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1. Silene tatarica microsatellites are frequently located in repetitive DNA

Author

R. Gudavalli, H. Neumeier, Christian Schlötterer, and N. Tero

Subjects
clone (Java method), DNA, Plant, Molecular Sequence Data, Biology, medicine.disease_cause, Polymerase Chain Reaction, Evolution, Molecular, chemistry.chemical_compound, Replication slippage, medicine, Cloning, Molecular, Silene, Repeated sequence, Ecology, Evolution, Behavior and Systematics, DNA Primers, Gene Library, Repetitive Sequences, Nucleic Acid, Sequence (medicine), Genetics, Cloning, Mutation, Base Sequence, chemistry, Microsatellite, Sequence Alignment, DNA, Microsatellite Repeats
Abstract

The genomic distribution of microsatellites can be explained by DNA slippage, slippage like processes and base substitutions. Nevertheless, microsatellites are also frequently associated with repetitive DNA, raising the question of the relative contributions of these processes to microsatellite genesis. We show that in Silene tatarica about 50% of the microsatellites isolated by an enrichment cloning protocol are associated with repetitive DNA. Based on the flanking sequences, we distinguished seven different classes of repetitive DNA. PCR primers designed for the flanking sequences of an individual clone amplified a heterogeneous family of repetitive DNA. Despite considerable variation in the flanking sequence (pi = 0.108), the microsatellite repeats did not show any evidence for decay. Rather, we observed the emergence of a new repeat type that probably arose by mutation and was spread by replication slippage. In fact, a complete repeat type switch could be observed among the analysed clones. We propose that the analysis of microsatellite sequences embedded in repetitive DNA provides a hitherto largely unexplored tool to study microsatellite evolution.

Published
2006
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2. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 June 2010 - 31 July 2010

Author

Cynthia Riginos, Rasanthi M. Gunasekera, James P. Hereward, Adam E. Vorsino, C. C. Vinson, Philippe Jarne, H. A. Rose, Joël Bried, Kittipath Prapayotin-Riveros, A. M. Risterucci, Angélique Quilichini, Mark G. Wright, Asta Audzijonyte, Hélène Delatte, Rebecca N. Johnson, Ryan A. Thum, Charles R. Vossbrinck, Yan Hong, Chunhong Li, Byeong-Wha Min, Akihiro Kijima, Pierre-Jean G. Malé, P. Charruau, Andrew J. Lowe, Karen-Ann Gray, Gregory J. Bugbee, A. Y. Ciampi, Woo-Jin Kim, Gudbjorg I. Aradottir, Steven J. Hanley, Minghui Liao, Jean-François Martin, Benjamin Fartek, Jae K. Noh, Manami Kanno, Bernard Reynaud, Hyun Chul Kim, K. Silbermayr, Paul J. DeBarro, Thibaut Malausa, D. Petro, Michelle D. Marko, Michael G. Gardner, Ania M. Wieczorek, Qi Jianfei, Chris Walzer, N. Tero, Samuel Nibouche, Kwan S. Kim, Emilie C. Bess, Ann E. Noack, Jeong-Ho Lee, Shotaro Hirase, G. Bourdel, Malvina Andris, Iracilda Sampaio, Mark D. B. Eldridge, Choul-Ji Park, Pamela A. Burger, Jang W. Lee, Nathan Havil, Jason C. White, D. Enkhbileg, Russell H. Messing, Jérôme Orivel, Laurent Costet, Jeong-In Myeong, Karen Miller, G. Arnau, Phillip R. England, Nathan Lo, Francesco Bonadonna, Elizabeth A. LaRue, Marivana Borges Silva, Marie-Pierre Dubois, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Department of Biomedical Sciences, Institute of Population Genetics, University of Veterinary Medicine, University of Veterinary Medicine, Research Institute of Wildlife Ecology, University of Veterinary Medicine, Department of Epidemiology, Biostatistics and Occupational Health [Montréal], McGill University, Institut de Chimie de Clermont-Ferrand (ICCF), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Sigma CLERMONT (Sigma CLERMONT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), School of Physics and Astronomy, University of Birmingham [Birmingham], Division of Cardiovascular Medicine, University of Cambridge [UK] (CAM), Birkbeck College [University of London], Department of Mathematical Sciences, TJ Watson, IBM, Southeast University [Jiangsu], State Key Lab. of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University [China], Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Ecologie des forêts de Guyane (ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université des Antilles et de la Guyane (UAG)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), School of Mechanical and Chemical Engineering, The University of Western Australia (UWA), Institut de recherche agricole pour le développement (IRAD), Ministère de la Recherche et de l'innovation, Department of Physics and Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology (KAIST), Paris-Jourdan Sciences Economiques (PSE), Centre National de la Recherche Scientifique (CNRS)-École des Ponts ParisTech (ENPC)-École des hautes études en sciences sociales (EHESS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Polymorphismes d'intérêt agronomique (UMR PIA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Technologie Servier, Institute of Arctic and Alpine Research (INSTAAR), University of Colorado [Boulder], Centre de recherche sur l'espace sonore et l'environnement urbain [1998-2014] (CRESSON [1998-2014]), Ambiances architecturales et urbaines (AAU), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Nantes (ECN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Nantes (ECN)-Ministère de la Culture et de la Communication (MCC), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), McGill University = Université McGill [Montréal, Canada], Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-SIGMA Clermont (SIGMA Clermont)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Recherche Agronomique (INRA)-École des hautes études en sciences sociales (EHESS)-École des Ponts ParisTech (ENPC)-Centre National de la Recherche Scientifique (CNRS), Institute of Arctic Alpine Research [University of Colorado Boulder] (INSTAAR), Centre de recherche sur l'espace sonore et l'environnement urbain (CRESSON), École Centrale de Nantes (ECN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Nantes (ECN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, École normale supérieure - Paris (ENS Paris), and Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture et de la Communication (MCC)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture et de la Communication (MCC)-École Centrale de Nantes (ECN)

Subjects
0106 biological sciences, Identification, [SDV]Life Sciences [q-bio], Banque de gènes, computer.software_genre, 01 natural sciences, F30 - Génétique et amélioration des plantes, GENBANK, Marqueur génétique, biology, Database, CATALOGUE, Dioscorea rotundata, Dioscorea trifida, Dioscorea, GENETIQUE DES POPULATIONS, Banque de données, ECOLOGIE, Biotechnology, Écologie, PHYLOGENY, Zoology, MOLECULAR MARKERS, Licania, ECOLOGY, 010603 evolutionary biology, Dioscorea transversa, Ressource génétique végétale, REFERENCEMENT, POPULATION GENETICS, Genetics, Ressource génétique animale, Dioscorea pentaphylla, Ecology, Evolution, Behavior and Systematics, Ressource génétique, Biologie moléculaire, TAXONOMY, biology.organism_classification, L10 - Génétique et amélioration des animaux, Tuberolachnus salignus, Hirtella, computer, 010606 plant biology & botany
Abstract

Correspondance: Molecular Ecology Resources Primer Development Consortium, E-mail: editorial.office@molecol.com; International audience; This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

Published
2011
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3. Local genetic population structure in an endangered plant species, Silene tatarica (Caryophyllaceae)

Author

Anne Jäkäläniemi, N. Tero, Jouni Aspi, and Pirkko Siikamäki

Subjects
DNA, Plant, Geography, Models, Genetic, Ecology, Silene tatarica, Caryophyllaceae, Genetic Variation, Biology, biology.organism_classification, Endangered plant species, Genetics, Population, Rivers, Botany, Seeds, Genetics, Pollen, Amplified fragment length polymorphism, Genetic population, Silene, Nucleic Acid Amplification Techniques, Genetics (clinical)
Abstract

Genetic substructuring in plant populations may evolve as a consequence of sampling events that occur when the population is founded or regenerated, or if gene dispersal by pollen and seeds is restricted within a population. Silene tatarica is an endangered, perennial plant species growing along periodically disturbed riverbanks in northern Finland. We investigated the mechanism behind the microspatial genetic structure of S. tatarica in four subpopulations using amplified fragment length polymorphism markers. Spatial autocorrelation revealed clear spatial genetic structure in each subpopulation, even though the pattern diminished in older subpopulations. Parentage analysis in an isolated island subpopulation indicated a very low level of selfing and avoidance of breeding between close relatives. The mean estimated pollen dispersal distance (24.10 m; SD = 10.5) was significantly longer and the mean seed dispersal distance (9.07 m; SD = 9.23) was considerably shorter than the mean distance between the individuals (19.20 m; SD = 13.80). The estimated indirect and direct estimates of neighbourhood sizes in this subpopulation were very similar, 32.1 and 37.6, respectively. Our results suggested that the local spatial genetic structure in S. tatarica was attributed merely to the isolation-by-distance process rather than founder effect, and despite free pollen movement across population, restricted seed dispersal maintains local genetic structure in this species.

Published
2005

4. Genetic structure and gene flow in a metapopulation of an endangered plant species, Silene tatarica

Author

Anne Jäkäläniemi, Juha Tuomi, Pirkko Siikamäki, Jouni Aspi, and N. Tero

Subjects
Population, Metapopulation, Biology, Linkage Disequilibrium, Gene flow, Coalescent theory, Russia, Rivers, Genetic variation, Genetics, Cluster Analysis, education, Silene, Ecology, Evolution, Behavior and Systematics, Finland, DNA Primers, education.field_of_study, Genetic diversity, Geography, Models, Genetic, Ecology, Genetic Variation, Bayes Theorem, Population bottleneck, Genetics, Population, Evolutionary biology, Genetic structure, Polymorphism, Restriction Fragment Length
Abstract

We investigated the distribution of genetic variation within and between seven subpopulations in a riparian population of Silene tatarica in northern Finland by using amplified fragment length polymorphism (AFLP) markers. A Bayesian approach-based clustering program indicated that the marker data contained not only one panmictic population, but consisted of seven clusters, and that each original sample site seems to consist of a distinct subpopulation. A coalescent-based simulation approach shows recurrent gene flow between subpopulations. Relative high FST values indicated a clear subpopulation differentiation. However, amova analysis and UPGMA-dendrogram did not suggest any hierarchical regional structuring among the subpopulations. There was no correlation between geographical and genetic distances among the subpopulations, nor any correlation between the subpopulation census size and amount of genetic variation. Estimates of gene flow suggested a low level of gene flow between the subpopulations, and the assignment tests proposed a few long-distance bidirectional dispersal events between the subpopulations. No apparent difference was found in within-subpopulation genetic diversity among upper, middle and lower regions along the river. Relative high amounts of linkage disequilibrium at subpopulation level indicated recent population bottlenecks or admixture, and at metapopulation levels a high subpopulation turnover rate. The overall pattern of genetic variation within and between subpopulations also suggested a 'classical' metapopulation structure of the species suggested by the ecological surveys.

Published
2003

5. Isolation and characterization of microsatellite loci from Silene tatarica

Author

Christian Schlötterer and N. Tero

Subjects
Genetics, education.field_of_study, Ecology, Population, Caryophyllaceae, Locus (genetics), Biology, biology.organism_classification, Biochemistry, General Biochemistry, Genetics and Molecular Biology, Loss of heterozygosity, Genotype, Microsatellite, Allele, education, Gene
Abstract

Five new microsatellite loci were isolated from the perennial plant, Silene tatarica. We characterized S. tatarica individuals originating from two riverbank populations in northern Finland and observed between four and nine alleles per locus. Observed heterozygosity was consistently lower than gene diversity (HO: 0.0450–0.2385, HE: 0.1919–0.6187). This deficiency of heterozygous genotypes was observed in most locus/population combinations, and is presumably caused by spatial genetic structuring due to restricted seed flow within subpopulations. The markers presented here are the first microsatellites reported for S. tatarica.

Published
2005
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6. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 June 2010 - 31 July 2010.

Author

Andris M, Aradottir GI, Arnau G, Audzijonyte A, Bess EC, Bonadonna F, Bourdel G, Bried J, Bugbee GJ, Burger PA, Chair H, Charruau PC, Ciampi AY, Costet L, Debarro PJ, Delatte H, Dubois MP, Eldridge MD, England PR, Enkhbileg D, Fartek B, Gardner MG, Gray KA, Gunasekera RM, Hanley SJ, Havil N, Hereward JP, Hirase S, Hong Y, Jarne P, Jianfei Q, Johnson RN, Kanno M, Kijima A, Kim HC, Kim KS, Kim WJ, Larue E, Lee JW, Lee JH, Li C, Liao M, Lo N, Lowe AJ, Malausa T, Malé PJ, Marko MD, Martin JF, Messing R, Miller KJ, Min BW, Myeong JI, Nibouche S, Noack AE, Noh JK, Orivel J, Park CJ, Petro D, Prapayotin-Riveros K, Quilichini A, Reynaud B, Riginos C, Risterucci AM, Rose HA, Sampaio I, Silbermayr K, Silva MB, Tero N, Thum RA, Vinson CC, Vorsino A, Vossbrinck CR, Walzer C, White JC, Wieczorek A, and Wright M

Abstract

This article documents the addition of 205 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Bagassa guianensis, Bulweria bulwerii, Camelus bactrianus, Chaenogobius annularis, Creontiades dilutus, Diachasmimorpha tryoni, Dioscorea alata, Euhrychiopsis lecontei, Gmelina arborea, Haliotis discus hannai, Hirtella physophora, Melanaphis sacchari, Munida isos, Thaumastocoris peregrinus and Tuberolachnus salignus. These loci were cross-tested on the following species: Halobaena caerulea, Procellaria aequinoctialis, Oceanodroma monteiroi, Camelus ferus, Creontiades pacificus, Dioscorea rotundata, Dioscorea praehensilis, Dioscorea abyssinica, Dioscorea nummularia, Dioscorea transversa, Dioscorea esculenta, Dioscorea pentaphylla, Dioscorea trifida, Hirtella bicornis, Hirtella glandulosa, Licania alba, Licania canescens, Licania membranaceae, Couepia guianensis and 7 undescribed Thaumastocoris species., (© 2010 Blackwell Publishing Ltd.)

Published
2010
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7. Local genetic population structure in an endangered plant species, Silene tatarica (Caryophyllaceae).

Author

Tero N, Aspi J, Siikamäki P, and Jäkäläniemi A

Subjects
DNA, Plant genetics, Genetics, Population, Geography, Nucleic Acid Amplification Techniques, Pollen, Rivers, Genetic Variation, Models, Genetic, Seeds genetics, Silene genetics
Abstract

Genetic substructuring in plant populations may evolve as a consequence of sampling events that occur when the population is founded or regenerated, or if gene dispersal by pollen and seeds is restricted within a population. Silene tatarica is an endangered, perennial plant species growing along periodically disturbed riverbanks in northern Finland. We investigated the mechanism behind the microspatial genetic structure of S. tatarica in four subpopulations using amplified fragment length polymorphism markers. Spatial autocorrelation revealed clear spatial genetic structure in each subpopulation, even though the pattern diminished in older subpopulations. Parentage analysis in an isolated island subpopulation indicated a very low level of selfing and avoidance of breeding between close relatives. The mean estimated pollen dispersal distance (24.10 m; SD = 10.5) was significantly longer and the mean seed dispersal distance (9.07 m; SD = 9.23) was considerably shorter than the mean distance between the individuals (19.20 m; SD = 13.80). The estimated indirect and direct estimates of neighbourhood sizes in this subpopulation were very similar, 32.1 and 37.6, respectively. Our results suggested that the local spatial genetic structure in S. tatarica was attributed merely to the isolation-by-distance process rather than founder effect, and despite free pollen movement across population, restricted seed dispersal maintains local genetic structure in this species.

Published
2005
Full Text
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8. Genetic structure and gene flow in a metapopulation of an endangered plant species, Silene tatarica.

Author

Tero N, Aspi J, Siikamäki P, Jäkäläniemi A, and Tuomi J

Subjects
Bayes Theorem, Cluster Analysis, DNA Primers, Finland, Geography, Linkage Disequilibrium, Polymorphism, Restriction Fragment Length, Rivers, Russia, Genetic Variation, Genetics, Population, Models, Genetic, Silene genetics
Abstract

We investigated the distribution of genetic variation within and between seven subpopulations in a riparian population of Silene tatarica in northern Finland by using amplified fragment length polymorphism (AFLP) markers. A Bayesian approach-based clustering program indicated that the marker data contained not only one panmictic population, but consisted of seven clusters, and that each original sample site seems to consist of a distinct subpopulation. A coalescent-based simulation approach shows recurrent gene flow between subpopulations. Relative high FST values indicated a clear subpopulation differentiation. However, amova analysis and UPGMA-dendrogram did not suggest any hierarchical regional structuring among the subpopulations. There was no correlation between geographical and genetic distances among the subpopulations, nor any correlation between the subpopulation census size and amount of genetic variation. Estimates of gene flow suggested a low level of gene flow between the subpopulations, and the assignment tests proposed a few long-distance bidirectional dispersal events between the subpopulations. No apparent difference was found in within-subpopulation genetic diversity among upper, middle and lower regions along the river. Relative high amounts of linkage disequilibrium at subpopulation level indicated recent population bottlenecks or admixture, and at metapopulation levels a high subpopulation turnover rate. The overall pattern of genetic variation within and between subpopulations also suggested a 'classical' metapopulation structure of the species suggested by the ecological surveys.

Published
2003
Full Text
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