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...
JEMU call for proposals 2016
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
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
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
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)
PROJECT TIME SCHEDULE
May 2016: expression of interest (informal)
June 2016: proposal submission
September 2016: project start (at latest)
May 2017: project completed
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
POTENTIAL APPLICATIONS
• Population genetics / genomics
• Phylogeography
• Phylogenetics / phylogenomics
• Museum genetics / museomics
• Ecological & evolutionary genetics / genomics
• Genomics of the microbiome
• DNA Barcoding identification / Forensics
• …
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
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
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
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
EVOLUTIONARY GENOMICS
Unravel the evolutionary history of a species assemblage
Molecular markers: single nucleotide polymorphism (SNPs)
Ex. CalosomaMethod: RADseq – SNP
Whole draft genome reconstruction
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
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
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
PILOT PROJECT
• Epigenetics Change in nucleotide sequence ↔ modification DNA molecule itself
Environmental induced DNA modifications
Methylation Modification histon tail
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
RADseq
Restriction digest
Adapter ligation
Shearing
Size selection
Adapter ligation
PCR amplification
Sequencing
C → C or C → U
M
RRBseq
Bisulfite Conversion
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