TECHNOLOGY

Whole Genome Sequencing

Host genomic analyses are based on resequencing the entire animal genomes to obtain the highest resolution

REFERENCE GENOMES

Whole Genome Sequencing (WGS) relies on the availability of high-quality reference genomes. Many of them are now being sequenced by multiple genomics consortia such as the Vertebrate Genomes Project.

SNP PROFILES

SNP profiles based on WGS provide the highest resolution to both identify genomic structure of species and populations and establish associations between genomic and microbial metagenomic traits.

POPULATION STRUCTURE

Acknowledging the structure of wild animal populations enables estimating population sizes, connectivity across populations and other relevant factors to understand the impact of host-microbiota interactions.

Shotgun Metagenomics

Whole genomes of microorganisms associated to hosts are reconstructed from metagenomic data

ASSEMBLY

Overlapping patterns of DNA sequences recovered from oral and anal swabs and faeces are used to generate long DNA sequences that are used to characterise microbial genomes.

BINNING

Bacterial genomes are reconstructed based on genetic properties and abundance patterns of DNA sequences characterised from metagenomic samples.

REFERENCE-FREE

The use of reference-free approaches enables detecting and characterising hidden diversity not still represented in public databases.

Automatised High-Throughput Workflows

Sample processing procedures are automatised to ensure high-throughput generation of reliable and reproducible results

STORAGE

We are currently trialing a standardised homemade preservation buffer which will reduce costs, commercial dependence and increase longevity of the Initiative. Samples will be registered using the QR codes of the tubes, and linked to the metadata provided by the field researchers. Biological samples will be stored in the sample storage facility of the EHI at -20ºC until DNA extraction is carried out.

LIQUID HANDLING ROBOTS

We are using robots to fill and label tubes included in the Sampling kits, as well as to extract DNA and prepare sequencing libraries. In doing so, we ensure rapid reaction to collaborators' needs for sampling material and high-throughput processing of biological samples.

DNA SEQUENCING

We multiplex libraries derived from multiple samples and taxa to sequence animal genomes and microbial metagenomes at the lowest fares and fastest throughput, using the most advanced sequencing technologies.

Cloud Services

Data and metadata are stored in Cloud services to ensure highest levels of sequrity and accessibility

DATABASE

Relevant metadata of the sampling events, sampled animals, processed samples and generated data are stored in the central EHI database.

RAW DATA

Genomic and metagenomic data belonging to each animal individual, as well as assemblies and bacterial MAGs derived from them, are stored at the European Nucleotide Archive (ENA), and are available to all researchers.

RESULTS

Results are disseminated via publishing articles under open access license, and participating in international conferences.

Address

Center for Evolutionary Hologenomics, GLOBE Institute
University of Copenhagen
Øster Farimagsgade 5, 7
1353 Copenhagen K, Denmark

Contact

Coordinator: Antton Alberdi, PhD
Email: ehi@sund.ku.dk