Göteborg coast line

First off, a big Thank you! to everyone who participated and everyone who helped to make PGEC 2021 a great success. We had over 700 people registered for virtual and almost 100 registered for in-person attendance

In particular, we want to thank our fantastic speakers who showed the great advances already made in pangenomics and the even greater excitement about the future potential in biology and medicine, and across all kingdoms of life.

We are indebted to our sponsors — the BioEnv department at the University of Gothenburg, the National Bioinformatics Infrastructure Sweden, the Harvard Museum for Comparative Zoology, and the Museums of Science and Culture at Harvard — for their genereous support. Many thanks to the many people who helped to make PGEC2021 a great event for our many virtual and in-person attendants: Diana at HMSC, Christian and the AV team, Marcelo and the Wallenberg Centre staff, the student volunteers — Joel, Adam, Yi and Ntwai —, and our session chairs.

Thanks again,
Scott & Alexander

PS: Recordings will be made available to registered participants. See below for info.

Pangenomes are revolutionizing biology, and new computational and technical tools are providing new insights into evolution and biodiversity. A pangenome is a catalog of all the genetic variation – single base changes, structural variants, regulatory regions and genes – found within a population, species or clade. Traditional short-read and computational approaches to high-throughput sequencing have provided enormous advances, but new approaches are needed to capture all the complex variation found in nature. A core perspective of pangenomics is eschewing a reference genome, leading to so-called reference-free genomics and providing a more comprehensive and inclusive platform to make new discoveries without the biases inherent in using any one genome as a reference.

We will bring together world experts in pangenomics on Wednesday, November 17, 2021, in Gothenburg, Sweden and remotely. Through a series of talks and discussions, we hope to summarize where the field of pangenomics is and what the next steps are. We highlight research in major clades of the tree of life – plants, bacteria, vertebrates, and other groups – as well as new computational algorithms that bring new approaches to capturing genomic variation. The symposium will be a welcome opportunity to interact in person with the pangenomics community and the streamed talks will expose pangenomics to an even wider audience remotely.


The list of distinguished speakers presenting in person or remotely includes:

  • Kerstin Lindblad-Toh, Uppsala Universitet, Sweden
  • Martin Mascher, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany
  • Doreen Ware, Cold Spring Harbor Laboratory, USA
  • Tobias Marschall, Uniklinik Düsseldorf, Germany
  • Marcel Martin, National Bioinformatics Infrastructure Sweden (NBIS), Sweden
  • Benedict Paten, UC Santa Cruz, USA
  • Kaisa Thorell, Sahlgrenska Academy, University of Gothenburg, Sweden
  • Heng Li, Dana Farber Cancer Institute, USA
  • Scott V. Edwards, Harvard University, USA
  • Leif Andersson, Uppsala University, Sweden
  • Shilpa Garg, University of Copenhagen, Denmark
  • Gianni Liti, IRCAN, Université Côte d’Azur (UCA), France
  • Gabriel David, Uppsala Universitet, Sweden

Date & Venue

PGEC 2021 will take place on Wednesday, November 17, 2021, from 9:00 until 17:30 in the Wallenberg Hall at the Conference Centre Wallenberg at the University of Gothenburg. The street address is Medicinaregatan 20A, 413 90 Göteborg, Sweden. Find the location and directions for travel on Google Maps.

Recordings of the presentations will be made available to those who have registered for in-person or virtual attendance. We are still sorting out some organizational questions, so please have patience. We will send email with access information to the address you used for registration.

The program is also available as a PDF document: PGEC2021-Program.pdf.

9:00-9:10 Opening

Scott V. Edwards (Harvard University, USA)

9:10-10:10 Session 1

Session chair: Christine Bacon (University of Gothenburg)
Kaisa Thorell (Sahlgrenska Academy, University of Gothenburg, Sweden)
Expanding Helicobacter pylori comparative genomics: a pangenome perspective
Martin Mascher (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany)
Pan-genomics for crop improvement

10:10-10:40 Coffee Break

Included with in-person registration.

10:40-12:10 Session 2

Session chair: Ana Tronholm (University of Gothenburg, Sweden)
Shilpa Garg (University of Copenhagen, Denmark)
Efficient, high-resolution computational methods for biodiversity genomics
Kerstin Lindblad-Toh (Uppsala University, Sweden)
Using comparative genomics at single-base resolution constraint to understand mammalian genome evolution and human disease
Tobias Marschall (Uniklinik Düsseldorf, Germany)
Structural variation and pangenome-based genome inference

12:10-13:30 Lunch

Included with in-person registration.

13:30-15:00 Session 3

Session chair: Bengt Oxelman (University of Gothenburg, Sweden)
Gabriel David (Uppsala University, Sweden)
Calling structural variants with confidence* from short-read data in wild bird populations
Marcel Martin (NBIS, National Bioinformatics Structure, Sweden)
One reference is not enough for Sweden
Scott V. Edwards (Harvard University, USA):
First glimpses of pangenomes from birds
Gianni Liti (IRCAN, Université Côte d’Azur (UCA), France)
Origin and evolution of yeast pangenomes

15:00-15:30 Coffee Break

Included with in-person registration.

15:30-17:30 Session 4

Session chair: Lars Arvestad (Stockholm University, Sweden)
Leif Andersson (Uppsala University, Sweden)
The genetics of evolutionary change — lessons from Atlantic herring and Darwin’s finches
Doreen Ware (USDA ARS, Cold Spring Harbor Laboratory, USA)
Fluid plant genomes: one of the strategies for plants success
Heng Li (Dana Farber Cancer Institute, USA)
Next-generation pangenome assembly
Benedict Paten (UC Santa Cruz, USA)
Building and using human pangenomes

17:30-17:35 Closing

Alexander Schliep (University of Gothenburg, Sweden)


The workshop is an event of the Department of Biological and Environmental Sciences (BioEnv) at the University of Gothenburg. It is organized by Scott V. Edwards (Harvard University and BioEnv, University of Gothenburg) and Alexander Schliep (Data Science & AI, CSE, University of Gothenburg). You can contact the organizers at pgec2021@schlieplab.org.

The organizers gratefully acknowledge generous support from the following sponsors.

GU logo NBIS logo MCZ logo HMSC logo