201
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Conservation genetics and geographic patterns of genetic variation of endangered shrub Ammopiptanthus (Fabaceae) in northwestern China. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0798-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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202
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Portnoy DS, Puritz JB, Hollenbeck CM, Gelsleichter J, Chapman D, Gold JR. Selection and sex-biased dispersal in a coastal shark: the influence of philopatry on adaptive variation. Mol Ecol 2015; 24:5877-85. [DOI: 10.1111/mec.13441] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/27/2015] [Accepted: 10/27/2015] [Indexed: 01/18/2023]
Affiliation(s)
- D. S. Portnoy
- Department of Life Sciences; Marine Genomics Laboratory; Harte Research Institute; Texas A&M University-Corpus Christi; 6300 Ocean Drive Corpus Christi TX 78412 USA
| | - J. B. Puritz
- Department of Life Sciences; Marine Genomics Laboratory; Harte Research Institute; Texas A&M University-Corpus Christi; 6300 Ocean Drive Corpus Christi TX 78412 USA
| | - C. M. Hollenbeck
- Department of Life Sciences; Marine Genomics Laboratory; Harte Research Institute; Texas A&M University-Corpus Christi; 6300 Ocean Drive Corpus Christi TX 78412 USA
| | - J. Gelsleichter
- University of North Florida; 1 UNF Drive Jacksonville FL 32224 USA
| | - D. Chapman
- Stony Brook University; Stony Brook NY 11776 USA
| | - J. R. Gold
- Department of Life Sciences; Marine Genomics Laboratory; Harte Research Institute; Texas A&M University-Corpus Christi; 6300 Ocean Drive Corpus Christi TX 78412 USA
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203
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Cellular Heterogeneity in the Level of mtDNA Heteroplasmy in Mouse Embryonic Stem Cells. Cell Rep 2015; 13:1304-1309. [DOI: 10.1016/j.celrep.2015.10.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 08/19/2015] [Accepted: 10/07/2015] [Indexed: 01/19/2023] Open
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204
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Muhammad Tahir H, Akhtar S. Services of DNA barcoding in different fields. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4463-4474. [DOI: 10.3109/19401736.2015.1089572] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Samreen Akhtar
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
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205
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Radojičić JM, Krizmanić I, Kasapidis P, Zouros E. Extensive mitochondrial heteroplasmy in hybrid water frog (Pelophylax spp.) populations from Southeast Europe. Ecol Evol 2015; 5:4529-41. [PMID: 26668720 PMCID: PMC4670067 DOI: 10.1002/ece3.1692] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/05/2015] [Accepted: 08/12/2015] [Indexed: 11/30/2022] Open
Abstract
Water frogs of the genus Pelophylax (previous Rana) species have been much studied in Europe for their outstanding reproductive mechanism in which sympatric hybridization between genetically distinct parental species produces diverse genetic forms of viable hybrid animals. The most common hybrid is P. esculentus that carries the genomes of both parental species, P. ridibundus and P. lessonae, but usually transfers the whole genome of only one parent to its offsprings (hybridogenesis). The evolutionary cost of transfer of the intact genome and hence the hemiclonal reproduction is the depletion of heterozygosity in the hybrid populations. Pelophylax esculentus presents an excellent example of the long‐term sustained hybridization and hemiclonal reproduction in which the effects of the low genetic diversity are balanced through the novel mutations and periodic recombinations. In this study, we analyzed the mitochondrial (mt) and microsatellites DNA variations in hybrid Pelophylax populations from southern parts of the Pannonian Basin and a north–south transect of the Balkan Peninsula, which are home for a variety of Pelophylax genetic lineages. The mtDNA haplotypes found in this study corresponded to P. ridibundus and P. epeiroticus of the Balkan – Anatolian lineage (ridibundus–bedriagae) and to P. lessonae and a divergent lessonae haplotype of the lessonae lineage. The mtDNA genomes showed considerable intraspecific variation and geographic differentiation. The Balkan wide distributed P. ridibundus was found in all studied populations and its nuclear genome, along with either the lessonae or the endemic epeiroticus genome, in all hybrids. An unexpected finding was that the hybrid populations were invariably heteroplasmic, that is, they contained the mtDNA of both parental species. We discussed the possibility that such extensive heteroplasmy is a result of hybridization and it comes from regular leakage of the paternal mtDNA from a sperm of one species that fertilizes eggs of another. In this case, the mechanisms that protect the egg from heterospecific fertilization and further from the presence of sperm mtDNA could become compromised due to their differences and divergence at both, mitochondrial and nuclear DNA. The heteroplasmy once retained in the fertilized egg could be transmitted by hybrid backcrossing to the progeny and maintained in a population over generations. The role of interspecies and heteroplasmic hybrid animals due to their genomic diversity and better fitness compare to the parental species might be of the special importance in adaptations to miscellaneous and isolated environments at the Balkan Peninsula.
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Affiliation(s)
- Jelena M Radojičić
- Hellenic Centre for Marine Research Institute of Marine Biology, Biotechnology and Aquaculture Heraklion Greece ; Department of Biology University of Crete Heraklion Greece
| | - Imre Krizmanić
- Faculty of Biology Institute of Zoology University of Belgrade Belgrade Serbia
| | - Panagiotis Kasapidis
- Hellenic Centre for Marine Research Institute of Marine Biology, Biotechnology and Aquaculture Heraklion Greece
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206
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Scarcelli N, Mariac C, Couvreur TLP, Faye A, Richard D, Sabot F, Berthouly‐Salazar C, Vigouroux Y. Intra‐individual polymorphism in chloroplasts from
NGS
data: where does it come from and how to handle it? Mol Ecol Resour 2015; 16:434-45. [DOI: 10.1111/1755-0998.12462] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/07/2015] [Accepted: 08/21/2015] [Indexed: 01/11/2023]
Affiliation(s)
- N. Scarcelli
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
| | - C. Mariac
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
| | - T. L. P. Couvreur
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
- Département des Sciences Biologiques Laboratoire de Botanique Systématique et d'Ecologie Ecole Normale Supérieure Université de Yaoundé I BP 047 Yaoundé Cameroon
| | - A. Faye
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
| | - D. Richard
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
| | - F. Sabot
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
| | - C. Berthouly‐Salazar
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
- Route des Hydrocarbures Centre de Recherche de Bel‐Air IRD/ISRA BP 1386 – 18524 Dakar Senegal
| | - Y. Vigouroux
- UMR DIADE IRD Montpellier 911 avenue Agropolis 34394 Montpellier Cedex 5 France
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207
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Szczecińska M, Sawicki J. Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae. Int J Mol Sci 2015; 16:22258-79. [PMID: 26389887 PMCID: PMC4613307 DOI: 10.3390/ijms160922258] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 11/25/2022] Open
Abstract
Background: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Methodology/principal findings: Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161–162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatillavernalis. Conclusions/significance: The determination of complete plastid genome and nuclear rRNA cluster sequences in three species of the genus Pulsatilla is an important contribution to our knowledge of the evolution and phylogeography of those endangered taxa. The resulting data can be used to identify regions that are particularly useful for barcoding, phylogenetic and phylogeographic studies. The investigated taxa can be identified at each stage of development based on their species-specific SNPs. The nuclear and plastid genomic resources enable advanced studies on hybridization, including identification of parent species, including their roles in that process. The identified nonsynonymous mutations could play an important role in adaptations to changing environments. The results of the study will also provide valuable information about the evolution of the plastome structure in the family Ranunculaceae.
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Affiliation(s)
- Monika Szczecińska
- Department of Botany and Nature Protection, University of Warmia and Mazury, 10-728 Olsztyn, Poland.
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury, 10-728 Olsztyn, Poland.
- Department of Biology and Ecology, University of Ostrava, 71000 Ostrava, Czech Republic.
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208
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Abstract
Mitochondrial DNA (mtDNA) is predominantly maternally inherited in eukaryotes. Diverse molecular mechanisms underlying the phenomenon of strict maternal inheritance (SMI) of mtDNA have been described, but the evolutionary forces responsible for its predominance in eukaryotes remain to be elucidated. Exceptions to SMI have been reported in diverse eukaryotic taxa, leading to the prediction that several distinct molecular mechanisms controlling mtDNA transmission are present among the eukaryotes. We propose that these mechanisms will be better understood by studying the deviations from the predominating pattern of SMI. This minireview summarizes studies on eukaryote species with unusual or rare mitochondrial inheritance patterns, i.e., other than the predominant SMI pattern, such as maternal inheritance of stable heteroplasmy, paternal leakage of mtDNA, biparental and strictly paternal inheritance, and doubly uniparental inheritance of mtDNA. The potential genes and mechanisms involved in controlling mitochondrial inheritance in these organisms are discussed. The linkage between mitochondrial inheritance and sex determination is also discussed, given that the atypical systems of mtDNA inheritance examined in this minireview are frequently found in organisms with uncommon sexual systems such as gynodioecy, monoecy, or andromonoecy. The potential of deviations from SMI for facilitating a better understanding of a number of fundamental questions in biology, such as the evolution of mtDNA inheritance, the coevolution of nuclear and mitochondrial genomes, and, perhaps, the role of mitochondria in sex determination, is considerable.
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Affiliation(s)
- Sophie Breton
- a Department of Biological Sciences, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Donald T Stewart
- b Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
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209
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Milani L, Ghiselli F, Pecci A, Maurizii MG, Passamonti M. The Expression of a Novel Mitochondrially-Encoded Gene in Gonadic Precursors May Drive Paternal Inheritance of Mitochondria. PLoS One 2015; 10:e0137468. [PMID: 26339998 PMCID: PMC4560408 DOI: 10.1371/journal.pone.0137468] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/17/2015] [Indexed: 12/02/2022] Open
Abstract
Mitochondria have an active role in germ line development, and their inheritance dynamics are relevant to this process. Recently, a novel protein (RPHM21) was shown to be encoded in sperm by the male-transmitted mtDNA of Ruditapes philippinarum, a species with Doubly Uniparental Inheritance (DUI) of mitochondria. In silico analyses suggested a viral origin of RPHM21, and we hypothesized that the endogenization of a viral element provided sperm mitochondria of R. philippinarum with the ability to invade male germ line, thus being transmitted to the progeny. In this work we investigated the dynamics of germ line development in relation to mitochondrial transcription and expression patterns using qPCR and specific antibodies targeting the germ line marker VASPH (R. philippinarum VASA homolog), and RPHM21. Based on the experimental results we conclude that both targets are localized in the primordial germ cells (PGCs) of males, but while VASPH is detected in all PGCs, RPHM21 appears to be expressed only in a subpopulation of them. Since it has been predicted that RPHM21 might have a role in cell proliferation and migration, we here suggest that PGCs expressing it might gain advantage over others and undertake spermatogenesis, accounting for RPHM21 presence in all spermatozoa. Understanding how foreign sequence endogenization and co-option can modify the biology of an organism is of particular importance to assess the impact of such events on evolution.
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Affiliation(s)
- Liliana Milani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Andrea Pecci
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Maria Gabriella Maurizii
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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210
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Hwang JY, Lee CK, Kim H, Nam BH, An CM, Park JY, Park KH, Huh CS, Kim EB. Comparative genomic analysis of mitochondrial protein-coding genes in Veneroida clams: Analysis of superfamily-specific genomic and evolutionary features. Mar Genomics 2015; 24 Pt 3:329-34. [PMID: 26343338 DOI: 10.1016/j.margen.2015.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/19/2015] [Accepted: 08/19/2015] [Indexed: 12/30/2022]
Abstract
Veneroida is the largest order of bivalves, and these clams are commercially important in Asian countries. Although numerous studies have focused on the genomic characters of individual species or genera in Veneroida, superfamily-specific genomic characters have not been determined. In this study, we performed a comparative genomic analysis of 12 mitochondrial protein coding genes (PCGs) from 25 clams in six Veneroida superfamilies to determine genomic and evolutionary features of each superfamily. Length and distribution of nucleotides encoding the PCGs were too variable to define superfamily-specific genomic characters. Phylogenetic analysis revealed that PCGs are suitable for classification of species in three superfamilies: Cardioidea, Mactroidea, and Veneroidea. However, one species classified in Tellinoidea, Sinonovacula constricta, was evolutionarily closer to Solenoidea clams than Tellinoidea clams. dN/dS analysis showed that positively selected sites in NADH dehydrogenase subunit, nd4 and subunit of ATP synthase, atp6 were present in Mactroidea. Differences in selected sites in the nd4 and atp6 could be caused by superfamily-level differences in sodium transport or ATP synthesis functions, respectively. These differences in selected sites in NADH may have conferred these animals, which have low motility and do not generally move, with increased flexibility to maintain homeostasis in the face of osmotic pressure. Our study provides insight into evolutionary traits as well as facilitates identification of veneroids.
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Affiliation(s)
- Jae Yeon Hwang
- Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Chang-Kyu Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921 Republic of Korea; Institute of Green Bio Science and Technology, Seoul National University, Kangwon-do 232-916, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921 Republic of Korea; Institute of Green Bio Science and Technology, Seoul National University, Kangwon-do 232-916, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
| | - Cheul Min An
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
| | - Kyu-Hyun Park
- Department of Animal Life System, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Chul-Sung Huh
- Graduate School of International Agricultural Technology/GBST, Seoul National University, Pyeongchang 232-916, Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea.
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211
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Fang F, Ji Y, Zhao Q, Wang Y, Gao W, Chu K, Sun H. Phylogeography of the Chinese endemic freshwater crabSinopotamon acutum(Brachyura, Potamidae). ZOOL SCR 2015. [DOI: 10.1111/zsc.12131] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fang Fang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Yongkun Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Qiang Zhao
- College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Yujuan Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Wei Gao
- College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Kelin Chu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Hongying Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
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212
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Pervasive Mitochondrial Sequence Heteroplasmy in Natural Populations of Wild Carrot, Daucus carota spp. carota L. PLoS One 2015; 10:e0136303. [PMID: 26295342 PMCID: PMC4546501 DOI: 10.1371/journal.pone.0136303] [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: 04/26/2015] [Accepted: 08/02/2015] [Indexed: 11/19/2022] Open
Abstract
Exceptions to the generally accepted rules that plant mitochondrial genomes are strictly maternally inherited and that within-individual sequence diversity in those genomes, i.e., heteroplasmy, should be minimal are becoming increasingly apparent especially with regard to sequence-level heteroplasmy. These findings raise questions about the potential significance of such heteroplasmy for plant mitochondrial genome evolution. Still studies quantifying the amount and consequences of sequence heteroplasmy in natural populations are rare. In this study, we report pervasive sequence heteroplasmy in natural populations of wild carrot, a close relative of the cultivated crop. In order to assay directly for this heteroplasmy, we implemented a quantitative PCR assay that can detect and quantify intra-individual SNP variation in two mitochondrial genes (Cox1 and Atp9). We found heteroplasmy in > 60% of all wild carrot populations surveyed and in > 30% of the 140 component individuals that were genotyped. Heteroplasmy ranged from a very small proportion of the total genotype (e.g., 0.995:0.005) to near even mixtures (e.g., 0.590:0.410) in some individuals. These results have important implications for the role of intra-genomic recombination in the generation of plant mitochondrial genome genotypic novelty. The consequences of such recombination are evident in the results of this study through analysis of the degree of linkage disequilibrium (LD) between the SNP sites at the two genes studied.
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213
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Hadjivasiliou Z, Iwasa Y, Pomiankowski A. Cell-cell signalling in sexual chemotaxis: a basis for gametic differentiation, mating types and sexes. J R Soc Interface 2015; 12:20150342. [PMID: 26156301 PMCID: PMC4535405 DOI: 10.1098/rsif.2015.0342] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/16/2015] [Indexed: 11/29/2022] Open
Abstract
While sex requires two parents, there is no obvious need for them to be differentiated into distinct mating types or sexes. Yet this is the predominate state of nature. Here, we argue that mating types could play a decisive role because they prevent the apparent inevitability of self-stimulation during sexual signalling. We rigorously assess this hypothesis by developing a model for signaller-detector dynamics based on chemical diffusion, chemotaxis and cell movement. Our model examines the conditions under which chemotaxis improves partner finding. Varying parameter values within ranges typical of protists and their environments, we show that simultaneous secretion and detection of a single chemoattractant can cause a multifold movement impediment and severely hinder mate finding. Mutually exclusive roles result in faster pair formation, even when cells conferring the same roles cannot pair up. This arrangement also allows the separate mating types to optimize their signalling or detecting roles, which is effectively impossible for cells that are both secretors and detectors. Our findings suggest that asymmetric roles in sexual chemotaxis (and possibly other forms of sexual signalling) are crucial, even without morphological differences, and may underlie the evolution of gametic differentiation among both mating types and sexes.
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Affiliation(s)
- Zena Hadjivasiliou
- Centre for Mathematics, Physics and Engineering in the Life Sciences and Experimental Biology (CoMPLEX), University College London, Gower Street, London WC1E 6BT, UK Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Yoh Iwasa
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Andrew Pomiankowski
- Centre for Mathematics, Physics and Engineering in the Life Sciences and Experimental Biology (CoMPLEX), University College London, Gower Street, London WC1E 6BT, UK Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
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214
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Chou JY, Leu JY. The Red Queen in mitochondria: cyto-nuclear co-evolution, hybrid breakdown and human disease. Front Genet 2015; 6:187. [PMID: 26042149 PMCID: PMC4437034 DOI: 10.3389/fgene.2015.00187] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 05/05/2015] [Indexed: 01/08/2023] Open
Abstract
Cyto-nuclear incompatibility, a specific form of Dobzhansky-Muller incompatibility caused by incompatible alleles between mitochondrial and nuclear genomes, has been suggested to play a critical role during speciation. Several features of the mitochondrial genome (mtDNA), including high mutation rate, dynamic genomic structure, and uniparental inheritance, make mtDNA more likely to accumulate mutations in the population. Once mtDNA has changed, the nuclear genome needs to play catch-up due to the intimate interactions between these two genomes. In two populations, if cyto-nuclear co-evolution is driven in different directions, it may eventually lead to hybrid incompatibility. Although cyto-nuclear incompatibility has been observed in a wide range of organisms, it remains unclear what type of mutations drives the co-evolution. Currently, evidence supporting adaptive mutations in mtDNA remains limited. On the other hand, it has been known that some mutations allow mtDNA to propagate more efficiently but compromise the host fitness (described as selfish mtDNA). Arms races between such selfish mtDNA and host nuclear genomes can accelerate cyto-nuclear co-evolution and lead to a phenomenon called the Red Queen Effect. Here, we discuss how the Red Queen Effect may contribute to the frequent observation of cyto-nuclear incompatibility and be the underlying driving force of some human mitochondrial diseases.
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Affiliation(s)
- Jui-Yu Chou
- Department of Biology, National Changhua University of Education , Changhua, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica , Taipei, Taiwan
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215
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Abstract
Transposable elements (TEs) are an important factor shaping eukaryotic genomes. Although a significant body of research has been conducted on the abundance of TEs in nuclear genomes, TEs in mitochondrial genomes remain elusive. In this study, we successfully assembled 28 complete yeast mitochondrial genomes and took advantage of the power of population genomics to determine mobile DNAs and their propensity. We have observed compelling evidence of GC clusters propagating within the mitochondrial genome and being horizontally transferred between species. These mitochondrial TEs experience rapid diversification by nucleotide substitution and, more importantly, undergo dynamic merger and shuffling to form new TEs. Given the hyper mobile and transformable nature of mitochondrial TEs, our findings open the door to a deeper understanding of eukaryotic mitochondrial genome evolution and the origin of nonautonomous TEs.
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216
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Lauron-Moreau A, Pitre FE, Argus GW, Labrecque M, Brouillet L. Phylogenetic relationships of American willows (Salix L., Salicaceae). PLoS One 2015; 10:e0121965. [PMID: 25880993 PMCID: PMC4399884 DOI: 10.1371/journal.pone.0121965] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/09/2015] [Indexed: 11/24/2022] Open
Abstract
Salix L. is the largest genus in the family Salicaceae (450 species). Several classifications have been published, but taxonomic subdivision has been under continuous revision. Our goal is to establish the phylogenetic structure of the genus using molecular data on all American willows, using three DNA markers. This complete phylogeny of American willows allows us to propose a biogeographic framework for the evolution of the genus. Material was obtained for the 122 native and introduced willow species of America. Sequences were obtained from the ITS (ribosomal nuclear DNA) and two plastid regions, matK and rbcL. Phylogenetic analyses (parsimony, maximum likelihood, Bayesian inference) were performed on the data. Geographic distribution was mapped onto the tree. The species tree provides strong support for a division of the genus into two subgenera, Salix and Vetrix. Subgenus Salix comprises temperate species from the Americas and Asia, and their disjunction may result from Tertiary events. Subgenus Vetrix is composed of boreo-arctic species of the Northern Hemisphere and their radiation may coincide with the Quaternary glaciations. Sixteen species have ambiguous positions; genetic diversity is lower in subg. Vetrix. A molecular phylogeny of all species of American willows has been inferred. It needs to be tested and further resolved using other molecular data. Nonetheless, the genus clearly has two clades that have distinct biogeographic patterns.
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Affiliation(s)
- Aurélien Lauron-Moreau
- Institut de recherche en biologie végétale, Université de Montréal, Montréal, QC, Canada
| | - Frédéric E. Pitre
- Institut de recherche en biologie végétale, Université de Montréal, Montréal, QC, Canada
| | | | - Michel Labrecque
- Institut de recherche en biologie végétale, Université de Montréal, Montréal, QC, Canada
- * E-mail:
| | - Luc Brouillet
- Institut de recherche en biologie végétale, Université de Montréal, Montréal, QC, Canada
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217
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Abstract
In virtually all multicellular eukaryotes, mitochondria are transmitted exclusively through one parent, usually the mother. In this short review, we discuss some of the major consequences of uniparental transmission of mitochondria, including deleterious effects in males and selection for increased transmission through females. Many of these consequences, particularly sex ratio distortion, have well-studied parallels in other maternally transmitted genetic elements, such as bacterial endosymbionts of arthropods. We also discuss the consequences of linkage between mitochondria and other maternally transmitted genetic elements, including the role of cytonuclear incompatibilities in maintaining polymorphism. Finally, as a case study, we discuss a recently discovered maternally transmitted sex ratio distortion in an insect that is associated with extraordinarily divergent mitochondria.
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218
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Kang AR, Kim MJ, Park IA, Kim KY, Kim I. Extent and divergence of heteroplasmy of the DNA barcoding region in Anapodisma miramae (Orthoptera: Acrididae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3405-14. [PMID: 25835040 DOI: 10.3109/19401736.2015.1022730] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A partial sequence of the mitochondrial cytochrome oxidase subunit I (COI) gene is widely used as a molecular marker for species identification in animals, also termed a DNA barcode. However, the presence of more than one sequence type in a single individual, also known as heteroplasmy, is one of the shortcomings of barcode identification. In this study, we examined the extent and divergence of COI heteroplasmy, including nuclear-encoded mitochondrial pseudogenes (NUMTs), at the genomic-DNA level from 13 insect species including orthopteran Anapodisma miramae, and a long fragment of mitochondrial DNA and cDNA from A. miramae as templates. When multiple numbers of clones originated from genomic DNA were sequenced, heteroplasmy was prevalent in all species and NUMTs were observed in five species. Long fragment DNA (∼13.5 kb) also is a source of heteroplasmic amplification, but the divergent haplotypes and NUMTs obtained from genomic DNA were not detected in A. miramae. On the other hand, cDNA was relatively heteroplasmy-free. Consistently, one dominant haplotype was always obtained from the genomic DNA-origin clones in all species and also from the long fragment- and cDNA-origin clones in the two tested individuals of A. miramae. Furthermore, the dominant haplotype was identical in sequence, regardless of the DNA source in A. miramae. Thus, one possible solution to avoid the barcoding problem in relationship to heteroplasmy could be the acquisition of multiple numbers of barcoding sequences to determine a dominant haplotype that can be assigned as barcoding sequence for a given species.
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Affiliation(s)
- Ah Rang Kang
- a College of Agriculture & Life Sciences, Chonnam National University , Gwangju , Korea and
| | - Min Jee Kim
- a College of Agriculture & Life Sciences, Chonnam National University , Gwangju , Korea and
| | - In Ah Park
- a College of Agriculture & Life Sciences, Chonnam National University , Gwangju , Korea and
| | - Kee Young Kim
- b Department of Agricultural Biology , National Academy of Agricultural Science , Wanju-gun , Korea
| | - Iksoo Kim
- a College of Agriculture & Life Sciences, Chonnam National University , Gwangju , Korea and
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219
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Kuijper B, Lane N, Pomiankowski A. Can paternal leakage maintain sexually antagonistic polymorphism in the cytoplasm? J Evol Biol 2015; 28:468-80. [PMID: 25653025 PMCID: PMC4413368 DOI: 10.1111/jeb.12582] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/05/2014] [Accepted: 01/06/2015] [Indexed: 12/13/2022]
Abstract
A growing number of studies in multicellular organisms highlight low or moderate frequencies of paternal transmission of cytoplasmic organelles, including both mitochondria and chloroplasts. It is well established that strict maternal inheritance is selectively blind to cytoplasmic elements that are deleterious to males – ’mother's curse’. But it is not known how sensitive this conclusion is to slight levels of paternal cytoplasmic leakage. We assess the scope for polymorphism when individuals bear multiple cytoplasmic alleles in the presence of paternal leakage, bottlenecks and recurrent mutation. When fitness interactions among cytoplasmic elements within an individual are additive, we find that sexually antagonistic polymorphism is restricted to cases of strong selection on males. However, when fitness interactions among cytoplasmic elements are nonlinear, much more extensive polymorphism can be supported in the cytoplasm. In particular, mitochondrial mutants that have strong beneficial fitness effects in males and weak deleterious fitness effects in females when rare (i.e. ’reverse dominance’) are strongly favoured under paternal leakage. We discuss how such epistasis could arise through preferential segregation of mitochondria in sex-specific somatic tissues. Our analysis shows how paternal leakage can dampen the evolution of deleterious male effects associated with predominant maternal inheritance of cytoplasm, potentially explaining why ’mother's curse’ is less pervasive than predicted by earlier work.
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Affiliation(s)
- B Kuijper
- CoMPLEX, Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London, UK; Department of Genetics, Evolution and Environment, University College London, London, UK
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220
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Wagner-Vogel G, Lämmer F, Kämper J, Basse CW. Uniparental mitochondrial DNA inheritance is not affected in Ustilago maydis Δatg11 mutants blocked in mitophagy. BMC Microbiol 2015; 15:23. [PMID: 25652096 PMCID: PMC4326477 DOI: 10.1186/s12866-015-0358-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/22/2015] [Indexed: 11/18/2022] Open
Abstract
Background Maternal or uniparental inheritance (UPI) of mitochondria is generally observed in sexual eukaryotes, however, the underlying mechanisms are diverse and largely unknown. Recently, based on the use of mutants blocked in autophagy, it has been demonstrated that autophagy is required for strict maternal inheritance in the nematode Caenorhabditis elegans. Uniparental mitochondrial DNA (mtDNA) inheritance has been well documented for numerous fungal species, and in particular, has been shown to be genetically governed by the mating-type loci in the isogamous species Cryptococcus neoformans, Phycomyces blakesleeanus and Ustilago maydis. Previously, we have shown that the a2 mating-type locus gene lga2 is decisive for UPI during sexual development of U. maydis. In axenic culture, conditional overexpression of lga2 triggers efficient loss of mtDNA as well as mitophagy. To assess a functional relationship, we have investigated UPI in U. maydis Δatg11 mutants, which are blocked in mitophagy. Results This study has revealed that Δatg11 mutants are not affected in pathogenic development and this has allowed us to analyse UPI under comparable developmental conditions between mating-compatible wild-type and mutant strain combinations. Explicitly, we have examined two independent strain combinations that gave rise to different efficiencies of UPI. We demonstrate that in both cases UPI is atg11-independent, providing evidence that mitophagy is not critical for UPI in U. maydis, even under conditions of strict UPI. Conclusions Until now, analysis of a role of mitophagy in UPI has not been reported for microbial species. Our study suggests that selective autophagy does not contribute to UPI in U. maydis, but is rather a consequence of selective mtDNA elimination in response to mitochondrial damage. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0358-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gaby Wagner-Vogel
- Department of Genetics, Institute for Applied Biosciences of the Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
| | - Frauke Lämmer
- Department of Genetics, Institute for Applied Biosciences of the Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
| | - Jörg Kämper
- Department of Genetics, Institute for Applied Biosciences of the Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
| | - Christoph W Basse
- Department of Genetics, Institute for Applied Biosciences of the Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
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221
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Sun M, Soltis DE, Soltis PS, Zhu X, Burleigh JG, Chen Z. Deep phylogenetic incongruence in the angiosperm clade Rosidae. Mol Phylogenet Evol 2015; 83:156-66. [DOI: 10.1016/j.ympev.2014.11.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 11/01/2014] [Accepted: 11/05/2014] [Indexed: 10/24/2022]
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222
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Wang Z, Wilson A, Xu J. Mitochondrial DNA inheritance in the human fungal pathogen Cryptococcus gattii. Fungal Genet Biol 2015; 75:1-10. [DOI: 10.1016/j.fgb.2015.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/18/2014] [Accepted: 01/02/2015] [Indexed: 01/19/2023]
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223
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Wang G, Xue T, Chen M, Guo L, Li J. Complete F-type mitochondrial genome of freshwater mussels Unio douglasiae. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4021-4022. [PMID: 25629504 DOI: 10.3109/19401736.2014.1003825] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete F-type mitochondrial genome of Unio douglasiae is reported for the first time in this research. It is 15,767 bp in size and contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Except for COI, ND2, CYTB, ND1, ND6, ND4L, ATP8 with ATA start codon, and ND4 with ATT start codon, the remaining protein-coding genes initiate with the orthodox ATG start codon. There are 25 noncoding regions found throughout the mitogenome of Unio douglasiae, ranging in the size from 1 to 312 bp, the largest of which is between tRNAGlu and ND2 (312 bp).
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Affiliation(s)
- Guiling Wang
- a Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture , Shanghai Ocean University , Shanghai , China
| | - Ting Xue
- a Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture , Shanghai Ocean University , Shanghai , China
| | - Meiling Chen
- a Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture , Shanghai Ocean University , Shanghai , China
| | - Liping Guo
- a Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture , Shanghai Ocean University , Shanghai , China
| | - Jiale Li
- a Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture , Shanghai Ocean University , Shanghai , China
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224
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Milani L, Ghiselli F, Maurizii MG, Nuzhdin SV, Passamonti M. Paternally transmitted mitochondria express a new gene of potential viral origin. Genome Biol Evol 2015; 6:391-405. [PMID: 24500970 PMCID: PMC3942028 DOI: 10.1093/gbe/evu021] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Mitochondrial ORFans (open reading frames having no detectable homology and with unknown function) were discovered in bivalve molluscs with doubly uniparental inheritance (DUI) of mitochondria. In these animals, two mitochondrial lineages are present, one transmitted through eggs (F-type), the other through sperm (M-type), each showing a specific ORFan. In this study, we used in situ hybridization and immunocytochemistry to provide evidence for the expression of Ruditapes philippinarum male-specific ORFan (orf21): both the transcript and the protein (RPHM21) were localized in spermatogenic cells and mature spermatozoa; the protein was localized in sperm mitochondria and nuclei, and in early embryos. Also, in silico analyses of orf21 flanking region and RPHM21 structure supported its derivation from viral sequence endogenization. We propose that RPHM21 prevents the recognition of M-type mitochondria by the degradation machinery, allowing their survival in the zygote. The process might involve a mechanism similar to that of Modulators of Immune Recognition, viral proteins involved in the immune recognition pathway, to which RPHM21 showed structural similarities. A viral origin of RPHM21 may also support a developmental role, because some integrated viral elements are involved in development and sperm differentiation of their host. Mitochondrial ORFans could be responsible for or participate in the DUI mechanism and their viral origin could explain the acquired capability of M-type mitochondria to avoid degradation and invade the germ line, that is what viruses do best: to elude host immune system and proliferate.
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Affiliation(s)
- Liliana Milani
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Italy
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225
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Abstract
Why the DNA-containing organelles, chloroplasts, and mitochondria, are inherited maternally is a long standing and unsolved question. However, recent years have seen a paradigm shift, in that the absoluteness of uniparental inheritance is increasingly questioned. Here, we review the field and propose a unifying model for organelle inheritance. We argue that the predominance of the maternal mode is a result of higher mutational load in the paternal gamete. Uniparental inheritance evolved from relaxed organelle inheritance patterns because it avoids the spread of selfish cytoplasmic elements. However, on evolutionary timescales, uniparentally inherited organelles are susceptible to mutational meltdown (Muller's ratchet). To prevent this, fall-back to relaxed inheritance patterns occurs, allowing low levels of sexual organelle recombination. Since sexual organelle recombination is insufficient to mitigate the effects of selfish cytoplasmic elements, various mechanisms for uniparental inheritance then evolve again independently. Organelle inheritance must therefore be seen as an evolutionary unstable trait, with a strong general bias to the uniparental, maternal, mode.
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Affiliation(s)
- Stephan Greiner
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - Johanna Sobanski
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
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226
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Li L, Hu L, Han LP, Ji H, Zhu Y, Wang X, Ge J, Xu M, Shen D, Dong H. Expression of turtle riboflavin-binding protein represses mitochondrial electron transport gene expression and promotes flowering in Arabidopsis. BMC PLANT BIOLOGY 2014; 14:381. [PMID: 25547226 PMCID: PMC4310184 DOI: 10.1186/s12870-014-0381-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 12/11/2014] [Indexed: 05/12/2023]
Abstract
BACKGROUND Recently we showed that de novo expression of a turtle riboflavin-binding protein (RfBP) in transgenic Arabidopsis increased H2O2 concentrations inside leaf cells, enhanced the expression of floral regulatory gene FD and floral meristem identity gene AP1 at the shoot apex, and induced early flowering. Here we report that RfBP-induced H2O2 presumably results from electron leakage at the mitochondrial electron transport chain (METC) and this source of H2O2 contributes to the early flowering phenotype. RESULTS While enhanced expression of FD and AP1 at the shoot apex was correlated with early flowering, the foliar expression of 13 of 19 METC genes was repressed in RfBP-expressing (RfBP+) plants. Inside RfBP+ leaf cells, cytosolic H2O2 concentrations were increased possibly through electron leakage because similar responses were also induced by a known inducer of electron leakage from METC. Early flowering no longer occurred when the repression on METC genes was eliminated by RfBP gene silencing, which restored RfBP+ to wild type in levels of FD and AP1 expression, H2O2, and flavins. Flowering was delayed by the external riboflavin application, which brought gene expression and flavins back to the steady-state levels but only caused 55% reduction of H2O2 concentrations in RfBP+ plants. RfBP-repressed METC gene expression remedied the cytosolic H2O2 diminution by genetic disruption of transcription factor NFXLl and compensated for compromises in FD and AP1 expression and flowering time. By contrast, RfBP resembled a peroxisomal catalase mutation, which augments the cytosolic H2O2, to enhance FD and AP1 expression and induce early flowering. CONCLUSIONS RfBP-repressed METC gene expression potentially causes electron leakage as one of cellular sources for the generation of H2O2 with the promoting effect on flowering. The repressive effect on METC gene expression is not the only way by which RfBP induces H2O2 and currently unappreciated factors may also function under RfBP+ background.
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Affiliation(s)
- Liang Li
- Department of Plant Pathology, Nanjing Agricultural University and State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 China
| | - Li Hu
- Department of Plant Pathology, Nanjing Agricultural University and State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 China
| | - Li-Ping Han
- Department of Plant Pathology, Nanjing Agricultural University and State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 China
| | - Hongtao Ji
- Department of Plant Pathology, Nanjing Agricultural University and State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 China
| | - Yueyue Zhu
- Department of Plant Pathology, Nanjing Agricultural University and State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 China
| | - Xiaobing Wang
- Department of Plant Pathology, Nanjing Agricultural University and State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 China
| | - Jun Ge
- Department of Plant Pathology, Nanjing Agricultural University and State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 China
| | - Manyu Xu
- Department of Plant Pathology, Nanjing Agricultural University and State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 China
| | - Dan Shen
- Department of Plant Pathology, Nanjing Agricultural University and State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 China
| | - Hansong Dong
- Department of Plant Pathology, Nanjing Agricultural University and State Ministry of Education Key Laboratory of Integrated Management of Crop Pathogens and Insect Pests, Nanjing, 210095 China
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227
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Nadimi M, Stefani FOP, Hijri M. The mitochondrial genome of the glomeromycete Rhizophagus sp. DAOM 213198 reveals an unusual organization consisting of two circular chromosomes. Genome Biol Evol 2014; 7:96-105. [PMID: 25527840 PMCID: PMC4316621 DOI: 10.1093/gbe/evu268] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2014] [Indexed: 01/02/2023] Open
Abstract
Mitochondrial (mt) genomes are intensively studied in Ascomycota and Basidiomycota, but they are poorly documented in basal fungal lineages. In this study, we sequenced the complete mtDNA of Rhizophagus sp. DAOM 213198, a close relative to Rhizophagus irregularis, a widespread, ecologically and economical relevant species belonging to Glomeromycota. Unlike all other known taxonomically close relatives harboring a full-length circular chromosome, mtDNA of Rhizophagus sp. reveals an unusual organization with two circular chromosomes of 61,964 and 29,078 bp. The large chromosome contained nine protein-coding genes (atp9, nad5, cob, nad4, nad1, nad4L, cox1, cox2, and atp8), small subunit rRNA gene (rns), and harbored 20 tRNA-coding genes and 10 orfs, while the small chromosome contained five protein-coding genes (atp6, nad2, nad3, nad6, and cox3), large subunit rRNA gene (rnl) in addition to 5 tRNA-coding genes, and 8 plasmid-related DNA polymerases (dpo). Although structural variation of plant mt genomes is well documented, this study is the first report of the presence of two circular mt genomes in arbuscular mycorrhizal fungi. Interestingly, the presence of dpo at the breakage point in intergenes cox1-cox2 and rnl-atp6 for large and small mtDNAs, respectively, could be responsible for the conversion of Rhizophagus sp. mtDNA into two chromosomes. Using quantitative real-time polymerase chain reaction, we found that both mtDNAs have an equal abundance. This study reports a novel mtDNA organization in Glomeromycota and highlights the importance of studying early divergent fungal lineages to describe novel evolutionary pathways in the fungal kingdom.
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Affiliation(s)
- Maryam Nadimi
- Département de Sciences Biologiques, Université de Montréal, Institut de Recherche en Biologie Végétale (IRBV), Quebec, Canada
| | - Franck O P Stefani
- Département de Sciences Biologiques, Université de Montréal, Institut de Recherche en Biologie Végétale (IRBV), Quebec, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Université de Montréal, Institut de Recherche en Biologie Végétale (IRBV), Quebec, Canada
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228
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Autophagy and ubiquitin-mediated proteolysis may not be involved in the degradation of spermatozoon mitochondria in mouse and porcine early embryos. ZYGOTE 2014; 24:31-41. [PMID: 25513816 DOI: 10.1017/s0967199414000689] [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] [Indexed: 12/15/2022]
Abstract
The mitochondrial genome is maternally inherited in animals, despite the fact that paternal mitochondria enter oocytes during fertilization. Autophagy and ubiquitin-mediated degradation are responsible for the elimination of paternal mitochondria in Caenorhabditis elegans; however, the involvement of these two processes in the degradation of paternal mitochondria in mammals is not well understood. We investigated the localization patterns of light chain 3 (LC3) and ubiquitin in mouse and porcine embryos during preimplantation development. We found that LC3 and ubiquitin localized to the spermatozoon midpiece at 3 h post-fertilization, and that both proteins were colocalized with paternal mitochondria and removed upon fertilization during the 4-cell stage in mouse and the zygote stage in porcine embryos. Sporadic paternal mitochondria were present beyond the morula stage in the mouse, and paternal mitochondria were restricted to one blastomere of 4-cell embryos. An autophagy inhibitor, 3-methyladenine (3-MA), did not affect the distribution of paternal mitochondria compared with the positive control, while an autophagy inducer, rapamycin, accelerated the removal of paternal mitochondria compared with the control. After the intracytoplasmic injection of intact spermatozoon into mouse oocytes, LC3 and ubiquitin localized to the spermatozoon midpiece, but remnants of undegraded paternal mitochondria were retained until the blastocyst stage. Our results show that paternal mitochondria colocalize with autophagy receptors and ubiquitin and are removed after in vitro fertilization, but some remnants of sperm mitochondrial sheath may persist up to morula stage after intracytoplasmic spermatozoon injection (ICSI).
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229
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Naue J, Hörer S, Sänger T, Strobl C, Hatzer-Grubwieser P, Parson W, Lutz-Bonengel S. Evidence for frequent and tissue-specific sequence heteroplasmy in human mitochondrial DNA. Mitochondrion 2014; 20:82-94. [PMID: 25526677 DOI: 10.1016/j.mito.2014.12.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 12/02/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
Mitochondrial point heteroplasmy is a common event observed not only in patients with mitochondrial diseases but also in healthy individuals. We here report a comprehensive investigation of heteroplasmy occurrence in human including the whole mitochondrial control region from nine different tissue types of 100 individuals. Sanger sequencing was used as a standard method and results were supported by cloning, minisequencing, and massively parallel sequencing. Only 12% of all individuals showed no heteroplasmy, whereas 88% showed at least one heteroplasmic position within the investigated tissues. In 66% of individuals up to 8 positions were affected. The highest relative number of heteroplasmies was detected in muscle and liver (79%, 69%), followed by brain, hair, and heart (36.7%-30.2%). Lower percentages were observed in bone, blood, lung, and buccal cells (19.8%-16.2%). Accumulation of position-specific heteroplasmies was found in muscle (positions 64, 72, 73, 189, and 408), liver (position 72) and brain (partial deletion at position 71). Deeper analysis of these specific positions in muscle revealed a non-random appearance and position-specific dependency on age. MtDNA heteroplasmy frequency and its potential functional importance have been underestimated in the past and its occurrence is ubiquitous and dependent at least on age, tissue, and position-specific mutation rates.
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Affiliation(s)
- Jana Naue
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany.
| | - Steffen Hörer
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany.
| | - Timo Sänger
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany.
| | - Christina Strobl
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020 Innsbruck, Austria.
| | - Petra Hatzer-Grubwieser
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020 Innsbruck, Austria.
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020 Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA.
| | - Sabine Lutz-Bonengel
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany.
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230
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Molecular phylogeography and intraspecific divergence of Spiraea alpina (Rosaceae) distributed in the Qinghai-Tibetan Plateau and adjacent regions inferred from nrDNA. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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231
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Huang DI, Hefer CA, Kolosova N, Douglas CJ, Cronk QCB. Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae). THE NEW PHYTOLOGIST 2014; 204:693-703. [PMID: 25078531 DOI: 10.1111/nph.12956] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/16/2014] [Indexed: 05/03/2023]
Abstract
As molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance - the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees - are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6-7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a 'ghost lineage' of a now-extinct North American poplar.
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Affiliation(s)
- Daisie I Huang
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
- Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Charles A Hefer
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
- Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Natalia Kolosova
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Carl J Douglas
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
- Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada
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232
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Zhihao S, Mingli Z. A range wide geographic pattern of genetic diversity and population structure of Hexinia polydichotoma (Asteraceae) in Tarim Basin and adjacent areas. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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233
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Dobler R, Rogell B, Budar F, Dowling DK. A meta-analysis of the strength and nature of cytoplasmic genetic effects. J Evol Biol 2014; 27:2021-34. [DOI: 10.1111/jeb.12468] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/25/2014] [Accepted: 07/27/2014] [Indexed: 01/07/2023]
Affiliation(s)
- R. Dobler
- Institute of Evolution and Ecology; University of Tübingen; Tübingen Germany
| | - B. Rogell
- School of Biological Sciences; Monash University; Clayton Vic. Australia
| | - F. Budar
- UMR 1318; Institut Jean-Pierre Bourgin; INRA; Versailles France
- UMR 1318; Institut Jean-Pierre Bourgin; AgroParisTech; Versailles France
| | - D. K. Dowling
- School of Biological Sciences; Monash University; Clayton Vic. Australia
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Heindryckx B, Neupane J, Vandewoestyne M, Christodoulou C, Jackers Y, Gerris J, Van den Abbeel E, Van Coster R, Deforce D, De Sutter P. Mutation-free baby born from a mitochondrial encephalopathy, lactic acidosis and stroke-like syndrome carrier after blastocyst trophectoderm preimplantation genetic diagnosis. Mitochondrion 2014; 18:12-7. [DOI: 10.1016/j.mito.2014.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 01/01/2023]
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Abstract
The lability in size, structure, and sequence content of mitochondrial genome (mtDNA) across plant species has sharply limited its use in taxonomic studies. However, due to the new opportunities offered by the availability of complete mtDNA sequence in plant species and the subsequent development of universal primers, the number of mtDNA-based molecular studies has recently increased. Historically, universal primers have enabled to characterize mtDNA polymorphism mainly by the RFLP technique. This methodology has been progressively replaced by Sanger DNA sequencing, which actually provides the full phylogenetic information content of a DNA fragment (single nucleotide, insertion/deletion, and single sequence repeat length polymorphism). This chapter presents a sequencing working protocol to be routinely used in mtDNA-based phylogenetic studies.
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236
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Politi Y, Gal L, Kalifa Y, Ravid L, Elazar Z, Arama E. Paternal mitochondrial destruction after fertilization is mediated by a common endocytic and autophagic pathway in Drosophila. Dev Cell 2014; 29:305-20. [PMID: 24823375 DOI: 10.1016/j.devcel.2014.04.005] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 01/16/2014] [Accepted: 04/02/2014] [Indexed: 12/12/2022]
Abstract
Almost all animals contain mitochondria of maternal origin only, but the exact mechanisms underlying this phenomenon are still vague. We investigated the fate of Drosophila paternal mitochondria after fertilization. We demonstrate that the sperm mitochondrial derivative (MD) is rapidly eliminated in a stereotypical process dubbed paternal mitochondrial destruction (PMD). PMD is initiated by a network of vesicles resembling multivesicular bodies and displaying common features of the endocytic and autophagic pathways. These vesicles associate with the sperm tail and mediate the disintegration of its plasma membrane. Subsequently, the MD separates from the axoneme and breaks into smaller fragments, which are then sequestered by autophagosomes for degradation in lysosomes. We further provide evidence for the involvement of the ubiquitin pathway and the autophagy receptor p62 in this process. Finally, we show that the ubiquitin ligase Parkin is not involved in PMD, implying a divergence from the autophagic pathway of damaged mitochondria.
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Affiliation(s)
- Yoav Politi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Liron Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yossi Kalifa
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Liat Ravid
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zvulun Elazar
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eli Arama
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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237
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Kuo HC, Chen SF, Fang YP, Flanders J, Rossiter SJ. Comparative rangewide phylogeography of four endemic Taiwanese bat species. Mol Ecol 2014; 23:3566-86. [DOI: 10.1111/mec.12838] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 06/09/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Hao-Chih Kuo
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
| | - Shiang-Fan Chen
- Center for General Education; National Taipei University; New Taipei City 23741 Taiwan
| | - Yin-Ping Fang
- Department of Biological Resources; National Chiayi University; Chiayi City 60004 Taiwan
| | - Jon Flanders
- School of Biological Sciences; University of Bristol; Bristol BS8 1UG UK
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences; Queen Mary University of London; London E1 4NS UK
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238
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Dokianakis E, Ladoukakis ED. Different degree of paternal mtDNA leakage between male and female progeny in interspecific Drosophila crosses. Ecol Evol 2014; 4:2633-41. [PMID: 25077015 PMCID: PMC4113288 DOI: 10.1002/ece3.1069] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 11/15/2013] [Accepted: 11/24/2013] [Indexed: 12/17/2022] Open
Abstract
Maternal transmission of mitochondrial DNA (mtDNA) in animals is thought to prevent the spread of selfish deleterious mtDNA mutations in the population. Various mechanisms have been evolved independently to prevent the entry of sperm mitochondria in the embryo. However, the increasing number of instances of paternal mtDNA leakage suggests that these mechanisms are not very effective. The destruction of sperm mitochondria in mammalian embryos is mediated by nuclear factors. Also, the destruction of paternal mitochondria in intraspecific crosses is more effective than in interspecific ones. These observations have led to the hypothesis that leakage of paternal mtDNA (and consequently mtDNA recombination owing to ensuing heteroplasmy) might be more common in inter- than in intraspecific crosses and that it should increase with phylogenetic distance of hybridizing species. We checked paternal leakage in inter- and intraspecific crosses in Drosophila and found little evidence for this hypothesis. In addition, we have observed a higher level of leakage among male than among female progeny from the same cross. This is the first report of sex-specific leakage of paternal mtDNA. It suggests that paternal mtDNA leakage might not be a stochastic result of an error-prone mechanism, but rather, it may be under complex genetic control.
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239
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Regulation of mitochondrial genome inheritance by autophagy and ubiquitin-proteasome system: implications for health, fitness, and fertility. BIOMED RESEARCH INTERNATIONAL 2014; 2014:981867. [PMID: 25028670 PMCID: PMC4083708 DOI: 10.1155/2014/981867] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/01/2014] [Accepted: 04/07/2014] [Indexed: 01/07/2023]
Abstract
Mitochondria, the energy-generating organelles, play a role in numerous cellular functions including adenosine triphosphate (ATP) production, cellular homeostasis, and apoptosis. Maternal inheritance of mitochondria and mitochondrial DNA (mtDNA) is universally observed in humans and most animals. In general, high levels of mitochondrial heteroplasmy might contribute to a detrimental effect on fitness and disease resistance. Therefore, a disposal of the sperm-derived mitochondria inside fertilized oocytes assures normal preimplantation embryo development. Here we summarize the current research and knowledge concerning the role of autophagic pathway and ubiquitin-proteasome-dependent proteolysis in sperm mitophagy in mammals, including humans. Current data indicate that sperm mitophagy inside the fertilized oocyte could occur along multiple degradation routes converging on autophagic clearance of paternal mitochondria. The influence of assisted reproductive therapies (ART) such as intracytoplasmic sperm injection (ICSI), mitochondrial replacement (MR), and assisted fertilization of oocytes from patients of advanced reproductive age on mitochondrial function, inheritance, and fitness and for the development and health of ART babies will be of particular interest to clinical audiences. Altogether, the study of sperm mitophagy after fertilization has implications in the timing of evolution and developmental and reproductive biology and in human health, fitness, and management of mitochondrial disease.
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240
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Zhang F, Broughton RE. Mitochondrial-nuclear interactions: compensatory evolution or variable functional constraint among vertebrate oxidative phosphorylation genes? Genome Biol Evol 2014; 5:1781-91. [PMID: 23995460 PMCID: PMC3814189 DOI: 10.1093/gbe/evt129] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Oxidative phosphorylation (OXPHOS), the major energy-producing pathway in aerobic organisms, includes protein subunits encoded by both mitochondrial (mt) and nuclear (nu) genomes. How these independent genomes have coevolved is a long-standing question in evolutionary biology. Although mt genes evolve faster than most nu genes, maintenance of OXPHOS structural stability and functional efficiency may involve correlated evolution of mt and nu OXPHOS genes. The nu OXPHOS genes might be predicted to exhibit accelerated evolutionary rates to accommodate the elevated substitution rates of mt OXPHOS subunits with which they interact. Evolutionary rates of nu OXPHOS genes should, therefore, be higher than that of nu genes that are not involved in OXPHOS (nu non-OXPHOS). We tested the compensatory evolution hypothesis by comparing the evolutionary rates (synonymous substitution rate dS and nonsynonymous substitution rate dN) among 13 mt OXPHOS genes, 60 nu OXPHOS genes, and 77 nu non-OXPHOS genes in vertebrates (7 fish and 40 mammal species). The results from a combined analysis of all OXPHOS subunits fit the predictions of the hypothesis. However, results from two OXPHOS complexes did not fit this pattern when analyzed separately. We found that the d(N) of nu OXPHOS genes for "core" subunits (those involved in the major catalytic activity) was lower than that of "noncore" subunits, whereas there was no significant difference in d(N) between genes for nu non-OXPHOS and core subunits. This latter finding suggests that compensatory changes play a minor role in the evolution of OXPHOS genes and that the observed accelerated nu substitution rates are due largely to reduced functional constraint on noncore subunits.
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Affiliation(s)
- Feifei Zhang
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma
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241
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Hilpold A, Vilatersana R, Susanna A, Meseguer AS, Boršić I, Constantinidis T, Filigheddu R, Romaschenko K, Suárez-Santiago VN, Tugay O, Uysal T, Pfeil BE, Garcia-Jacas N. Phylogeny of the Centaurea group (Centaurea, Compositae) - geography is a better predictor than morphology. Mol Phylogenet Evol 2014; 77:195-215. [PMID: 24784974 DOI: 10.1016/j.ympev.2014.04.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/17/2014] [Accepted: 04/18/2014] [Indexed: 10/25/2022]
Abstract
The Centaurea group is part of the Circum-Mediterranean Clade (CMC) of genus Centaurea subgenus Centaurea, a mainly Mediterranean plant group with more than 200 described species. The group is traditionally split on morphological basis into three sections: Centaurea, Phalolepis and Willkommia. This division, however, is doubtful, especially in light of molecular approaches. In this study we try to resolve this phylogenetic problem and to consolidate the circumscription and delimitation of the entire group against other closely related groups. We analyzed nuclear (internal transcribed spacer of the ribosomal genes) and chloroplast (rpl32-trnL intergenic spacer) DNA regions for most of the described species of the Centaurea group using phylogenetic and network approaches, and we checked the data for recombination. Phylogeny was used to reconstruct the evolution of the lacerate-membranaceous bract appendages using parsimony. The magnitude of incomplete lineage sorting was tested estimating the effective population sizes. Molecular dating was performed using a Bayesian approach, and the ancestral area reconstruction was conducted using the Dispersal-Extinction-Cladogenesis method. Monophyly of the Centaurea group is confirmed if a few species are removed. Our results do not support the traditional sectional division. There is a high incongruence between the two markers and between genetic data and morphology. However, there is a clear relation between geography and the structure of the molecular data. Diversification in the Centaurea group mainly took place during the Pliocene and Pleistocene. The ancestral area infered for the Circum-Mediterranean Clade of Centaurea is the Eastern Mediterranean, whereas for the Centaurea group it is most likely NW-Africa. The large incongruencies, which hamper phylogenetic reconstruction, are probably the result of introgression, even though the presence of incomplete lineage sorting as an additional factor cannot be ruled out. Convergent evolution of morphological traits may have led to incongruence between morphology-based, traditional systematics and molecular results. Our results also cast major doubts about current species delimitation.
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Affiliation(s)
- Andreas Hilpold
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Pg. del Migdia s/n, ES-08038 Barcelona, Spain.
| | - Roser Vilatersana
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Pg. del Migdia s/n, ES-08038 Barcelona, Spain
| | - Alfonso Susanna
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Pg. del Migdia s/n, ES-08038 Barcelona, Spain
| | - Andrea S Meseguer
- Real Jardín Botánico de Madrid (RJB-CSIC), Plaza de Murillo, 2, ES-28014 Madrid, Spain
| | - Igor Boršić
- State Institute for Nature Protection, Trg. Mažuranića 5, HR-10000 Zagreb, Croatia
| | - Theophanis Constantinidis
- Department of Ecology & Systematics, Faculty of Biology, National & Kapodistrian University of Athens, Panepistimiopolis, GR-15784 Athens, Greece
| | - Rossella Filigheddu
- Dipartimento di Scienze Botaniche, Ecologiche e Geologiche, Università degli Studi di Sassari, Via Piandanna 4, I-07100 Sassari, Italy
| | - Konstantin Romaschenko
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Pg. del Migdia s/n, ES-08038 Barcelona, Spain
| | - Víctor N Suárez-Santiago
- Departamento de Botánica, Facultad de Ciencias, Universidad de Granada, Severo Ochoa s/n, ES-18071 Granada, Spain
| | - Osman Tugay
- Faculty of Science and Art, Selçuk University, TR-42031 Konya, Turkey
| | - Tuna Uysal
- Faculty of Science and Art, Selçuk University, TR-42031 Konya, Turkey
| | - Bernard E Pfeil
- Department of Biological and Environmental Sciences, University of Göteborg, Box 461, SE-40530 Göteborg, Sweden
| | - Núria Garcia-Jacas
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Pg. del Migdia s/n, ES-08038 Barcelona, Spain
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242
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Povelones ML. Beyond replication: division and segregation of mitochondrial DNA in kinetoplastids. Mol Biochem Parasitol 2014; 196:53-60. [PMID: 24704441 DOI: 10.1016/j.molbiopara.2014.03.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/18/2014] [Accepted: 03/25/2014] [Indexed: 11/29/2022]
Abstract
The mitochondrial genome of kinetoplastids, called kinetoplast DNA (kDNA) is a complex structure that must be faithfully duplicated exactly once per cell cycle. Despite many years of thorough investigation into the kDNA replication mechanism, many of the molecular details of the later stages of the process, particularly kDNA division and segregation, remain mysterious. In addition, perturbation of several cellular activities, some only indirectly related to kDNA, can lead to asymmetric kDNA division and other segregation defects. This review will examine unifying features and possible explanations for these phenotypes in the context of current models for kDNA division and segregation.
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243
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Sańko TJ, Burzyński A. Co-expressed mitochondrial genomes: recently masculinized, recombinant mitochondrial genome is co-expressed with the female-transmitted mtDNA genome in a male Mytilus trossulus mussel from the Baltic Sea. BMC Genet 2014; 15:28. [PMID: 24575766 PMCID: PMC3941564 DOI: 10.1186/1471-2156-15-28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 02/13/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Few exceptions have been described from strict maternal inheritance of mitochondrial DNA in animals, including sea mussels (Mytilidae), clams (Donacidae, Veneridae and Solenidae) and freshwater mussels (Unionoidae) order. In these bivalves mitochondria and their DNA are transferred through two separate routes. The females inherit only the maternal mitochondrial DNA whereas the males inherit maternal as well as paternal mitochondrial DNA, which is usually present only in gonads and sperm. The mechanism controlling this phenomenon is unclear but leads to the existence of two separate mitochondrial DNA lineages in a single species. The lineages are usually well differentiated: up to 20-50% divergence in nucleotide sequence. Occasionally, a maternal mitochondrial DNA can invade the paternal transmission route, eventually replacing the diverged M-type and lowering the divergence. Such role reversal (masculinization) event has happened recently in the Mytilus population of the Baltic Sea which consists of M. edulis × M. trossulus hybrids, but the functional status of the resulting mitochondrial genome was unknown. RESULTS In this paper we sequenced transcripts from one specimen that was identified as male carrying both the female mitochondrial genome and a recently masculinized mitochondrial genome. Additionally, the analysis of the control region has showed that the recently masculinized, recombinant genome, not only has an M-type control region and all coding regions derived from the F-type, but also is transcriptionally active along side the maternally inherited F-type genome. In the comparative analysis, the two genomes exhibit different substitution patterns, typical for the M vs. F genome comparisons. The genetic distances and ratios of non-synonymous substitutions also suggest that one of the genomes is transitioning from the maternal to the paternal inheritance mode, consistent with its recent masculinization. CONCLUSION We have shown, for the first time, that the recently masculinized mitochondrial genome is active and that it accumulates excess of non-synonymous substitutions across its coding sequence. This suggests, that, under certain cytonuclear incompatibility conditions, masculinization may serve to restore the endangered functionality of the paternally inherited genome. This is also another example of a mitochondrial genome in which the recombination in the control region predated its transition from paternal to maternal transmission route.
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Affiliation(s)
- Tomasz J Sańko
- Genetics and Marine Biotechnology Department, Institute of Oceanology of Polish Academy of Sciences, Powstańców Warszawy 55, Sopot 81-712, Poland.
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244
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Wei W, Ning LW, Ye YN, Li SJ, Zhou HQ, Huang J, Guo FB. SMAL: A Resource of Spontaneous Mutation Accumulation Lines. Mol Biol Evol 2014; 31:1302-8. [DOI: 10.1093/molbev/msu073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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245
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Neupane J, Vandewoestyne M, Heindryckx B, Ghimire S, Lu Y, Qian C, Lierman S, Van Coster R, Gerris J, Deroo T, Deforce D, De Sutter P. A systematic analysis of the suitability of preimplantation genetic diagnosis for mitochondrial diseases in a heteroplasmic mitochondrial mouse model. Hum Reprod 2014; 29:852-9. [DOI: 10.1093/humrep/deu016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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246
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Friedman JR, Nunnari J. Mitochondrial form and function. Nature 2014; 505:335-43. [PMID: 24429632 DOI: 10.1038/nature12985] [Citation(s) in RCA: 1212] [Impact Index Per Article: 121.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/22/2013] [Indexed: 02/08/2023]
Abstract
Mitochondria are one of the major ancient endomembrane systems in eukaryotic cells. Owing to their ability to produce ATP through respiration, they became a driving force in evolution. As an essential step in the process of eukaryotic evolution, the size of the mitochondrial chromosome was drastically reduced, and the behaviour of mitochondria within eukaryotic cells radically changed. Recent advances have revealed how the organelle's behaviour has evolved to allow the accurate transmission of its genome and to become responsive to the needs of the cell and its own dysfunction.
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Affiliation(s)
- Jonathan R Friedman
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, California 95616, USA
| | - Jodi Nunnari
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, California 95616, USA
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247
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Mudd EA, Madesis P, Avila EM, Day A. Excision of plastid marker genes using directly repeated DNA sequences. Methods Mol Biol 2014; 1132:107-23. [PMID: 24599849 DOI: 10.1007/978-1-62703-995-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Excision of marker genes using DNA direct repeats makes use of the predominant homologous recombination pathways present in the plastids of algae and plants. The method is simple, efficient, and widely applicable to plants and microalgae. Marker excision frequency is dependent on the length and number of directly repeated sequences. When two repeats are used a repeat size of greater than 600 bp promotes efficient excision of the marker gene. A wide variety of sequences can be used to make the direct repeats. Only a single round of transformation is required, and there is no requirement to introduce site-specific recombinases by retransformation or sexual crosses. Selection is used to maintain the marker and ensure homoplasmy of transgenic plastid genomes. Release of selection allows the accumulation of marker-free plastid genomes generated by marker excision, which is spontaneous, random, and a unidirectional process. Positive selection is provided by linking marker excision to restoration of the coding region of an herbicide resistance gene from two overlapping but incomplete coding regions. Cytoplasmic sorting allows the segregation of cells with marker-free transgenic plastids. The marker-free shoots resulting from direct repeat-mediated excision of marker genes have been isolated by vegetative propagation of shoots in the T0 generation. Alternatively, accumulation of marker-free plastid genomes during growth, development and flowering of T0 plants allows the collection of seeds that give rise to a high proportion of marker-free T1 seedlings. The simplicity and convenience of direct repeat excision facilitates its widespread use to isolate marker-free crops.
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Affiliation(s)
- Elisabeth A Mudd
- Faculty of Life Sciences, The University of Manchester, Manchester, UK
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248
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Zhao Y, Yin J, Guo H, Zhang Y, Xiao W, Sun C, Wu J, Qu X, Yu J, Wang X, Xiao J. The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng. FRONTIERS IN PLANT SCIENCE 2014; 5:696. [PMID: 25642231 PMCID: PMC4294130 DOI: 10.3389/fpls.2014.00696] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 11/23/2014] [Indexed: 05/21/2023]
Abstract
Panax ginseng C.A. Meyer (P. ginseng) is an important medicinal plant and is often used in traditional Chinese medicine. With next generation sequencing (NGS) technology, we determined the complete chloroplast genome sequences for four Chinese P. ginseng strains, which are Damaya (DMY), Ermaya (EMY), Gaolishen (GLS), and Yeshanshen (YSS). The total chloroplast genome sequence length for DMY, EMY, and GLS was 156,354 bp, while that for YSS was 156,355 bp. Comparative genomic analysis of the chloroplast genome sequences indicate that gene content, GC content, and gene order in DMY are quite similar to its relative species, and nucleotide sequence diversity of inverted repeat region (IR) is lower than that of its counterparts, large single copy region (LSC) and small single copy region (SSC). A comparison among these four P. ginseng strains revealed that the chloroplast genome sequences of DMY, EMY, and GLS were identical and YSS had a 1-bp insertion at base 5472. To further study the heterogeneity in chloroplast genome during domestication, high-resolution reads were mapped to the genome sequences to investigate the differences at the minor allele level; 208 minor allele sites with minor allele frequencies (MAF) of ≥0.05 were identified. The polymorphism site numbers per kb of chloroplast genome sequence for DMY, EMY, GLS, and YSS were 0.74, 0.59, 0.97, and 1.23, respectively. All the minor allele sites located in LSC and IR regions, and the four strains showed the same variation types (substitution base or indel) at all identified polymorphism sites. Comparison results of heterogeneity in the chloroplast genome sequences showed that the minor allele sites on the chloroplast genome were undergoing purifying selection to adapt to changing environment during domestication process. A study of P. ginseng chloroplast genome with particular focus on minor allele sites would aid in investigating the dynamics on the chloroplast genomes and different P. ginseng strains typing.
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Affiliation(s)
- Yongbing Zhao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jinlong Yin
- School of Pharmaceutical Sciences, Changchun University of Chinese MedicineChangchun, China
| | - Haiyan Guo
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
| | - Yuyu Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Wen Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Chen Sun
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jiayan Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
| | - Xiaobo Qu
- School of Pharmaceutical Sciences, Changchun University of Chinese MedicineChangchun, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
| | - Xumin Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
- *Correspondence: Jingfa Xiao and Xumin Wang, Beijing Institute of Genomics, Chinese Academy of Sciences. NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China e-mail: ;
| | - Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
- *Correspondence: Jingfa Xiao and Xumin Wang, Beijing Institute of Genomics, Chinese Academy of Sciences. NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China e-mail: ;
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249
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Milani L, Ghiselli F, Guerra D, Breton S, Passamonti M. A comparative analysis of mitochondrial ORFans: new clues on their origin and role in species with doubly uniparental inheritance of mitochondria. Genome Biol Evol 2013; 5:1408-34. [PMID: 23824218 PMCID: PMC3730352 DOI: 10.1093/gbe/evt101] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite numerous comparative mitochondrial genomics studies revealing that animal mitochondrial genomes are highly conserved in terms of gene content, supplementary genes are sometimes found, often arising from gene duplication. Mitochondrial ORFans (ORFs having no detectable homology and unknown function) were found in bivalve molluscs with Doubly Uniparental Inheritance (DUI) of mitochondria. In DUI animals, two mitochondrial lineages are present: one transmitted through females (F-type) and the other through males (M-type), each showing a specific and conserved ORF. The analysis of 34 mitochondrial major Unassigned Regions of Musculista senhousia F- and M-mtDNA allowed us to verify the presence of novel mitochondrial ORFs in this species and to compare them with ORFs from other species with ascertained DUI, with other bivalves and with animals showing new mitochondrial elements. Overall, 17 ORFans from nine species were analyzed for structure and function. Many clues suggest that the analyzed ORFans arose from endogenization of viral genes. The co-option of such novel genes by viral hosts may have determined some evolutionary aspects of host life cycle, possibly involving mitochondria. The structure similarity of DUI ORFans within evolutionary lineages may also indicate that they originated from independent events. If these novel ORFs are in some way linked to DUI establishment, a multiple origin of DUI has to be considered. These putative proteins may have a role in the maintenance of sperm mitochondria during embryo development, possibly masking them from the degradation processes that normally affect sperm mitochondria in species with strictly maternal inheritance.
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Affiliation(s)
- Liliana Milani
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Bologna, Italy.
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Baltazar-Soares M, Biastoch A, Harrod C, Hanel R, Marohn L, Prigge E, Evans D, Bodles K, Behrens E, Böning CW, Eizaguirre C. Recruitment collapse and population structure of the European eel shaped by local ocean current dynamics. Curr Biol 2013; 24:104-108. [PMID: 24374306 DOI: 10.1016/j.cub.2013.11.031] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 09/24/2013] [Accepted: 11/15/2013] [Indexed: 11/17/2022]
Abstract
Worldwide, exploited marine fish stocks are under threat of collapse [1]. Although the drivers behind such collapses are diverse, it is becoming evident that failure to consider evolutionary processes in fisheries management can have drastic consequences on a species' long-term viability [2]. The European eel (Anguilla anguilla; Linnaeus, 1758) is no exception: not only does the steep decline in recruitment observed in the 1980s [3, 4] remain largely unexplained, the punctual detection of genetic structure also raises questions regarding the existence of a single panmictic population [5-7]. With its extended Transatlantic dispersal, pinpointing the role of ocean dynamics is crucial to understand both the population structure and the widespread decline of this species. Hence, we combined dispersal simulations using a half century of high-resolution ocean model data with population genetics tools. We show that regional atmospherically driven ocean current variations in the Sargasso Sea were the major driver of the onset of the sharp decline in eel recruitment in the beginning of the 1980s. The simulations combined with genotyping of natural coastal eel populations furthermore suggest that unexpected evidence of coastal genetic differentiation is consistent with cryptic female philopatric behavior within the Sargasso Sea. Such results demonstrate the key constraint of the variable oceanic environment on the European eel population.
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Affiliation(s)
- Miguel Baltazar-Soares
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany.
| | - Arne Biastoch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Chris Harrod
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Instituto de Ciencias Naturales Alexander Von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Reinhold Hanel
- Thünen-Institute of Fisheries Ecology, Palmaille 9, 22767 Hamburg, Germany
| | - Lasse Marohn
- Thünen-Institute of Fisheries Ecology, Palmaille 9, 22767 Hamburg, Germany
| | - Enno Prigge
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Derek Evans
- Fisheries and Aquatic Ecosystems Branch, Agri-Food and Biosciences Institute, Newforge Lane, Belfast BT9 5PX, UK
| | - Kenneth Bodles
- School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Erik Behrens
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Claus W Böning
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Christophe Eizaguirre
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany; School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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