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