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Marti, G.; Eparvier, V.; Litaudon, M.; Grellier, P.; Gueritte, F. |
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Title |
A New Xanthone from the Bark Extract of Rheedia acuminata and Antiplasmodial Activity of Its Major Compounds |
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Journal Article |
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Year |
2010 |
Publication |
Molecules |
Abbreviated Journal  |
Molecules |
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Volume |
15 |
Issue |
10 |
Pages |
7106-7114 |
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Rheedia acuminata, Clusiaceae; xanthones; antiplasmodial activity; cytotoxicity |
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Bioassay-guided fractionation of the ethyl acetate bark extract of Rheedia acuminata led to the isolation of the new compound 1,5,6-trihydroxy-3-methoxy-7-geranyl-xanthone (1), together with four known compounds 2-5. These compounds were tested in vitro for their antiplasmodial activity on a chloroquine-resistant strain of Plasmodium falciparum (FcB1) and for their cytotoxicity against the human diploid embryonic lung cell line MRC-5. |
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[Eparvier, Veronique] CNRS, UPS2561, F-97300 Cayenne, France, Email: guillaume.marti@icsn.cnrs-gif.fr |
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MDPI AG |
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1420-3049 |
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ISI:000283587400030 |
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EcoFoG @ webmaster @ |
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282 |
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Csilléry, K.; Lalague, H.; Vendramin, G.G.; González-Martínez, S.C.; Fady, B.; Oddou-Muratorio, S. |
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Title |
Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations |
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Journal Article |
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Year |
2014 |
Publication |
Molecular Ecology |
Abbreviated Journal |
Molecular Ecology |
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Volume |
23 |
Issue |
19 |
Pages |
4696-4708 |
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abiotic stress; budburst phenology; FST outlier; gene network; haplotype; Ohta's test; variance components of linkage disequilibrium |
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Detecting signatures of selection in tree populations threatened by climate change is currently a major research priority. Here, we investigated the signature of local adaptation over a short spatial scale using 96 European beech (Fagus sylvatica L.) individuals originating from two pairs of populations on the northern and southern slopes of Mont Ventoux (south-eastern France). We performed both single and multilocus analysis of selection based on 53 climate-related candidate genes containing 546 SNPs. FST outlier methods at the SNP level revealed a weak signal of selection, with three marginally significant outliers in the northern populations. At the gene level, considering haplotypes as alleles, two additional marginally significant outliers were detected, one on each slope. To account for the uncertainty of haplotype inference, we averaged the Bayes factors over many possible phase reconstructions. Epistatic selection offers a realistic multilocus model of selection in natural populations. Here, we used a test suggested by Ohta based on the decomposition of the variance of linkage disequilibrium. Overall populations, 0.23% of the SNP pairs (haplotypes) showed evidence of epistatic selection, with nearly 80% of them being within genes. One of the between gene epistatic selection signals arose between an FST outlier and a nonsynonymous mutation in a drought response gene. Additionally, we identified haplotypes containing selectively advantageous allele combinations which were unique to high or low elevations and northern or southern populations. Several haplotypes contained nonsynonymous mutations situated in genes with known functional importance for adaptation to climatic factors. |
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CIFOR-INIA, Forest Research Centre, Carretera de La Coruña km 7.5Madrid 28040, Spain |
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Export Date: 13 January 2015 |
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EcoFoG @ webmaster @ |
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579 |
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Hamon, P.; Duroy, P.-O.; Dubreuil-Tranchant, C.; Mafra D'Almeida Costa, P.; Duret, C.; Razafinarivo, N.J.; Couturon, E.; Hamon, S.; De Kochko, A.; Poncet, V.; Guyot, R. |
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Title |
Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae) |
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Journal Article |
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Year |
2011 |
Publication |
Molecular Genetics and Genomics |
Abbreviated Journal |
Mol. Genet. Genomics |
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Volume |
285 |
Issue |
6 |
Pages |
447-460 |
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Keywords |
Coffea; Evolution; Genetic diversity; LTR-retrotransposons; article; coffee; controlled study; Divo; gene amplification; gene dosage; gene expression; gene insertion; gene locus; gene sequence; genetic identification; genetic polymorphism; genetic variability; molecular cloning; Nana; nonhuman; nucleotide sequence; phylogeny; plant evolution; plant gene; priority journal; Psilanthus; random amplified microsatellite; retroposon; Rubiaceae; species differentiation; tree; Ty1 copia gene; Coffea; Genes, Plant; Genome, Plant; Phylogeny; Retroelements |
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Abstract |
In the study, we developed new markers for phylogenetic relationships and intraspecies differentiation in Coffea. Nana and Divo, two novel Ty1-copia LTR-retrotransposon families, were isolated through C. canephora BAC clone sequencing. Nana- and Divo-based markers were used to test their: (1) ability to resolve recent phylogenetic relationships; (2) efficiency in detecting intra-species differentiation. Sequence-specific amplification polymorphism (SSAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and retrotransposon-based insertion polymorphism (RBIP) approaches were applied to 182 accessions (31 Coffea species and one Psilanthus accession). Nana- and Divo-based markers revealed contrasted transpositional histories. At the BAC clone locus, RBIP results on C. canephora demonstrated that Nana insertion took place prior to C. canephora differentiation, while Divo insertion occurred after differentiation. Combined SSAP and REMAP data showed that Nana could resolve Coffea lineages, while Divo was efficient at a lower taxonomic level. The combined results indicated that the retrotransposon-based markers were useful in highlighting Coffea genetic diversity and the chronological pattern of speciation/differentiation events. Ongoing complete sequencing of the C. canephora genome will soon enable exhaustive identification of LTR-RTN families, as well as more precise in-depth analyses on contributions to genome size variation and Coffea evolution. © 2011 Springer-Verlag. |
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IRD, UMR DIADE, BP 50172, Sainte Clotilde Cedex, La Réunion 97492, France |
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16174615 (Issn) |
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Export Date: 21 October 2011; Source: Scopus; Coden: Mggoa; doi: 10.1007/s00438-011-0617-0; PubMed ID: 21505885; Language of Original Document: English; Correspondence Address: Hamon, P.; IRD, UMR DIADE, BP 64501, Montpellier Cedex 5, France; email: perla.hamon@ird.fr; Molecular Sequence Numbers: GENBANK: DV666936, HM755952, HM755953;; Chemicals/CAS: Retroelements |
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EcoFoG @ webmaster @ |
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344 |
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Andris, M.; Aradottir, G.I.; Arnau, G.; Audzijonyte, A.; Bess, E.C.; Bonadonna, F.; Bourdel, G.; Bried, J.; Bugbee, G.J.; Burger, P.A.; Chair, H.; Charruau, P.C.; Ciampi, A.Y.; Costet, L.; Debarro, P.J.; Delatte, H.; Dubois, M.P.; Eldridge, M.D.B.; England, P.R.; Enkhbileg, D.; Fartek, B.; Gardner, M.G.; Gray, K.A.; Gunasekera, R.M.; Hanley, S.J.; Havil, N.; Hereward, J.P.; Hirase, S.; Hong, Y.; Jarne, P.; Qi, J.F.; Johnson, R.N.; Kanno, M.; Kijima, A.; Kim, H.C.; Kim, K.S.; Kim, W.J.; Larue, E.; Lee, J.W.; Lee, J.H.; Li, C.H.; Liao, M.H.; Lo, N.; Lowe, A.J.; Malausa, T.; Male, P.J.G.; Marko, M.D.; Martin, J.F.; Messing, R.; Miller, K.J.; Min, B.W.; Myeong, J.I.; Nibouche, S.; Noack, A.E.; Noh, J.K.; Orivel, J.; Park, C.J.; Petro, D.; Prapayotin-Riveros, K.; Quilichini, A.; Reynaud, B.; Riginos, C.; Risterucci, A.M.; Rose, H.A.; Sampaio, I.; Silbermayr, K.; Silva, M.B.; Tero, N.; Thum, R.A.; Vinson, C.C.; Vorsino, A.; Vossbrinck, C.R.; Walzer, C.; White, J.C.; Wieczorek, A.; Wright, M. |
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Title |
Permanent Genetic Resources added to Molecular Ecology Resources Database 1 June 2010-31 July 2010 |
Type |
Journal Article |
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Year |
2010 |
Publication |
Molecular Ecology Resources |
Abbreviated Journal |
Mol. Ecol. Resour. |
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Volume |
10 |
Issue |
6 |
Pages |
1106-1108 |
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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. |
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[Andris, Malvina; Bried, Joel] Univ Acores, Ctr IMAR, Dept Oceanog & Pescas, P-9901862 Horta, Acores, Portugal, Email: editorial.office@molecol.com |
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WILEY-BLACKWELL PUBLISHING, INC |
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1755-098X |
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ISI:000282876300024 |
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EcoFoG @ eric.marcon @ |
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28 |
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Arranz, S.E.; Avarre, J.-C.; Balasundaram, C.; Bouza, C.; Calcaterra, N.B.; Cezilly, F.; Chen, S.-L.; Cipriani, G.; Cruz, V.P.; D'Esposito, D.; Daniel, C.; Dejean, A.; Dharaneedharan, S.; Díaz, J.; Du, M.; Durand, J.-D.; Dziadek, J.; Foresti, F.; Peng-Cheng, F.; Gao, Q.-B.; García, G.; Gauffre-Autelin, P.; Giovino, A.; Goswami, M.; Guarino, C.; Guerra-Varela, J.; Gutiérrez, V.; Harris, D.J.; Heo, M.-S.; Khan, G.; Kim, M.; Lakra, W.S.; Lauth, J.; Leclercq, P.; Lee, J.; Lee, S.-H.; Lee, S.; Lee, T.; Li, Y.-H.; Liu, H.; Liu, S.; Malé, P.-J.G.; Mandhan, R.P.; Martinez, P.; Mayer, V.E.; Mendel, J.; Mendes, N.J.; Mendonça, F.F.; Minias, A.; Minias, P.; Oh, K.-S.; Oliveira, C.; Orivel, J.; Orsini, L.; Pardo, B.G.; Perera, A.; Procaccini, G.; Rato, C.; Ríos, N.; Scibetta, S.; Sharma, B.S.; Sierens, T.; Singh, A.; Terer, T.; Triest, L.; Urbánková, S.; Vera, M.; Villanova, G.V.; Voglmayr, H.; Vyskočilová, M.; Wang, H.; Wang, J.-L.; Wattier, R.A.; Xing, R.; Yadav, K.; Yin, G.; Yuan, Y.; Yun, J.-C.; Zhang, F.-Q.; Zhang, J.-H.; Zhuang, Z. |
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Title |
Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2012-31 January 2013 |
Type |
Journal Article |
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Year |
2013 |
Publication |
Molecular Ecology Resources |
Abbreviated Journal |
Mol. Ecol. Resour. |
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Volume |
13 |
Issue |
3 |
Pages |
546-549 |
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This article documents the addition of 268 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alburnoides bipunctatus, Chamaerops humilis, Chlidonias hybrida, Cyperus papyrus, Fusarium graminearum, Loxigilla barbadensis, Macrobrachium rosenbergii, Odontesthes bonariensis, Pelteobagrus vachelli, Posidonia oceanica, Potamotrygon motoro, Rhamdia quelen, Sarotherodon melanotheron heudelotii, Sibiraea angustata, Takifugu rubripes, Tarentola mauritanica, Trimmatostroma sp. and Wallago attu. These loci were cross-tested on the following species: Alburnoides fasciatus, Alburnoides kubanicus, Alburnoides maculatus, Alburnoides ohridanus, Alburnoides prespensis, Alburnoides rossicus, Alburnoides strymonicus, Alburnoides thessalicus, Alburnoides tzanevi, Carassius carassius, Fusarium asiaticum, Leucaspius delineatus, Loxigilla noctis dominica, Pelecus cultratus, Phoenix canariensis, Potamotrygon falkneri, Trachycarpus fortune and Vimba vimba. © 2013 Blackwell Publishing Ltd. |
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Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, China |
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1755098x (Issn) |
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Export Date: 2 May 2013; Source: Scopus; :doi 10.1111/1755-0998.12095; Language of Original Document: English; Correspondence Address: Arranz, S.E.; Molecular Ecology Resources Editorial Office, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada; email: editorial.office@molecol.com |
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no |
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EcoFoG @ webmaster @ |
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484 |
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Malé, P.-J.G.; Bardon, L.; Besnard, G.; Coissac, E.; Delsuc, F.; Engel, J.; Lhuillier, E.; Scotti-Saintagne, C.; Tinaut, A.; Chave, J. |
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Title |
Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family |
Type |
Journal Article |
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Year |
2014 |
Publication |
Molecular Ecology Resources |
Abbreviated Journal |
Mol. Ecol. Resour. |
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Volume |
14 |
Issue |
5 |
Pages |
966-975 |
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Next-generation sequencing; Organellar genome; Phylogenomics; Tropical trees |
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Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000×, 450× and 120× sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups. © 2014 John Wiley & Sons Ltd. |
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GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, F-31326, France |
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Blackwell Publishing Ltd |
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17550998 (Issn) |
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Export Date: 1 September 2014; Correspondence Address: Malé, P.-J.G.; UMR 5174 Laboratoire Évolution and Diversité Biologique, CNRS, Université Paul Sabatier, ENFA, 118 route de Narbonne, Toulouse, F-31062, France; email: pjg.male@gmail.com |
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no |
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EcoFoG @ webmaster @ |
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559 |
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Sommeria-Klein, G.; Zinger, L.; Coissac, E.; Iribar, A.; Schimann, H.; Taberlet, P.; Chave, J. |
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Title |
Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA-based census of soil biodiversity from a tropical forest |
Type |
Journal Article |
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Year |
2020 |
Publication |
Molecular Ecology Resources |
Abbreviated Journal |
Mol. Ecol. Resour. |
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Volume |
20 |
Issue |
2 |
Pages |
371-386 |
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Keywords |
community ecology; environmental DNA; metabarcoding; OTU presence–absence; soil microbiome; topic modelling; bacterium; biodiversity; biology; classification; eukaryote; fungus; genetics; high throughput sequencing; isolation and purification; microbiology; parasitology; procedures; soil; Bacteria; Biodiversity; Computational Biology; Eukaryota; Fungi; High-Throughput Nucleotide Sequencing; Soil; Soil Microbiology |
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Abstract |
High-throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retrieving and interpreting the structure of such data sets requires efficient methods for dimensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA samples into overlapping assemblages of co-occurring taxa. It is a flexible model-based method adapted to uneven sample sizes and to large and sparse data sets. Here, we compare LDA performance on abundance and occurrence data, and we quantify the robustness of the LDA decomposition by measuring its stability with respect to the algorithm's initialization. We then apply LDA to a survey of 1,131 soil DNA samples that were collected in a 12-ha plot of primary tropical forest and amplified using standard primers for bacteria, protists, fungi and metazoans. The analysis reveals that bacteria, protists and fungi exhibit a strong spatial structure, which matches the topographical features of the plot, while metazoans do not, confirming that microbial diversity is primarily controlled by environmental variation at the studied scale. We conclude that LDA is a sensitive, robust and computationally efficient method to detect and interpret the structure of large DNA-based biodiversity data sets. We finally discuss the possible future applications of this approach for the study of biodiversity. © 2019 John Wiley & Sons Ltd |
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Laboratoire d’Ecologie des Forêts de Guyane (EcoFoG, UMR 745), INRA, AgroParisTech, CIRAD, CNRS, University of the French West Indies, University of French Guiana, Kourou, France |
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Blackwell Publishing Ltd |
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1755098x (Issn) |
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no |
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EcoFoG @ webmaster @ |
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981 |
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Le Guen, V.; Rodier-Goud, M.; Troispoux, V.; Xiong, T.C.; Brottier, P.; Billot, C.; Seguin, M. |
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Title |
Characterization of polymorphic microsatellite markers for Microcyclus ulei, causal, agent of South American leaf blight of rubber trees |
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Journal Article |
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Year |
2004 |
Publication |
Molecular Ecology Notes |
Abbreviated Journal |
Mol. Ecol. Notes |
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Volume |
4 |
Issue |
1 |
Pages |
122-124 |
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Keywords |
Hevea brasiliensis; Microcyclus ulei; microsatellite markers; phytopathogenic fungi; South American leaf blight |
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Abstract |
South American leaf blight caused by the ascomycete Microcyclus Wei is the most harmful disease of the rubber tree in Latin America and a potential threat to Asiatic and African natural rubber production. Until now, the variability of this fungus was assessed through observation of pathogenicity of isolates on a range of rubber tree clones with known resistance reactions. The present study describes the process used to design 11 microsatellite markers and evaluates their usefulness in detecting genetic polymorphism. Nine of these markers were polymorphic among six isolates from Brazil (with two to three alleles per locus) and five markers were polymorphic among four isolates from French Guiana (with two to four alleles per locus). |
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CIRAD, F-97387 Kourou, France, Email: vincent.le_guen@cirad.fr |
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BLACKWELL PUBLISHING LTD |
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1471-8278 |
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Notes |
ISI:000189159500037 |
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no |
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EcoFoG @ eric.marcon @ |
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265 |
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Author |
Duminil, J.; Caron, H.; Scotti, I.; Cazal, S.O.; Petit, R.J. |
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Title |
Blind population genetics survey of tropical rainforest trees |
Type |
Journal Article |
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Year |
2006 |
Publication |
Molecular Ecology |
Abbreviated Journal |
Mol. Ecol. |
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Volume |
15 |
Issue |
12 |
Pages |
3505-3513 |
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Keywords |
Bayesian assignment tests; genetic diversity; geographical structure; South America; species delimitation |
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Abstract |
Rainforest tree species can be difficult to identify outside of their period of reproduction. Vascular tissues from Carapa spp. individuals were collected during a short field trip in French Guiana and analysed in the laboratory with nuclear and chloroplast markers. Using a Bayesian approach, > 90% of the samples could be assigned to one of two distinct clusters corresponding to previously described species, making it possible to estimate the genetic structure of each species and to identify cases of introgression. We argue that this blind procedure represents a first-choice rather than a fallback option whenever related taxa are investigated. |
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INRA, UMR Biodivers Genes & Ecosyst, F-33612 Cestas, France, Email: caron@pierroton.inra.fr |
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BLACKWELL PUBLISHING |
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0962-1083 |
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ISI:000241157400002 |
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EcoFoG @ eric.marcon @ |
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175 |
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Author |
Hardy, O.J.; Maggia, L.; Bandou, E.; Breyne, P.; Caron, H.; Chevallier, M.H.; Doligez, A.; Dutech, C.; Kremer, A.; Latouche-Halle, C.; Troispoux, V.; Veron, V.; Degen, B. |
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Title |
Fine-scale genetic structure and gene dispersal inferences in 10 Neotropical tree species |
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Journal Article |
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2006 |
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Molecular Ecology |
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Mol. Ecol. |
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15 |
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2 |
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559-571 |
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French Guiana; gene dispersal; seed dispersal; spatial genetic structure; tropical trees |
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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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Univ Libre Bruxelles, Serv Ecoethol Evolut, B-1050 Brussels, Belgium, Email: ohardy@ulb.ac.be |
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BLACKWELL PUBLISHING |
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0962-1083 |
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ISI:000235045500021 |
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EcoFoG @ eric.marcon @ |
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183 |
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