). FISH PHYSIOLOGY AND BIOCHEMISTRY 2010; 36:263-272. [PMID: 18815893 DOI: 10.1007/s10695-008-9251-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 07/21/2008] [Indexed: 05/26/2023]
Abstract
The entire sequences of the mitochondrial (mt)DNA control region (CR) and portions of its flanking genes in the red crucian carp (RC) and blunt snout bream (BSB) as well as their polyploid hybrids (3nRB, 4nRB and 5nRB) were determined and subjected to a comparative analysis. The mtDNA-CRs of these five fish species ranged from 923 to 937 bp in length, they had the same flanking gene arrangement as other vertebrates and the pattern of nucleotide substitution bias was also similar to that in other vertebrates. Our data are consistent with the viewpoint of three domains [extended terminal associated sequence (ETAS domain), central conserved sequence block domain and conserved sequence block (CSB) domain] within the mtDNA-CR of mammals. On the basis our comparative analysis of the mtDNA-CRs of these five fish species, we were able to identify the consensus sequences of functional conserved units, including the ETAS, CSB-F, CSB-D, CSB-E, CSB1, CSB2 and CSB3 and putative promoter. The percentage of variable nucleotide positions (41.98%) in the central domain was lower than those in the ETAS and conserved domain (71.70 and 47.12%, respectively), suggesting that the central domain was the most conserved part of the mtDNA-CR. These results provide useful and important information for the further study of mtDNA-CR structure in fish. The sequence similarities of mtDNA-CR among the 3nRB, 4nRB, 5nRB hybrids and their respective female parents were higher than those among the 3nRB, 4nRB, 5nRB hybrids and their respective male parents, providing the direct evidence of stringent maternal inheritance of mtDNA-CR in the 3nRB, 4nRB and 5nRB hybrids.
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Affiliation(s)
- Jinpeng Yan
- College of Life Science, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
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47
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Birstein VJ, Desalle R, Doukakis P, Hanner R, Ruban GI, Wong E. Testing taxonomic boundaries and the limit of DNA barcoding in the Siberian sturgeon,Acipenser baerii. ACTA ACUST UNITED AC 2009; 20:110-8. [DOI: 10.3109/19401730903168182] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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48
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Zhang Y, Nie L, Huang Y, Pu Y, Zhang L. The mitochondrial DNA control region comparison studies of four hinged turtles and its phylogentic significance of the genusCuora sensu lato (Testudinata: Geoemydidae). Genes Genomics 2009. [DOI: 10.1007/bf03191253] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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White MM, Martin HR. Structure and conservation of tandem repeats in the mitochondrial DNA control region of the Least Brook lamprey (Lampetra aepyptera). J Mol Evol 2009; 68:715-23. [PMID: 19449051 DOI: 10.1007/s00239-009-9246-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 04/21/2009] [Accepted: 04/27/2009] [Indexed: 10/20/2022]
Abstract
Tandemly repeated sequences are a common feature of vertebrate mitochondrial DNA control regions. However, questions still remain about their mode of evolution, function, and phylogenetic distribution. We report phylogenetic and geographic patterns of variation of control region repeat sequence and number in a nonparasitic lamprey, Lampetra aepyptera. A survey of populations from throughout the species' range revealed remarkably low repeat sequence polymorphism but some interpopulation variation in repeat number. The high sequence similarity extended to repeats observed in other species in the genus Lampetra and other lamprey genera. The very low levels of variation suggest a high copy turnover. Our data are consistent with the illegitimate elongation model of repeat gain and loss and further suggest that repeat change occurs at internal copies. However, the limited variation across some species of lamprey suggests that functional constraints may further limit variation.
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Affiliation(s)
- Matthew M White
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA.
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50
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Xiao B, Ma F, Sun Y, Li QW. Comparative analysis of complete mitochondrial DNA control region of four species of Strigiformes. ACTA ACUST UNITED AC 2009; 33:965-74. [PMID: 17112967 DOI: 10.1016/s0379-4172(06)60131-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Accepted: 07/17/2006] [Indexed: 11/30/2022]
Abstract
The sequence of the whole mitochondrial (mt) DNA control region (CR) of four species of Strigiformes was obtained. Length of the CR was 3,290 bp, 2,848 bp, 2,444 bp, and 1,771 bp for Asio flammeus, Asio otus, Athene noctua, and Strix aluco, respectively. Interestingly, the length of the control region was maximum in Asio flammeus among all the avian mtDNA control regions sequenced thus far. In addition, the base composition and organization of mtDNA CR of Asio flammeus were identical to those reported for other birds. On the basis of the differential frequencies of base substitutions, the CR may be divided two variable domains, I and III, and a central conserved domain, II. The 3' end of the CR contained many tandem repeats of varying lengths and repeat numbers. In Asio flammeus, the repeated sequences consisted of a 126 bp sequence that was repeated seven times and a 78 bp sequence that was repeated 14 times. In Asio otus, there were also two repeated sequences, namely a 127 bp sequence that was repeated eight times and a 78 bp sequence that was repeated six times. The control region of Athene noctua contained three sets of repeats: a 89 bp sequence that was repeated three times, a 77 bp sequence that was repeated four times, and a 71 bp sequence that was repeated six times. Strix aluco, however, had only one repeated sequence, a 78 bp sequence that was repeated five times. The results of this study seem to indicate that these tandem repeats may have resulted from slipped-strand mispairing during mtDNA replication. Moreover, there are many conserved motifs within the repeated units. These sequences could form stable stem-loop secondary structures, which suggests that these repeated sequences play an important role in regulating transcription and replication of the mitochondrial genome.
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Affiliation(s)
- Bing Xiao
- College of Life Sciences, Liaoning Normal University, Dalian 116029, China
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