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Adriaens T, Baert K, Breyne P, Casaer J, Devisscher S, Onkelinx T, Pieters S, Stuyck J. Successful eradication of a suburban Pallas’s squirrel Callosciurus erythraeus (Pallas 1779) (Rodentia, Sciuridae) population in Flanders (northern Belgium). Biol Invasions 2015. [DOI: 10.1007/s10530-015-0898-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Frantz AC, McDevitt AD, Pope LC, Kochan J, Davison J, Clements CF, Elmeros M, Molina-Vacas G, Ruiz-Gonzalez A, Balestrieri A, Van Den Berge K, Breyne P, Do Linh San E, Ågren EO, Suchentrunk F, Schley L, Kowalczyk R, Kostka BI, Ćirović D, Šprem N, Colyn M, Ghirardi M, Racheva V, Braun C, Oliveira R, Lanszki J, Stubbe A, Stubbe M, Stier N, Burke T. Revisiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations. Heredity (Edinb) 2014; 113:443-53. [PMID: 24781805 PMCID: PMC4220720 DOI: 10.1038/hdy.2014.45] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 02/04/2014] [Accepted: 02/14/2014] [Indexed: 11/09/2022] Open
Abstract
Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples from western Europe, making it difficult to draw robust conclusions about the location of refugia, patterns of postglacial expansion and recent demography. In the present study, continent-wide sampling and analyses with multiple markers provided evidence for two glacial refugia (Iberia and southeast Europe) that contributed to the genetic variation observed in badgers in Europe today. Approximate Bayesian computation provided support for a colonisation of Scandinavia from both Iberian and southeastern refugia. In the whole of Europe, we observed a decline in genetic diversity with increasing latitude, suggesting that the reduced diversity in the peripheral populations resulted from a postglacial expansion processes. Although MSVAR v.1.3 also provided evidence for recent genetic bottlenecks in some of these peripheral populations, the simulations performed to estimate the method's power to correctly infer the past demography of our empirical populations suggested that the timing and severity of bottlenecks could not be established with certainty. We urge caution against trying to relate demographic declines inferred using MSVAR with particular historic or climatological events.
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Affiliation(s)
- A C Frantz
- NERC Biomolecular Analysis Facility,
Department of Animal and Plant Sciences, University of Sheffield,
Sheffield, UK
- Musée National d'Histoire
Naturelle, Luxembourg, Luxembourg
| | - A D McDevitt
- School of Biology and Environmental
Science, University College Dublin, Dublin,
Ireland
| | - L C Pope
- School of Biological Science, University
of Queensland, St Lucia, Queensland,
Australia
| | - J Kochan
- Department of Genetics and Animal
Breeding, Wrocław University of Environmental and Life Sciences,
Wrocław, Poland
| | - J Davison
- Institute of Ecology and Earth Sciences,
University of Tartu, Tartu, Estonia
| | - C F Clements
- NERC Biomolecular Analysis Facility,
Department of Animal and Plant Sciences, University of Sheffield,
Sheffield, UK
| | - M Elmeros
- Department of Bioscience, Aarhus
University, Rønde, Denmark
| | - G Molina-Vacas
- Animal Biology Department, University of
Barcelona, Barcelona, Spain
| | - A Ruiz-Gonzalez
- Department of Zoology, Biogeography and
Population Dynamics Research Group, University of the Basque Country,
UPV/EHU, Vitoria-Gasteiz, Spain
| | - A Balestrieri
- Department of Biosciences, University
of Milan, Milan, Italy
| | - K Van Den Berge
- Research Institute for Nature and
Forest, Geraardsbergen, Belgium
| | - P Breyne
- Research Institute for Nature and
Forest, Geraardsbergen, Belgium
| | - E Do Linh San
- Department of Zoology and Entomology,
University of Fort Hare, Alice, South Africa
| | - E O Ågren
- National Veterinary Institute,
Department of Pathology and Wildlife Diseases, Uppsala,
Sweden
| | - F Suchentrunk
- Research Institute of Wildlife Ecology,
University of Veterinary Medicine Vienna, Vienna,
Austria
| | - L Schley
- Administration de la nature et des
forêts, Luxembourg, Luxembourg
| | - R Kowalczyk
- Mammal Research Institute,
Bialowieza, Poland
| | - B I Kostka
- Queen's University Belfast,
Northern Ireland, UK
| | - D Ćirović
- Faculty of Biology, University of
Belgrade, Belgrade, Serbia
| | - N Šprem
- Department of Fisheries, Beekeeping,
Game Management and Special Zoology, University of Zagreb,
Zagreb, Croatia
| | - M Colyn
- CNRS, UMR 6553, ECOBIO,
Université de Rennes 1, Rennes, France
| | - M Ghirardi
- Università degli Studi di
Torino, Torino, Italy
| | - V Racheva
- Balkani Wildlife Society,
Sofia, Bulgaria
| | - C Braun
- 9 chemin du Kilbs,
Bischoffsheim, France
| | - R Oliveira
- Departamento de Zoologia e
Antropologia, Faculdade de Ciências da Universidade do Porto,
Porto, Portugal
| | - J Lanszki
- Department of Nature Conservation,
University of Kaposvár, Kaposvár,
Hungary
| | - A Stubbe
- Domplatz 4,
Halle/Saale, Germany
| | - M Stubbe
- Domplatz 4,
Halle/Saale, Germany
| | - N Stier
- Institute of Forest Botany and Forest
Zoology, Dresden University of Technology, Tharandt,
Germany
| | - T Burke
- NERC Biomolecular Analysis Facility,
Department of Animal and Plant Sciences, University of Sheffield,
Sheffield, UK
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Vandepitte K, Honnay O, Mergeay J, Breyne P, Roldán-Ruiz I, De Meyer T. SNP discovery using Paired-End RAD-tag sequencing on pooled genomic DNA of Sisymbrium austriacum (Brassicaceae). Mol Ecol Resour 2012; 13:269-75. [PMID: 23231662 DOI: 10.1111/1755-0998.12039] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 10/22/2012] [Accepted: 10/30/2012] [Indexed: 12/22/2022]
Abstract
Single nucleotide polymorphisms SNPs are rapidly replacing anonymous markers in population genomic studies, but their use in non model organisms is hampered by the scarcity of cost-effective approaches to uncover genome-wide variation in a comprehensive subset of individuals. The screening of one or only a few individuals induces ascertainment bias. To discover SNPs for a population genomic study of the Pyrenean rocket (Sisymbrium austriacum subsp. chrysanthum), we undertook a pooled RAD-PE (Restriction site Associated DNA Paired-End sequencing) approach. RAD tags were generated from the PstI-digested pooled genomic DNA of 12 individuals sampled across the species distribution range and paired-end sequenced using Illumina technology to produce ~24.5 Mb of sequences, covering ~7% of the specie's genome. Sequences were assembled into ~76 000 contigs with a mean length of 323 bp (N(50) = 357 bp, sequencing depth = 24x). In all, >15 000 SNPs were called, of which 47% were annotated in putative genic regions based on homology with the Arabidopsis thaliana genome. Gene ontology (GO) slim categorization demonstrated that the identified SNPs covered extant genic variation well. The validation of 300 SNPs on a larger set of individuals using a KASPar assay underpinned the utility of pooled RAD-PE as an inexpensive genome-wide SNP discovery technique (success rate: 87%). In addition to SNPs, we discovered >600 putative SSR markers.
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Affiliation(s)
- K Vandepitte
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Kasteelpark Arenberg 31, Heverlee, B-3001, Belgium.
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4
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Jacquemyn H, Van Looy K, Breyne P, Honnay O. The Meuse river as a corridor for range expansion of the exotic plant species Sisymbrium austriacum: evidence for long-distance seed dispersal. Biol Invasions 2009. [DOI: 10.1007/s10530-009-9461-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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De Cock K, Vander Mijnsbrugge K, Breyne P, Van Bockstaele E, Van Slycken J. Morphological and AFLP-based differentiation within the taxonomical complex section Caninae (subgenus Rosa). Ann Bot 2008; 102:685-97. [PMID: 18723861 PMCID: PMC2712374 DOI: 10.1093/aob/mcn151] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS The taxonomical structure of the polymorphic subgenus Rosa section Caninae is highly complex due to the combination of some unusual features: the unique polyploid chromosomal constitution, the heterogamic canina meiosis, the ability to hybridize interspecifically, and the predominantly matroclinal inheritance. Although most taxonomists agree on the subdivision of the section into three morphologically well-defined groups (Rubigineae, Vestitae, and Caninae), they disagree on the existence of smaller groups such as Tomentellae. The aim was to gain insight in the taxonomical structure and investigate the interpopulation differentiation of the polymorphic section Caninae by analysing morphological and AFLP-based characters of the seven most common Belgian dog-rose taxa. METHODS The intersubsectional and -specific relationships within the dog-roses were examined using morphological and molecular-genetic markers. AFLP data were analysed with basic descriptive genetic statistics because of the lack of Hardy-Weinberg equilibrium due to the polyploid genetic structure and heterogamic meiosis. KEY RESULTS Both the morphological and AFLP-based analyses supported the subdivision of the dog-roses in three well-defined though partly overlapping groups, Rubigineae, Vestitae and Caninae. However, it was not possible to distinguish between the morphologically well-defined taxa within the same subsection using AFLP-based data. In addition, the results suggested a high similarity of Rosa balsamica with subsection Caninae taxa. Small-scale geographical AFLP-based differentiation was observed within several dog-rose taxa. Surprisingly, individuals sampled at one locality and belonging to morphologically distinct dog-rose taxa displayed higher genetic similarities in comparison to their congeners sampled at different localities. CONCLUSIONS The hybridogenic character of the dog-roses was reflected in the vague boundaries between the subsections and on the species level within the subsections. Indications were found for current or historical hybridization on the genetic structure of the population. No morphological or AFLP-based evidence was obtained to support the existence of the separate subsection Tomentellae.
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Affiliation(s)
- Katrien De Cock
- Research Institute for Nature and Forest (INBO), Scientific Institute of the Flemish Government, Kliniekstraat 25, B-1070 Brussels, Belgium
| | - Kristine Vander Mijnsbrugge
- Research Institute for Nature and Forest (INBO), Scientific Institute of the Flemish Government, Kliniekstraat 25, B-1070 Brussels, Belgium
| | - Peter Breyne
- Research Institute for Nature and Forest (INBO), Scientific Institute of the Flemish Government, Kliniekstraat 25, B-1070 Brussels, Belgium
- For correspondence. E-mail
| | - Erik Van Bockstaele
- Institute for Agricultural and Fisheries Research (ILVO), Scientific Institute of the Flemish Government, Burg. Van Gansbergelaan 96 bus 1,B-9820 Merelbeke, Belgium
| | - Jos Van Slycken
- Research Institute for Nature and Forest (INBO), Scientific Institute of the Flemish Government, Kliniekstraat 25, B-1070 Brussels, Belgium
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De Cock K, Vander Mijnsbrugge K, Breyne P, Nybom H, Smulders M, Van Slycken J, De Riek J. THE DIVERSITY OF AUTOCHTHONOUS ROSES IN FLANDERS (BELGIUM) IN THE VIEW OF THE EUROPEAN GENEROSE REFERENCE FRAMEWORK. ACTA ACUST UNITED AC 2007. [DOI: 10.17660/actahortic.2007.760.88] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Scheppers TLJ, Roper TJ, Frantz AC, Schaul M, Engel E, Breyne P, Schley L. Estimating social group size of Eurasian badgers Meles meles by genotyping remotely plucked single hairs. Wildlife Biology 2007. [DOI: 10.2981/0909-6396(2007)13[195:esgsoe]2.0.co;2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Measey GJ, Galbusera P, Breyne P, Matthysen E. Gene flow in a direct-developing, leaf litter frog between isolated mountains in the Taita Hills, Kenya. CONSERV GENET 2007. [DOI: 10.1007/s10592-006-9272-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Morreel K, Goeminne G, Storme V, Sterck L, Ralph J, Coppieters W, Breyne P, Steenackers M, Georges M, Messens E, Boerjan W. Genetical metabolomics of flavonoid biosynthesis in Populus: a case study. Plant J 2006; 47:224-37. [PMID: 16774647 DOI: 10.1111/j.1365-313x.2006.02786.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Genetical metabolomics [metabolite profiling combined with quantitative trait locus (QTL) analysis] has been proposed as a new tool to identify loci that control metabolite abundances. This concept was evaluated in a case study with the model tree Populus. Using HPLC, the peak abundances were analyzed of 15 closely related flavonoids present in apical tissues of two full-sib poplar families, Populus deltoides cv. S9-2 x P. nigra cv. Ghoy and P. deltoides cv. S9-2 x P. trichocarpa cv. V24, and correlation and QTL analysis were used to detect flux control points in flavonoid biosynthesis. Four robust metabolite quantitative trait loci (mQTL), associated with rate-limiting steps in flavonoid biosynthesis, were mapped. Each mQTL was involved in the flux control to one or two flavonoids. Based on the identities of the affected metabolites and the flavonoid pathway structure, a tentative function was assigned to three of these mQTL, and the corresponding candidate genes were mapped. The data indicate that the combination of metabolite profiling with QTL analysis is a valuable tool to identify control points in a complex metabolic pathway of closely related compounds.
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Affiliation(s)
- Kris Morreel
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, B-9052 Gent, Belgium
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Pertoldi C, Breyne P, Cabria MT, Halfmaerten D, Jansman HAH, Van Den Berge K, Madsen AB, Loeschcke V. Genetic structure of the European polecat (
Mustela putorius
) and its implication for conservation strategies. J Zool (1987) 2006. [DOI: 10.1111/j.1469-7998.2006.00095.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C. Pertoldi
- Department of Ecology and Genetics, University of Aarhus, Ny Munkegade, Aarhus C, Denmark
- Department of Applied Biology, Estación Biológica Doñana, CSIC, Pabellón del Perú, Seville, Spain
- Department of Wildlife Ecology and Biodiversity, National Environmental Research Institute, Rønde, Denmark
| | - P. Breyne
- Institute for Forestry and Game Management, Gaverstraat, Geraardsbergen, Belgium
| | - M. T. Cabria
- Departamento Zoologia y BCA, Facultad Farmacia, Universidad del Pais Vasco, Vitoria‐Gasteiz, Spain
| | - D. Halfmaerten
- Institute for Forestry and Game Management, Gaverstraat, Geraardsbergen, Belgium
| | - H. A. H. Jansman
- Alterra‐Centre for Ecosystem Studies, AA Wageningen, The Netherlands
| | - K. Van Den Berge
- Institute for Forestry and Game Management, Gaverstraat, Geraardsbergen, Belgium
| | - A. B. Madsen
- Department of Wildlife Ecology and Biodiversity, National Environmental Research Institute, Rønde, Denmark
| | - V. Loeschcke
- Department of Ecology and Genetics, University of Aarhus, Ny Munkegade, Aarhus C, Denmark
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Jacquemyn H, Honnay O, Van Looy K, Breyne P. Spatiotemporal structure of genetic variation of a spreading plant metapopulation on dynamic riverbanks along the Meuse River. Heredity (Edinb) 2006; 96:471-8. [PMID: 16622473 DOI: 10.1038/sj.hdy.6800825] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Long-distance seed dispersal is a crucial determinant of within-population genetic variability and among-population genetic differentiation in plant metapopulations undergoing recurrent local extinctions and (re-)colonization. We investigated the spatial and temporal structure of genetic variation in a metapopulation of Sisymbrium austriacum located along a dynamic river system using dominant AFLP markers. Data on riverbank dynamics and colonization history allowed separating populations based on their age (< or =5 vs >5 years old). Bayesian analysis of population genetic structure indicated that populations were significantly differentiated from each other, but Mantel tests revealed that there was no relationship between pairwise geographic and genetic distances, suggesting that long-distance seed dispersal partly determines spatial genetic structure. Recent populations were less differentiated from each other than old populations. Analysis of molecular variance (AMOVA) indicated that both spatial factors and population age significantly determined genetic diversity, the effects of age being more important than spatial location. Clustering analysis revealed five large clusters, which were related primarily to population age and to a minor extent to geographical location. Our results indicate that the recurrent formation and destruction of riverbank habitats following peak flow events have a large impact on genetic diversity of riparian plant species.
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Affiliation(s)
- H Jacquemyn
- Division Forest, Nature and Landscape Research, Catholic University of Leuven, Celestijnenlaan 200E, Leuven B-3001, Belgium.
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Hardy OJ, Maggia L, Bandou E, Breyne P, Caron H, Chevallier MH, Doligez A, Dutech C, Kremer A, Latouche-Hallé C, Troispoux V, Veron V, Degen B. Fine-scale genetic structure and gene dispersal inferences in 10 neotropical tree species. Mol Ecol 2006; 15:559-71. [PMID: 16448421 DOI: 10.1111/j.1365-294x.2005.02785.x] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics of tropical tree species, but directly monitoring seed and pollen movement is a difficult task. However, indirect estimates of historical gene dispersal can be obtained from the fine-scale spatial genetic structure of populations at drift-dispersal equilibrium. Using an approach that is based on the slope of the regression of pairwise kinship coefficients on spatial distance and estimates of the effective population density, we compare indirect gene dispersal estimates of sympatric populations of 10 tropical tree species. We re-analysed 26 data sets consisting of mapped allozyme, SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA) or AFLP (amplified fragment length polymorphism) genotypes from two rainforest sites in French Guiana. Gene dispersal estimates were obtained for at least one marker in each species, although the estimation procedure failed under insufficient marker polymorphism, limited sample size, or inappropriate sampling area. Estimates generally suffered low precision and were affected by assumptions regarding the effective population density. Averaging estimates over data sets, the extent of gene dispersal ranged from 150 m to 1200 m according to species. Smaller gene dispersal estimates were obtained in species with heavy diaspores, which are presumably not well dispersed, and in populations with high local adult density. We suggest that limited seed dispersal could indirectly limit effective pollen dispersal by creating higher local tree densities, thereby increasing the positive correlation between pollen and seed dispersal distances. We discuss the potential and limitations of our indirect estimation procedure and suggest guidelines for future studies.
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Affiliation(s)
- Olivier J Hardy
- Université Libre de Bruxelles, Service d'Eco-Ethologie Evolutive, CP 160/12, 50 Av. F. Roosevelt, B-1050 Brussels, Belgium.
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Maertens I, Breyne P, Steenackers M, Gheysen G. Identification of genes involved in vertical rust resistance in poplar. Commun Agric Appl Biol Sci 2004; 69:171-3. [PMID: 15560214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Affiliation(s)
- Inge Maertens
- Vakgroep Moleculaire Biotechnologie, Universiteit Gent, Coupure links 653, B-9000 Gent, Belgium
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Breyne P, Dreesen R, Cannoot B, Rombaut D, Vandepoele K, Rombauts S, Vanderhaeghen R, Inzé D, Zabeau M. Quantitative cDNA-AFLP analysis for genome-wide expression studies. Mol Genet Genomics 2003; 269:173-9. [PMID: 12756529 DOI: 10.1007/s00438-003-0830-6] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2002] [Accepted: 02/05/2003] [Indexed: 11/25/2022]
Abstract
An improved cDNA-AFLP method for genome-wide expression analysis has been developed. We demonstrate that this method is an efficient tool for quantitative transcript profiling and a valid alternative to microarrays. Unique transcript tags, generated from reverse-transcribed messenger RNA by restriction enzymes, were screened through a series of selective PCR amplifications. Based on in silico analysis, an enzyme combination was chosen that ensures that at least 60% of all the mRNAs were represented by an informative sequence tag. The sensitivity and specificity of the method allows one to detect poorly expressed genes and distinguish between homologous sequences. Accurate gene expression profiles were determined by quantitative analysis of band intensities, and subtle differences in transcriptional activity were revealed. A detailed screen for cell cycle-modulated genes in tobacco demonstrates the usefulness of the technology for genome-wide expression analysis.
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Affiliation(s)
- P Breyne
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, K.L. Ledeganckstraat 35, Belgium
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Lowe AJ, Jourde B, Breyne P, Colpaert N, Navarro C, Wilson J, Cavers S. Fine-scale genetic structure and gene flow within Costa Rican populations of mahogany (Swietenia macrophylla). Heredity (Edinb) 2003; 90:268-75. [PMID: 12634811 DOI: 10.1038/sj.hdy.6800247] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Fine-scale structure of genetic diversity and gene flow were analysed in three Costa Rican populations of mahogany, Swietenia macrophylla. Population differentiation estimated using AFLPs and SSRs was low (38.3 and 24%) and only slightly higher than previous estimates for Central American populations based on RAPD variation (20%). Significant fine-scale spatial structure was found in all of the surveyed mahogany populations and is probably strongly influenced by the limited seed dispersal range of the species. Furthermore, a survey of progeny arrays from selected mother trees in two of the plots indicated that most pollinations involved proximate trees. These data indicate that very little gene flow, via either pollen or seed, is occurring between blocks of mahogany within a continuous or disturbed forest landscape. Thus, once diversity is removed from a forest population of mahogany, these data suggest that recovery would be difficult via seed or pollen dispersal, and provides an explanation for mahogany's apparent susceptibility to the pressures of logging. Evidence is reviewed from other studies of gene flow and seedling regeneration to discuss alternative extraction strategies that may maintain diversity or allow recovery of genetic resources.
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Affiliation(s)
- A J Lowe
- Centre for Ecology and Hydrology-Edinburgh, Bush Estate, Penicuik, Midlothian EH26 0QB, Scotland, UK.
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Breyne P, Dreesen R, Vandepoele K, De Veylder L, Van Breusegem F, Callewaert L, Rombauts S, Raes J, Cannoot B, Engler G, Inzé D, Zabeau M. Transcriptome analysis during cell division in plants. Proc Natl Acad Sci U S A 2002; 99:14825-30. [PMID: 12393816 PMCID: PMC137503 DOI: 10.1073/pnas.222561199] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2002] [Accepted: 09/16/2002] [Indexed: 11/18/2022] Open
Abstract
Using synchronized tobacco Bright Yellow-2 cells and cDNA-amplified fragment length polymorphism-based genomewide expression analysis, we built a comprehensive collection of plant cell cycle-modulated genes. Approximately 1,340 periodically expressed genes were identified, including known cell cycle control genes as well as numerous unique candidate regulatory genes. A number of plant-specific genes were found to be cell cycle modulated. Other transcript tags were derived from unknown plant genes showing homology to cell cycle-regulatory genes of other organisms. Many of the genes encode novel or uncharacterized proteins, indicating that several processes underlying cell division are still largely unknown.
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Affiliation(s)
- Peter Breyne
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, K.L. Ledeganckstraat 35, Belgium
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17
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Van Droogenbroeck B, Breyne P, Goetghebeur P, Romeijn-Peeters E, Kyndt T, Gheysen G. AFLP analysis of genetic relationships among papaya and its wild relatives (Caricaceae) from Ecuador. Theor Appl Genet 2002; 105:289-297. [PMID: 12582531 DOI: 10.1007/s00122-002-0983-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2001] [Accepted: 03/04/2002] [Indexed: 05/24/2023]
Abstract
The AFLP technique was used to assess the genetic relationships among the cultivated papaya ( Carica papaya L.) and related species native to Ecuador. Genetic distances based on AFLP data were estimated for 95 accessions belonging to three genera including C. papaya, at least eight Vasconcella species and two Jacaratia species. Cluster analysis using different methods and principal co-ordinate analysis (PCO), based on the AFLP data from 496 polymorphic bands generated with five primer combinations, was performed. The resulted grouping of accessions of each species corresponds largely with their taxonomic classifications and were found to be consistent with other studies based on RAPD, isozyme and cpDNA data. The AFLP analysis supports the recent rehabilitation of the Vasconcella group as a genus; until recently Vasconcella was considered as a section within the genus Carica. Both cluster and PCO analysis clearly separated the species of the three genera and illustrated the large genetic distance between C. papaya accessions and the Vasconcella group. The specific clustering of the highly diverse group of Vasconcella x heilbornii accessions also suggests that these genotypes may be the result of bi-directional introgression events between Vasconcella stipulata and Vasconcella cundinamarcensis.
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Affiliation(s)
- B. Van Droogenbroeck
- Department of Molecular Biotechnology, Faculty of Agricultural and Applied Biological Sciences, Ghent University, Coupure links 653, B-9000 Gent, Belgium
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18
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Abstract
Genome-wide expression analysis is rapidly becoming an essential tool for identifying and analysing genes involved in, or controlling, various biological processes ranging from development to responses to environmental cues. The control of cell division involves the temporal expression of different sets of genes, allowing the dividing cell to progress through the different phases of the cell cycle. A landmark study using DNA microarrays to follow the patterns of gene expression in synchronously dividing yeast cells has allowed the identification of several hundreds of genes that are involved in the cell cycle. Although DNA microarrays provide a convenient tool for genome-wide expression analysis, their use is limited to organisms for which the complete genome sequence or a large cDNA collection is available. For other organisms, including most plant species, DNA fragment analysis based methods, such as cDNA-AFLP, provide a more appropriate tool for genome-wide expression analysis. Furthermore, cDNA-AFLP exhibits properties that complement DNA microarrays and, hence, constitutes a useful tool for gene discovery.
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Affiliation(s)
- P Breyne
- Departement Plantengenetica, Vlaams Interuniversitair Instituut voor Biotechnologie, Universiteit Gent, K.L. Ledeganckstraat 35, B-9000, Gent, Belgium
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19
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Neves-Borges AC, Collares WM, Pontes JA, Breyne P, Farinelli L, de Oliveira DE. Coat protein RNAs-mediated protection against Andean potato mottle virus in transgenic tobacco. Plant Sci 2001; 160:699-712. [PMID: 11448745 DOI: 10.1016/s0168-9452(00)00452-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The expression of translatable sequences of either one of the two Andean potato mottle virus (APMoV) coat protein (CP) genes (CP22 and CP42) and of the nontranslatable sequence of CP42 in transgenic tobacco provided protection against APMoV. Resistance was mediated by CP transgene RNAs rather than the protein, as an inverse correlation between resistance and the accumulation levels of CPs transgene mRNAs was observed. These data indicated that a post-transcriptional gene silencing (PTGS) mechanism is likely involved in the APMoV CP RNA-mediated protection. Moreover, the HindIII-AccI restriction pattern of the CP22 transgene was different in susceptible and resistant transgenic plants, suggesting the involvement of methylation in PTGS. Southern blot experiments also revealed that CPs transgene insertion loci and organisation in the plant genome may play a role in determining the degree of protection.
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Affiliation(s)
- A C. Neves-Borges
- Laboratório de Genética Molecular Vegetal, Departamento de Genética, Instituto de Biologia, CCS, UFRJ, CEP 21944-970, RJ, Rio de Janeiro, Brazil
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20
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Breyne P, Rombaut D, Van Gysel A, Van Montagu M, Gerats T. AFLP analysis of genetic diversity within and between Arabidopsis thaliana ecotypes. Mol Gen Genet 1999; 261:627-34. [PMID: 10394899 DOI: 10.1007/s004380050005] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The degree of genetic diversity within and between 21 Arabidopsis thaliana (L.) Heynh ecotypes was estimated by AFLP analysis. Within seven of the 21 ecotypes, a low but significant level of polymorphism was detected, and for five of these ecotypes two or three distinct subgroups could be distinguished. As these ecotypes represent natural populations, this intraecotypic diversity reflects natural genetic variation and diversification within the ecotypes. The source of this diversity remains unclear but is intriguing in view of the predominantly self-fertilizing nature of Arabidopsis. Interrelationships between the different ecotypes were estimated after AFLP fingerprinting using two enzyme combinations (EcoRI/MseI and SacI/MseI) and a number of selective primer pairs. SacI recognition sites are less evenly distributed in the genome than EcoRI sites, and occur more frequently in coding sequences. In most cases, AFLP data from only one enzyme combination are used for genetic diversity analysis. Our results show that the use of two enzyme combinations can result in significantly different classifications of the ecotypes both in cluster and ordination analysis. This difference most probably reflects differences in the genomic distribution of the AFLP fragments generated, depending on the enzymes and selective primers used. For closely related varieties, as in the case of Arabidopsis ecotypes, this can preclude reliable classification.
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Affiliation(s)
- P Breyne
- Department of Plant Genetics, Flanders Interuniversity Institute for Biotechnology, University of Gent, Belgium
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21
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Van Gysel A, Cnops G, Breyne P, Van Montagu M, Cervera MT. Chromosome landing using an AFLP-based strategy. Methods Mol Biol 1998; 82:305-14. [PMID: 9664434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- A Van Gysel
- Laboratorium voor Genetica, Universiteit Gent, Belgium
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22
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Breyne P, Van Montagu M, Gheysen G. The role of scaffold attachment regions in the structural and functional organization of plant chromatin. Transgenic Res 1994; 3:195-202. [PMID: 8025597 DOI: 10.1007/bf01973987] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Studies on nuclear scaffolds and scaffold attachment regions (SARs) have recently been extended to different plant species and indicate that SARs are involved in the structural and functional organization of the plant genome, as is the case for other eukaryotes. One type of SAR seems to delimit structural chromatin loops and may also border functional units of gene expression and DNA replication. Another group of SARs map close to regulatory elements and may be directly involved in gene expression. In this overview, we summarize the structural and functional properties of plant SARs in comparison with those of SARs from animals and yeast.
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Affiliation(s)
- P Breyne
- Laboratorium voor Genetica, Universiteit Gent, Belgium
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23
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Abstract
T-DNA vectors were constructed which carry a beta-glucuronidase (gusA) gene fused to the promoter of the nopaline synthase (nos) gene and the 3' end of the octopine synthase (ocs) gene. This reporter gene was cloned at different locations and orientations towards the right T-DNA border. For each construct, between 30 and 60 stably transformed calli were analysed for beta-glucuronidase activity. Depending on the T-DNA configuration, distinct populations of gusA-expressing calli were obtained. Placing the reporter gene in the middle of the T-DNA results in relatively low expression levels and a limited inter-transformant variability. Placing the gene with its promoter next to the right border led to an increase in both the mean activity and the variability level. With this construct, some of the calli expressed the gusA gene at levels four to five times higher than the mean. In all these series, at least 30% of the calli contained reporter gene activities that were less than half of the mean expression level. Separating the gusA gene from the right T-DNA border by an additional 3'-untranslated region, derived from the nos gene, resulted in an increase in the mean expression to a level almost four times higher than that of constructions carrying the reporter gene in the middle of the T-DNA. Moreover, the number of transformants with extremely low activities decreased by at least 50% and this resulted in significantly lower inter-transformant variability independently of the orientation of the reporter gene on the T-DNA.
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MESH Headings
- Agrobacterium tumefaciens/enzymology
- Agrobacterium tumefaciens/genetics
- Amino Acid Oxidoreductases/genetics
- Analysis of Variance
- Cloning, Molecular
- Conjugation, Genetic
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- Gene Expression Regulation, Bacterial
- Gene Expression Regulation, Enzymologic
- Genes, Bacterial
- Genetic Vectors
- Glucuronidase/genetics
- Nucleic Acid Conformation
- Plants, Toxic
- Promoter Regions, Genetic
- Restriction Mapping
- Nicotiana
- Transcription, Genetic
- Transformation, Genetic
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Affiliation(s)
- P Breyne
- Laboratorium voor Genetica, Universiteit Gent, Belgium
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24
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Breyne P, van Montagu M, Depicker N, Gheysen G. Characterization of a plant scaffold attachment region in a DNA fragment that normalizes transgene expression in tobacco. Plant Cell 1992; 4:463-71. [PMID: 1498604 PMCID: PMC160145 DOI: 10.1105/tpc.4.4.463] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Using a low-salt extraction procedure, we isolated nuclear scaffolds from tobacco that bind specific plant DNA fragments in vitro. One of these fragments was characterized in more detail; this characterization showed that it contains sequences with structural properties analogous to animal scaffold attachment regions (SARs). We showed that scaffold attachment is evolutionarily conserved between plants and animals, although different SARs have different binding affinities. Furthermore, we demonstrated that flanking a chimeric transgene with the characterized SAR-containing fragment reduces significantly the variation in expression in series of transformants with an active insertion, whereas a SAR fragment from the human beta-globin locus does not. Moreover, the frequency distribution patterns of transgene activities showed that most of the transformants containing the plant SAR fragment had expression levels clustered around the mean. These data suggest that the particular plant DNA fragment can insulate the reporter gene from expression-influencing effects exerted from the host chromatin.
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Affiliation(s)
- P Breyne
- Laboratorium voor Genetica, Universteit Gent, Belgium
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25
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Abstract
When a promoterless marker gene is transformed into the plant genome using the Agrobacterium vector system, on average 30% of the T-DNA inserts produce gene fusions. This suggests that the T-DNA is preferentially integrated into transcribed regions. Here, we proposed that this transcriptional activity is responsible for some of the variation in expression frequently observed among independent transformants. Using hybrid gene constructions, we show that transcriptional readthrough into a downstream gene with opposite orientation substantially reduces expression of this gene both in transient expression and in transgenic plants. Furthermore, a poly(A) signal/terminator can block readthrough and restore the expression of the gene. Finally, enzymatic analysis of calli suggests that less variation in neomycin phosphotransferase II synthesis is observed when the gene is separated from plant DNA by promoter and terminator elements.
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Affiliation(s)
- I Ingelbrecht
- Laboratorium voor Genetica, Universiteit Gent, Belgium
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26
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Abstract
Transgenic plants produced by Agrobacterium-mediated transformation usually have one or a few stable and intact T-DNA insertions. However, in a significant number of the transformants Southern blot analysis has revealed the occurrence of aberrant T-DNA insertions missing one or both ends. During the study of this phenomenon, we obtained KmR Nicotiana tabacum clones after cocultivation with an Agrobacterium strain containing a promoterless nptII gene located internally in the T-DNA. Expression of this nptII gene requires a break in the T-DNA region upstream from the nptII-coding sequence and insertion of the truncated T-DNA in a transcriptionally active plant DNA region. The most conspicuous result from Southern analyses on four such KmR plant clones is that they contain several T-DNAs truncated at other positions besides the upstream region of the nptII sequence. Four truncated T-DNA insertions have been cloned. Two insertions contain the nptII gene fused to plant expression signals and are missing the right part of the T-DNA. Another is missing the left T-DNA part and the last T-DNA is lacking both ends. Sequence analysis of the T-DNA::plant junctions has shown that the T-DNA breakpoints are randomly distributed and do not show obvious homologies to one another or to the border consensus sequence. S1-type mapping of the most strongly expressed plant genome::nptII fusion revealed a specific transcription start point and putative TATA and CAAT boxes in the upstream plant DNA region; the steady-state nptII mRNA in these plants is about 20 times more abundant than in transgenic Pnos-nptII plants.
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Affiliation(s)
- G Gheysen
- Laboratorium voor Genetica, Rijksuniversiteit Gent, Belgium
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