RADseq platform

Restriction site Associated DNA (RAD) sequencing is an effective methodology to produce genomic data at population level even in non-model organisms. It can be employed in SNPs discovery and genotyping, genotype-phenotype association mapping, linkage mapping, QTL analysis, hybridization and gene flow analysis, phylogeography, population genetics ...

The approach

Genomic DNA is digested by restriction enzymes and tagged with barcode sequences in each sample. Tagged individuals/populations can then be pooled and sequenced on a next-generation sequencer (ILLUMINA sequencer MiSeq/HiSeq2000/2500 at the Norwegian Sequencing Centre).

Currently, we have 62 TGCA-overhang  P1-adapter in use (they can be ligated to SbfI, PstI, etc, digested DNA) and this is a graphic protocol kindly provided by one of our users.

We use the STACKS pipeline to analyze our raw sequence data.

We recommend to visit the UK RAD Sequencing Wiki for more info 

Contact us to use our RADseq platform.

NEW! - RAD sequencing is now offered as a service through the Norwegian Sequencing Centre. Contact us for more info!

We are using it for...

Evolutionary response of two African Rodent species (Hystrix sp) to climate changes: the study of the past as an estimate of the future
Emiliano Trucchi, Nils Christian Stenseth.

Tags: phylogeography and population genetics

Population genomics of penguins
Celine Le Bohec, Emiliano Trucchi, Jason Whittington, Nils Christian Stenseth & Yvon Le Maho.

Tags: population genetics and connectivity

Investigating the genomic signature of non-plated stickleback (Gatserosteus aculeatus)
Anna Mazzarella, Kjartan Østbye, Kjetill S. Jakobsen, Asbjørn Vøllestad.

Tags: phenotype/genotype mapping, population genetics

Ecological genomics of Atlantic cod (Gadus morhua): adaptive responses to changing selection regimes
Paul R. Berg, Bastiaan Star, Sissel Jentoft, Kjetill S. Jakobsen. 

Tags: population genetics, adaptation, spatial structuring
 

Speciation genomics in the brassy ringlets (Erebia cassioides) species complex 
Paolo Gratton et al (University of Roma Tor Vergata, Italy).

Tags: phylogeography, population genetics, speciation
 

Population genetics of the wood tick Ixodes ricinus: new insights into dispersal capacity and relation with host
Margherita Collini et al (Edmund Mach Foundation, Trento, Italy).

Tags: population genetics, gene-flow, host-identification
 

Phylogeography and speciation in bluethroat and common redstart  
Gunnhild Marthinsen, Arild Johnsen, et al (NHM, University of Oslo).

Tags: population genetics, phylogeography, subspecies.
 

 

Tags: Population genetics, Adaptation, Genomics, Evolutionary genomics
Published May 2, 2012 3:50 PM - Last modified May 14, 2014 8:40 PM

Contact

Emiliano Trucchi

Participants

Detailed list of participants