JEMU call for proposals 2016jemu.myspecies.info/sites/jemu.myspecies.info/files/JEMU...GOAL • The...
Transcript of JEMU call for proposals 2016jemu.myspecies.info/sites/jemu.myspecies.info/files/JEMU...GOAL • The...
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JEMU call for proposals 2016
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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
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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
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BUDGET
• total financial contribution of 20.000 €
• one or two research projects financed / co-financed (tentatively 10.000 € / 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
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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)
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PROJECT TIME SCHEDULE
May 2016: expression of interest (informal)
June 2016: proposal submission
September 2016: project start (at latest)
May 2017: project completed
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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
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POTENTIAL APPLICATIONS
• Population genetics / genomics
• Phylogeography
• Phylogenetics / phylogenomics
• Museum genetics / museomics
• Ecological & evolutionary genetics / genomics
• Genomics of the microbiome
• DNA Barcoding identification / Forensics
• …
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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, biodiversityinventory, agriculture, food safety, etc.
Congolese vertebrates, Malagasy reptiles, flies, amphipods, ants, butterflies
DNA barcoding
Species boundaries flatworms, annelid worms, flies, snails
Sanger sequencing & NGS
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EasternAfricanRegion
West-Central
AfricanRegionSouthernAfrican
Region
Con
nentalScale
EasternRegion
SouthernRegion West-CentralRegion
A
B
C
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. Syncerus caffer 8 identified populationsMethod: GBS- SNP and SSR
Ex. Bulinus truncatusMethod: GBS- SNP
S.c. nanus
S.c. caffer
S.c. aequinoctialis
S.c. brachyceros
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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. Syncerus caffer (4 morphological subspecies) 2 identified lineagesMethod: D-Loop sequence
Ex. African Goshawk Accipiter tachiro (8 subspecies) min. 2 speciesMethod: COI sequence
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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
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EVOLUTIONARY GENOMICS
Unravel the evolutionary history of a species assemblage
Molecular markers: single nucleotide polymorphism (SNPs)
Ex. CalosomaMethod: RADseq – SNP
Whole draft genome reconstruction
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DNA-BASED SPECIES IDENTIFICATION
Ex. Malagasy reptiles Ex. Congolese vertebrates Ex. ants from Ecuador (genus Solenopsis)
Exploring biodiversity and building a reference library of DNA barcodes
Species delineation
Species identification
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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 SERVICESEx. Barcoding Organisms and tissues of Policy Concern
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Environmental DNA, diet analysis, symbiont diversity
Barcode marker (16S rRNA, COI, …) or whole genomes
METABARCODING / METAGENOMICS
Ex. microbiomics (SYMDIV PROJECT, 2016-2018)• Characterizing bacterial assemblages of insect pests with different feeding strategies• Correlating assemblage diversity and composition to insect life history traits and
geographic origin
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PILOT PROJECT
• Epigenetics Change in nucleotide sequence ↔ modification DNA molecule itself
Environmental induced DNA modifications
Methylation Modification histon tail
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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
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RADseq
Restriction digest
Adapter ligation
Shearing
Size selection
Adapter ligation
PCR amplification
Sequencing
C → C or C → U
M
RRBseq
Bisulfite Conversion
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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 www.jemu.myspecies.info