class: hide_logo, inverse, center, middle exclude: false # La base Arthemis et le barcode au CBGP &#128526; .large[Centre de Biologie pour la Gestion des Populations] <img src="im/cbgp.jpg" width="550px"/> .large[J.-P. Rossi, J.-C. Streito, E. Pierre, G. Genson, A Cruaud, J.-Y. Rasplus] .large[Journée d'échanges INRAE - DSF | 14 Avril 2022] .remark-slide-number { display: none; } <div> <style type="text/css">.xaringan-extra-logo { width: 50px; height: 128px; z-index: 0; background-image: url(im0/logo_inrae.png); background-size: contain; background-repeat: no-repeat; position: absolute; top:1em;right:1em; } </style> <script>(function () { let tries = 0 function addLogo () { if (typeof slideshow === 'undefined') { tries += 1 if (tries < 10) { setTimeout(addLogo, 100) } } else { document.querySelectorAll('.remark-slide-content:not(.title-slide):not(.inverse):not(.hide_logo)') .forEach(function (slide) { const logo = document.createElement('div') logo.classList = 'xaringan-extra-logo' logo.href = null slide.appendChild(logo) }) } } document.addEventListener('DOMContentLoaded', addLogo) })()</script> </div> --- exclude: false ### .center[Arthemis] ###.center[.red[ARTH]ropod .red[E]cology, .red[M]olecular .red[I]dentification and .red[S]ystematics] <br> .center[<img src="im/arthemisDB@se.png" title="Arthemis" alt="Arthemis" width="700"/> ] https://arthemisdb.supagro.inra.fr/ --- exclude: false ### Arthemis : contenu de la base - Des informations sur les spécimens des collections du CBGP (+ anciens : 1850) * Taxonomie * Biologie * biogéographie * Photographies - Séquence d'ADN produites par le labo : * Barcode standard Cytochrome Oxydase I (COI) * ITS2 * Autres gènes selon les projets/espèces - Outils d'identification des séquences de l'utilisateur par comparaison avec les séquences de référence de la base https://arthemisdb.supagro.inra.fr/ .content-box-red[ `\(\rightarrow\)` Arthemis est bien plus qu'une base de données barcode !] --- exclude: false ### Arthemis : quelles espèces ? - **Arthropodes ravageurs** et leurs **ennemis naturels** et quelques espèces d'intérêt patrimonial (carabes...) - Pas de limite géographique - Au premier avril 2022 : * 3060 espèces dont 2303 présentes en Fance * 28879 spécimens * 942 espèces séquencées dont 623 espèces Françaises * 10134 barcodes dont 4582 sur du matériel Français --- exclude: false ### Chronologie - Création par J.-Y. Raslus et A. Cruaud en 2010 | projet QBOL (Quanrantine Barcode Of Life) [CBGP / URZF / Pays-Bas] - Prise en charge de la base de données (QBANK) par l'OEPP à la fin du projet QBOL (2015) - CBGP devient curateur pour la partie Arthropodes (J.-C. Streito, E. Pierre) - Arthemis incorpore les données QBANK et les données de nombreux projets du CBGP ### Espèces ciblées, financements - Espèces étudiées dans le cadre de projets dédiés barcode (QBOL, BIOFIS, LYCOVITIS, QUINTRO, XYLELLA,...) - Espèces étudiées dans des projets non spécifiquement barcode (Epidisarth, ...) - Espèces documentées hors projet financé (actualité phytosanitaire) .content-box-red[ `\(\rightarrow\)` Financement opportuniste ! On abonde la base dès que possible...] --- ### Que contient la base ? - Arthropodes ravageurs d'intérêt agronomique en agriculture comme en forêt Exemple : phytophages associés aux **arbres et arbustes** | Groupes | Nb espèces France | Nb espèces monde | |:-----------:|:-----------------:|:----------------:| | Coleoptera | 202 (46) | 272 (97) | | Hemiptera | 179 (95) | 228 (112) | | Lepidoptera | 302 (56) | 322 (71) | | ... | ... | ... | .center[(nombre d'espèces séquencées)] Exemple : Arthemis contient 3 espèces du genre *Xylosandrus*: - *Xylosandrus compactus* : 15 COI - *Xylosandrus crassiusculus* : 11 COI - *Xylosandrus germanus* : 3 COI --- ### Que contient la base ? - Arthropodes ravageurs d'intérêt agronomique en agriculture comme en forêt Exemple : Phytophages d'importance **agricole** | Groupes | Nb espèces France | Nb espèces monde | |:-----------:|:-----------------:|:----------------:| | Coleoptera | 338 (48) | 486 (154) | | Hemiptera | 378 (173) | 505 (237) | | Lepidoptera | 380 (77) | 515 (110) | | ... | ... | ... | .center[(nombre d'espèces séquencées)] <br> .center[.content-box-red[&#128226; Arthemis s'intéresse à tous les ravageurs !]] --- ### Que contient la base ? - Parasitoïdes et prédateurs .pull-left.w60[ | Groupes | Nb espèces séquencées | |:------------:|:---------------------:| | Parasitoïdes | 442 | | Prédateurs | 286 | ] .pull-right.w40[.center[<img src="im/ooctonus_vulgatus.png" title="Ooctonus vulgatus" alt="Ooctonus vulgatus" width="300"/> ]] .center[.content-box-red[&#9763;&#65039; Les agents de biocontrôle commercialisés sont souvent mal identifiés... ]] --- exclude: false ### `\(\rightarrow\)` Vecteurs de *Xylella fastidiosa* en Europe - Identification morphologique sur le terrain parfois difficile (oeufs, larves) - Plusieurs projets depuis 2015 - Arthemis : 681 séquences barcode * 74 espèces de vecteurs potentiels * 536 séquences représentant 42 espèces Européennes * 145 séquences pour 32 espèces non-Européennes .center[<img src="im/vecteurs-Xf.png" title="Draeculacepha robinsoni" alt="Draeculacepha robinsoni" width="420"/> ] --- ### `\(\rightarrow\)` Données vecteurs *Xylella* en 2017 <div id="htmlwidget-9f9185ace33089f5d69d" style="width:800px;height:500px;" class="leaflet html-widget"></div> <script type="application/json" data-for="htmlwidget-9f9185ace33089f5d69d">{"x":{"options":{"crs":{"crsClass":"L.CRS.EPSG3857","code":null,"proj4def":null,"projectedBounds":null,"options":{}}},"calls":[{"method":"addTiles","args":["//{s}.tile.openstreetmap.org/{z}/{x}/{y}.png",null,"OSM (default)",{"minZoom":0,"maxZoom":18,"tileSize":256,"subdomains":"abc","errorTileUrl":"","tms":false,"noWrap":false,"zoomOffset":0,"zoomReverse":false,"opacity":1,"zIndex":1,"detectRetina":false,"attribution":"© <a href=\"http://openstreetmap.org\">OpenStreetMap<\/a> contributors, <a 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L'exemple de *Brachyplatys vahlii* & *B. subaeneus* .pull-right.w20[.right[<img src="im/Brachyplatys_subaeneus.png" title="Brachyplatys subaeneus" alt="Brachyplatys subaeneus" width="150"/>]] - *Brachyplatys vahlii* signalée au Panama en 2016 - Mauvaise identification des séquences dans BOLD - Mais photographies associées au signalement... - `\(\rightarrow\)` correction par un taxonomiste - Identification de *Brachyplatys subaeneus* ...invasif devenu important aux Antilles par la suite... .content-box-red[ Identification morphologique **et** moléculaire de qualité pour : - La recherche - La surveillance du territoire - La législation ] --- exclude: false ### La stratégie du CBGP - Faire les séquences en interne - Conserver tous les spécimens, tous les ADN - Faire des photos de qualité optimale - Stocker toutes les données dans une base que nous contrôlons à 100% - Ressource : une collection de plusieurs millions de spécimens - Ressource : une bibliothèque "taxonomie" de plusieurs milliers de documents - Demande du personnel qualifié (taxinomistes insectes & acariens) &#128293;&#128293; - Demande du temps &#128293; .center[ <img src="im/Collections-quarantaine.jpg" title="" alt="" height="150"/> <img src="im/collections-CBGP.jpg" title="" alt="" height="150"/> <img src="im/conditionnement-des-vouchers-Arthropodes-en-ethanol_medium.jpg" title="" alt="" height="150"/>] --- ### Vers l'infini et au-delà ! Distribution géographique des espèces et changement climatique - Arthemis contient de nombreuses données d'occurrence **fiables** - Macroécologie, modélisation d'aire de distribution - Prévision de l'impact du changement climatique - Géographie du risque phytosanitaire, soutien aux politiques publiques .center[ <img src="im/Ov_fig.png" title="Ooctonus vulgatus" alt="Ooctonus vulgatus" height="350"/> ] --- ### Le projet CHACRA *CHAngement Climatique et Risque punAise* .pull-left.w85[ - Vaste groupe d'insectes diversifié en Europe - Ravageurs plus ou moins importants selon les espèces - On étudie plusieurs centaines d'espèces - `\(\rightarrow\)` Espèces en expansion vers le nord - `\(\rightarrow\)` Contraction d'aire au sud ? - `\(\rightarrow\)` Evolution globale du risque ] .pull-right.w15[ .right[<img src="im/CHACRA-logo-v03.png" title="CHACRA" alt="CHACRA" width="150"/>] ] --- ### Projet scolyte en cours de réflexion .pull-left.w85[ - Appel à Projets Joint Linkage Call (JLC) - University of Florida, Institute of Food and Agricultural Sciences (UF/IFAS) - Topic Forest Health and Invasive Species ] .pull-right.w15[ .right[<img src="im/UFIFAS.png" title="UF-IFAS" alt="UF-IFAS" width="100"/>] ] --- class: inverse <br> <br> <br> # Merci de votre attention ! <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br> https://slides.yihui.org/xaringan/#1 ??? ## PDF