JEMU call for proposals 2016

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1 JEMU call for proposals 2016

2 THE JOINT EXPERIMENTAL MOLECULAR UNIT (JEMU) Established in 2007 Royal Belgian Institute of Natural Sciences (RBINS) Royal Museum for Central Africa (RMCA) Mission: supporting DNA research activities related to the use of the natural history collections of both institutes Current team members: Nathalie Smitz (RMCA), Gontran Sonet (RBINS) Carl Vangestel (RBINS), Massimiliano Virgilio (RMCA) Coordinators: Thierry Backeljau (RBINS) & Marc De Meyer (RMCA) Previous members: Zoltan Nagy, Kurt Jordaens, Floris Breman, Jeroen Van Houdt

3 GOAL The goal of this call is to support novel or already ongoing research projects coordinated by scientists of RBINS and RMCA. JEMU CONTRIBUTION TO YOUR RESEARCH expertise on the most appropriate DNA techniques in relation to the research aims and scientific issues to be addressed support to the laboratory activities and collection of DNA data statistical analyses of the data collected co-authorship in scientific papers financial contribution to the working costs

4 BUDGET total financial contribution of one or two research projects financed / co-financed (tentatively / project) ELIGIBILITY Individual researchers or research teams led by individuals working at the RBINS or RMCA Collaborative projects involving RBINS / RMCA / other research institutes in Belgium and abroad

5 PROJECT REQUIREMENTS all specimens/tissue samples must be available by the end of August 2016 samples and sample data prepared and stored according to the RBINS /RMCA standard for long term storage (2D barcoded tubes, spreadsheet templates) budget only used to support the DNA work (e.g. consumables)

6 PROJECT TIME SCHEDULE May 2016: expression of interest (informal) June 2016: proposal submission September 2016: project start (at latest) May 2017: project completed

7 TECHNOLOGY Sanger Sequencing Microsatellite genotyping Next-generation sequencing (NGS) Reduced representation of genome (GBS, RADseq) Reduced representation of methylome Mitogenomics High-throughput sequencing of PCR amplicons Genomic characterization of the microbiome The use of novel sequencing technologies (NGS) is warmly encouraged, but support on more traditional techniques remains also available

8 POTENTIAL APPLICATIONS Population genetics / genomics Phylogeography Phylogenetics / phylogenomics Museum genetics / museomics Ecological & evolutionary genetics / genomics Genomics of the microbiome DNA Barcoding identification / Forensics

9 EXAMPLES FROM PREVIOUS JEMU PROJECTS (ca. 20 projects) Field Organism DNA Approach Population genetics / genomics flies, snails, African buffalo microsatellites, NGS Phylogeography birds, African buffalo Sanger sequencing Phylogenetics & phylogenomics termites, amphipods, snakes multi-locus Sanger seq & NGS Museum genetics / museomics flies, Congolese vertebrates DNA preservation, NGS Ecology sawflies Sanger sequencing DNA-based species identification for forensics, biodiversity inventory, agriculture, food safety, etc. Congolese vertebrates, Malagasy reptiles, flies, amphipods, ants, butterflies DNA barcoding Species boundaries flatworms, annelid worms, flies, snails Sanger sequencing & NGS

10 POPULATION GENETICS / GENOMICS Population structure, gene flow and recent evolutionary history Genetic management of populations: effective population size, inbreeding, genetic drift Molecular markers: microsatellites (SSR), single nucleotide polymorphism (SNPs) Ex. Bulinus truncatus Method: GBS- SNP Ex. Syncerus caffer 8 identified populations Method: GBS- SNP and SSR A Southern African Region Eastern African Region West-Central African Region S.c. caffer Con nental Scale B Southern Region West-Central Region S.c. nanus Eastern Region S.c. aequinoctialis C S.c. brachyceros

11 PHYLOGEOGRAPHY Evolutionary history of a species in the context of the Earth s geoclimatic history (population expansion, bottleneck, vicariance and migration) Molecular markers: variable mtdna fragment Ex. African Goshawk Accipiter tachiro (8 subspecies) min. 2 species Method: COI sequence Ex. Syncerus caffer (4 morphological subspecies) 2 identified lineages Method: D-Loop sequence

12 MUSEUM GENETICS / MUSEOMICS Longitudinal studies: genetic effects after fragmentation, climate change, poaching, Museum specimens as a tool to delineate the base-line situation Molecular markers: microsatellites (SSR) Ex. Passer domesticus

13 EVOLUTIONARY GENOMICS Unravel the evolutionary history of a species assemblage Molecular markers: single nucleotide polymorphism (SNPs) Ex. Calosoma Method: RADseq SNP Whole draft genome reconstruction

14 DNA-BASED SPECIES IDENTIFICATION Exploring biodiversity and building a reference library of DNA barcodes Species delineation Species identification Ex. Malagasy reptiles Ex. Congolese vertebrates Ex. ants from Ecuador (genus Solenopsis)

15 DNA-BASED SPECIES IDENTIFICATION Exploring biodiversity and building a reference library of DNA barcodes Species delineation Species identification Ex. flies of forensic interest Ex. vectors of diseases (mosquitoes) BUT NOT SERVICES Ex. Barcoding Organisms and tissues of Policy Concern

16 METABARCODING / METAGENOMICS Environmental DNA, diet analysis, symbiont diversity Barcode marker (16S rrna, COI, ) or whole genomes Ex. microbiomics (SYMDIV PROJECT, ) Characterizing bacterial assemblages of insect pests with different feeding strategies Correlating assemblage diversity and composition to insect life history traits and geographic origin

17 PILOT PROJECT Epigenetics Change in nucleotide sequence modification DNA molecule itself Environmental induced DNA modifications Methylation Modification histon tail

18 PILOT PROJECT Epigenetics Example: methylation of the agouti gene in mice Environmentally induced: diet mother Reduced Representation Bisulphite Sequencing Wet lab: very similar to RADseq Bioinformatical analysis: some caveats Resource polyphenism

19 Restriction digest RADseq RRBseq Adapter ligation Shearing Size selection Adapter ligation Bisulfite Conversion M C C or C U PCR amplification Sequencing

20 DEADLINES TO REMEMBER Deadline for sending an expression of interest: 17 May 2016 name and contact of the coordinator (must be at RBINS/RMCA) a few lines briefly describing the project the research issues to be investigated a list of the biological material available (end of August) a suggestion of methodological approach (optional) contacts of potential external partners Deadline for the submission of the proposal: 30 June 2016 JEMU proposal submission form 2016 More info on

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