Section: Partnerships and Cooperations

International Initiatives

Supervised clustering

One way to build an inventory in a community on a molecular basis is to map unknown reads onto a taxonomically annotated reference database. We (AF, PC, JMF, FS) have developed a cooperation with UMR Carrtel (A. Bouchez, F. Rimet) and SLU at Uppsala (Sweden, M. Kahlert) for industrializing molecular based inventories from data production (NGS facilities, PGTB, Pierroton) to data analysis. Molecular based inventories of about 200 samples have been done, for diatoms Mayotte rivers, and the same number for diatoms in Fennoscandian rivers. The method has been published in [13]. As far as those tools and metagenomics are concerned, a complementary partnership has been established with UMR BioGER (V. Laval) on metabarcoding of fungal communities.

Metagenomics for zoonoses

In the framework of CEBA Cluster of Excellence (Centre d'Etude de la Biodiversité Amazonienne), Pleiade team has been successful in an application for being part of a so called long term strategic project (2017-2019) called microbiome, chaired by Institut Pasteur in Cayenne and UMR MIVEGEC (CNRS-IRD) at Montpellier. The role of the team is twofold: $\left(i\right)$ develop methods for metabarcoding of viral and bacterial communities in some hosts (bats, birds, ...) and $\left(ii\right)$ run some data analysis for scaling up from microbiomes to landscape ecology, having in mind the dilution effect, i.e. pristine forest offer a better protection against disease spread than disturbed ones. The project starts on January 1, 2017.

Historical biogeography of plant families

In the framework of CEBA too, AF and David Sherman have worked in providing some tools for mapping paleoclimatic conditions on the Earth over geological times, elaborating on datasets of paleoclimates produced by running General Circulation Models (work done by UMR LSCE, Orsay, in a previous ANR project lead by AF). These maps will be part of a collaboration established with The Royal Botanical Gardens at Kew (UK) and several Brasilian Universities in a join project on historical biogeography of Myrtaceae, a large family of trees and shrubs, well developed in the Neotropoics. A. Franc has been visiting E. Lucas, at Kew Botanical gardens, in March 2016 for setting up a cooperation. A first workshop has been organized by F. Salgeiro and AF at Rio in May 2016. The next one will be held in August 2017, organized by E. Lucas and coll. An an open access paper on historical biogeography of the genus Quercus, in collaboration with University of Padova and Museum of Natural History of Stockholm, is [11].

Informal International Partners

Pleiade collaborates with Rodrigo Assar of the Universidad Andrès Bello, and Nicolás Loira and Alessandro Maass of the Center for Genomic Regulation, in Santiago de Chile (Chile). Our focus is inference of metabolic and regulatory models by comparative genomics, and their description using stochastic transition systems.