Résumé
The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources. In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs. The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species.
Auteurs, date et publication :
Auteurs Louise Brousseau , Alexandra Tinaut , Caroline Duret , Tiange Lang , Pauline Garnier-Gere , Ivan Scotti
Publication : BMC Genomics
Date : 2014
Volume : 15
Issue : 1
Pages : 238
Catégorie(s)
#CIRAD #FORET ParacouAuteurs, date et publication :
Auteurs Louise Brousseau , Damien Bonal , Jeremy Cigna , Ivan Scotti
Publication : Annals of Botany
Date : 2013
Volume : 112
Issue : 6
Pages : 1169–1179
Catégorie(s)
#CIRAD #FORET ParacouAuteurs, date et publication :
Auteurs Romain Lehnebach , Hélène Morel , Julie Bossu , Gilles Le Moguédec , Nadine Amusant , Jacques Beauchêne , Eric Nicolini
Publication : Trees
Date : 2017
Volume : 31
Issue : 1
Pages : 199–214
Catégorie(s)
#CIRAD #FORET ParacouRésumé
textlessptextgreaterLes aménagements futurs nécessaires au développement rapide de la Guyane vont entraîner la conversion de terres fores- tières, participant ainsi au changement global. Les décideurs guyanais devront conjuguer ces aménagements avec la pré- servation des services écosystémiques forestiers. Le projet GuyaSim avait comme objectif l'approfondissement des connaissances sur ces services (stock de carbone, biodiversité et qualité du sol) et le transfert d'un logiciel aux décideurs pour faciliter l'intégration de ces connais- sances dans les politiques d'aménage- ment du territoire. L'article présente les caractéristiques et les fonctionnalités de ce logiciel GuyaSim. Il s'agit d'un logiciel libre de type Sig, destiné a priori aux ser- vices d'aménagement des collectivités et du domaine forestier de Guyane. Le logiciel offre deux grands types de fonc- tionnalité : la mise à disposition d'infor- mations et l'aide à l'aménagement. Les informations mises à disposition sont les scénarios de développement socio-éco- nomique, les scénarios climatiques et les valeurs des services écosystémiques. L'aide à l'aménagement consiste en des outils de construction des scénarios d'aménagement du territoire (change- ment d'usage des terres) et d'aménage- ment forestier (exploitation forestière), fournissant des informations sur l'impact environnemental. Les fonctionnalités du logiciel sont limitées par les connais- sances sur les écosystèmes guyanais. Les avancées des projets de recherche en cours permettront de mettre à jour le logiciel à moyen terme.textless/ptextgreater
Auteurs, date et publication :
Auteurs Vivien Rossi , Thomas Dolley , Guillaume Cornu , Stéphane Guitet , Bruno Hérault
Publication : Bois et Forêts des Tropiques
Date : 2015
Volume : 326
Issue : 326
Pages : 67
Catégorie(s)
#CIRAD #FORET ParacouRésumé
Opossums and rodents were sampled by live-trapping at Paracou, French Guiana to study habitat use. Tomahawk and Sherman traps were placed on the ground and at various heights in the subcanopy and canopy. We captured 10 species of opossums and seven species of rodents. We measured 14 microhabitat variables at each of 485 sampling stations. Presence or absence at a trap station of the three most abundant species of opossums (Didelphis albiventris, Didelphis marsupialis, and Micoureus demerarae) and two rodents (Oecomys rutilus and Proechimys cuvieri) were related by logistic regression analysis to the microhabitat variables. All five species were associated with at least one habitat variable. Linear analysis of categorical data was used to determine the degree of arboreality. Didelphis marsupialis and P. cuvieri were more commonly captured on the ground, D. albiventris was equitably distributed between ground and arboreal traps, and the remaining species were mostly arboreal. Linear analysis was used to compare the distribution of arboreal captures among two substrate types, two heights, and two substrate diameters. Oecomys rutilus was more commonly captured on lianas, D. albiventris and O. rutilus were more commonly captured at lower heights, and D. marsupialis demonstrated a preference for larger arboreal substrates.
Auteurs, date et publication :
Auteurs Gregory H. Adler , Alejandra Carvajal , Shannon L. Davis-Foust , Jacob W. Dittel
Publication : Mammalian Biology
Date : 2012
Volume : 77
Issue : 2
Pages : 84–89
Catégorie(s)
#CIRAD #FORET ParacouRésumé
In this work, the role of volume scattering obtained from ground and volume decomposition of P-band synthetic aperture radar (SAR) data as a proxy for biomass is investigated. The analysis here presented originates from the BIOMASS L2 activities, part of which were focused on strengthening the physical foundations of the SAR-based retrieval of forest above-ground biomass (AGB). A critical analysis of the observed strong correlation between tomographic intensity and AGB is done in order to propose simplified AGB proxies to be used during the interferometric phase of BIOMASS. In particular, the aim is to discuss whether, and to what extent, volume scattering obtained from ground/volume decomposition can provide a reasonable alternative to tomography. To do this, both are tested on P-band data collected at Paracou during the TropiSAR campaign and cross-validated against in-situ AGB measurements. Results indicate that volume backscattered power as obtained by ground/volume decomposition is weakly correlated to AGB, notwithstanding different solutions for volume scattering are tested, and support the conclusion that forest structure actually plays a non-negligible role in AGB retrieval in dense tropical forests.
Auteurs, date et publication :
Auteurs Francesco Banda , Mauro Mariotti d’Alessandro , Stefano Tebaldini
Publication : Remote Sensing
Date : 2020
Volume : 12
Issue : 2
Pages : 240
Catégorie(s)
#CIRAD #FORET ParacouAuteurs, date et publication :
Auteurs Ho Tong Minh Dinh , Stefano Tebaldini , Fabio Rocca , Thierry Koleck , Pierre Borderies , Clement Albinet , Ludovic Villard , Alia Hamadi , Thuy Le Toan
Publication : IEEE Transactions on Geoscience and Remote Sensing
Date : 2013
Volume : 51
Issue : 8
Pages : 4460–4472
Catégorie(s)
#CIRAD #FORET ParacouRésumé
Plant phenology characterises the seasonal cyclicity of biological events such as budburst, flowering, fructification, leaf senescence and leaf fall. These biological events are genetically pre-determined but also strongly modulated by climatic conditions, particularly temperature, daylength and water availability. Therefore, the timing of these events is considered as a good indicator of climate change impacts and as a key parameter for understanding and modelling vegetation–climate interactions. In situ observations, empirical or bioclimatic models and remotely sensed time-series data constitute the three possible ways for monitoring the timing of plant phenological events. Remote sensing has the advantage of being the only way of surface sampling at high temporal frequency and, in the case of satellite-based remote sensing, over large regions. Nevertheless, exogenous factors, particularly atmospheric conditions, lead to some uncertainties on the seasonal course of surface reflectance and cause bias in the identification of vegetation phenological events. Since 2005, a network of forest and herbaceous sites has been equipped with laboratory made NDVI sensors to monitor the temporal dynamics of canopy structure and phenology at an intra-daily time step. In this study, we present recent results obtained in several contrasting biomes in France, French Guiana, Belgium and Congo. These sites represent a gradient of vegetation ecosystems: the main evergreen and deciduous forest ecosystems in temperate climate region, an evergreen tropical rain forest in French Guiana, an herbaceous savanna ecosystem in Congo, and a succession of three annual crops in Belgium. In this paper, (1) we provide an accurate description of the seasonal dynamics of vegetation cover in these different ecosystems (2) we identify the most relevant remotely sensed markers from NDVI time-series for determining the dates of the main phenological events that characterize these ecosystems and (3) we discuss the relationships between temporal canopy dynamics and climate factors. In addition to its importance for phenological studies, this ground-based Network of NDVI measurement provides data needed for the calibration and direct validation of satellite observations and products.
Auteurs, date et publication :
Auteurs K. Soudani , G. Hmimina , N. Delpierre , J.-Y. Pontailler , M. Aubinet , D. Bonal , B. Caquet , A. de Grandcourt , B. Burban , C. Flechard , D. Guyon , A. Granier , P. Gross , B. Heinesh , B. Longdoz , D. Loustau , C. Moureaux , J.-M. Ourcival , S. Rambal , L. Saint André
Publication : Remote Sensing of Environment
Date : 2012
Volume : 123
Pages : 234–245
Catégorie(s)
#CIRAD #CNRS #FORET Paracou #FORET PuechabonRésumé
Plant functional traits directly affect ecosystem functions. At the species level, trait combinations depend on trade-offs representing different ecological strategies, but at the community level trait combinations are expected to be decoupled from these trade-offs because different strategies can facilitate co-existence within communities. A key question is to what extent community-level trait composition is globally filtered and how well it is related to global versus local environmental drivers. Here, we perform a global, plot-level analysis of trait–environment relationships, using a database with more than 1.1 million vegetation plots and 26,632 plant species with trait information. Although we found a strong filtering of 17 functional traits, similar climate and soil conditions support communities differing greatly in mean trait values. The two main community trait axes that capture half of the global trait variation (plant stature and resource acquisitiveness) reflect the trade-offs at the species level but are weakly associated with climate and soil conditions at the global scale. Similarly, within-plot trait variation does not vary systematically with macro-environment. Our results indicate that, at fine spatial grain, macro-environmental drivers are much less important for functional trait composition than has been assumed from floristic analyses restricted to co-occurrence in large grid cells. Instead, trait combinations seem to be predominantly filtered by local-scale factors such as disturbance, fine-scale soil conditions, niche partitioning and biotic interactions.
Auteurs, date et publication :
Auteurs Helge Bruelheide , Jürgen Dengler , Oliver Purschke , Jonathan Lenoir , Borja Jiménez-Alfaro , Stephan M Hennekens , Zoltán Botta-Dukát , Milan Chytrý , Richard Field , Florian Jansen , Jens Kattge , Valério D Pillar , Franziska Schrodt , Miguel D Mahecha , Robert K Peet , Brody Sandel , Peter van Bodegom , Jan Altman , Esteban Alvarez-Dávila , Mohammed A S Arfin Khan
Publication : Nature Ecology & Evolution
Date : 2025
Catégorie(s)
#CIRAD #FORET ParacouAuteurs, date et publication :
Auteurs Maarja Öpik , Martin Zobel , Juan J. Cantero , John Davison , José M. Facelli , Inga Hiiesalu , Teele Jairus , Jesse M. Kalwij , Kadri Koorem , Miguel E. Leal , Jaan Liira , Madis Metsis , Valentina Neshataeva , Jaanus Paal , Cherdchai Phosri , Sergei Põlme , Ülle Reier , Ülle Saks , Heidy Schimann , Odile Thiéry
Publication : Mycorrhiza
Date : 2013
Volume : 23
Issue : 5
Pages : 411–430