Pan-genomes Doorstep Meeting

Evolutionary Applications of Pan-genomes PEQG Doorstep Meeting

Tuesday, June 9, 1:00-4:00 p.m. PDT, Asilomar Conference Grounds

Led by John Lovell and Avril Harder, Genome Sequencing Center, HudsonAlpha Institute for Biotechnology

The availability of many reference genomes within and across species provides a powerful foundation to discover the causes and consequences of molecular evolution. When integrated into a single resource, these “pan-genomes” can capture the full spectrum of sequence and functional variation across individuals, populations, species, and higher order taxonomic groups. This richer framework can enable more accurate read mapping, variant discovery, and evolutionary inference, particularly in diverse or non-model systems.

This three-hour workshop will probe the challenges and benefits of pangenomics, through the lens of evolutionary, population, and quantitative genetics. Invited presentations, discussions, and hands-on tutorials will cover topics including:

• Pan-genome construction and analysis across very diverse taxa
• Phylogenetic inference in the context of multiple reference genomes
• Annotation of genes, structural variants, and functional effects
• Pan-genome graph construction and quality control

Attendance is limited to allow for plenty of interaction and in-depth discussion. Bring your fully charged laptop to the meeting.

Meeting Agenda

1:00–2:00 p.m.	Part 1: Basics of pangenomics—Alignments and annotations	Speaker
1:00 p.m.	Introductions and overview	John Lovell, Moderator
1:10 p.m.	Whole genome alignments and graph construction: Why and how of pangenome graphs Tutorial: Summarizing and quality-controlling pangenome graphs	Avril Harder, HudsonAlpha Institute for Biotechnology
1:35 p.m.	Protein-coding genes: considerations for consistent annotations across pangenomes Tutorial: Evaluating consistency of pan-genome annotations	Tomáš Brůna, DOE Joint Genome Institute
2:00–3:00 p.m.	Part 2: Large-scale genome evolution
2:00 p.m.	Examining gene function and presence–absence variation in Salmonidae Tutorial: Identifying gene presence/absence from alignments	Airianna McGuire, University of Connecticut
2:25 p.m.	Synteny and structural variation in Carnivoran sex chromosomes Tutorial: Mapping synteny with GENESPACE	Ellie Armstrong, University of California, Riverside
2:50 p.m.	Group discussion and break
3:00–4:00 p.m.	Part 3: Pushing the envelope—New methods in pangenomics
3:00 p.m.	Scalable phylopangenomic analysis using PanMAMA and PanMAN	Russ Corbett-Detig, University of California, Santa Cruz
3:25 p.m.	Many genomes, many scales: new pan-vertebrate and pan-human resources for comparative and population genomics	Benedict Paten, University of California, Santa Cruz
3:50 p.m.	Airing of the grievances	John Lovell, Moderator

This meeting will enhance your PEQG 2026 experience, but space is limited so act now! Separate reservation for $99 is required.