Pacific Arctic Group (PAG) logo is a polar bear walking on sea ice. The PAG is part of the International Arctic Science Committee (IASC).

We are looking forward to providing an update on the latest observations of #OceanAcidification at the Pacfic Arctic Group meeting in Seoul Korea next week! 🙌
#PAG2025 🇰🇷🧪🌊🦑

pag.arcticportal.org

🌲🧬🦀 Calling conservation genomics scientists! 🦀🧬🌲

@uconneeb.bsky.social & @nanoporetech.com's ORG.one hosts “Genomes for Conservation of Endangered Species” workshop at #PAG33. Submit abstracts by Monday, Oct 27! Join us to advance genomic resources for conservation. #PAG2025

HERRO was one of the heroes from #PAG2025 | #PAG32

Great presentation from our institute director Dr. Nicole Riddle at PAG32! 🧬 #PAG2025 #AgingResearch

IISAGE hosted a workshop at the Plant and Animal Genome Conference (PAG) in San Diego, CA! The session, "Genomics and Epigenomics of Aging," highlighted recent breakthroughs in aging research across species. Big thanks to all the amazing speakers! #Genomics #AgingResearch #PAG2025

GENESPACE tracks regions of interest and gene copy number variation across multiple genomes GENESPACE lets users track related chromosomal sequences across multiple reference genomes.

But even this can be too much, especially since many genomic analyses often focus on genes. One great example for analyzing and visualizing how genes vary in a pangenome is GENESPACE (this came up over and over again at #PAG32 | #PAG2025) elifesciences.org/articles/785...

So long San Diego! Here’s my opinionated meeting report from #PAG2025 | #PAG32. What else did I miss???

Huge thanks to Dr. Elinor Karlsson for her amazing session at PAG yesterday on whole exome sequencing in at-risk companion dogs and clonal hematopoiesis! 🧬 🐾 Thanks to everyone who joined us for the workshop and reception—we had a great time connecting and learning more about your research. #PAG2025

Great presentation from @johannconfais.bsky.social at #PAG2025 #PAG32 on the first result obtained with panREPET tool a non reference centric approach

#PAG2025 | #PAG32 continues! Todays highlights are the Bioinformatics session (starting now in Pacific A) and the Galaxy Workshop (starting at 4pm in T&C D)!

Bookmarking the thread, #bookmark #pag32 #pag2025 I liked the conclusion slide “if you search for pangenome graph benchmark, all you get is the image of Mark Twain sitting on a bench”

Excited to present at the #PAG2025 @nanoporetech.com workshop tomorrow! Come along to hear more about how we incorporate ONT methylation sequencing for sea turtle conservation! 🐢🧬

🌱 Our #PAG2025 workshop is starting soon! Head to Pacific D ballroom to hear Dr. Elinor Karlsson of the Broad Institute share how #AVITI  & Trinity™ #sequencing unlocks novel insights into clonal hematopoiesis in at-risk companion dogs.

🗓️ Jan 13 | 4:00-6:10 PM | Pacific D Ballroom

A Novel Methodology for a Comprehensive Analysis of Genomic Sequence-to-Graph Alignment Tools Genome graphs have proved to be a more compact and efficient way of representing genetic inter- and intra-individual variability. Although they overcome the traditional sequence-based genome reference...

#PAG32 | #PAG2025
Dr. Wattenburger
New publication about evaluation:
ieeexplore.ieee.org/document/108...
Other tools to develop pan-genome graphs
PGGB: www.nature.com/articles/s41...

#PAG32 | #PAG2025
Dr. Wattenburger
2) Completeness and Contents
- Coding regions well represented, clearer relationship to traits, better placement certainty

Mysterious missing regions are research opportunites
-Maize Knobs
- Repetition
- Non-systematic regions

Pangenome graph construction from genome alignments with Minigraph-Cactus - PubMed Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers ...

#PAG32 | #PAG2025
Dr. Wattenburger
Assessing genome graph quality using Minigraph-cactus
1) Structural stability
- Issues: Complexity, genome order and Clipping
- variability was very low
2) Completeness and contents
pubmed.ncbi.nlm.nih.gov/37165083/

Plant pangenomes for crop improvement, biodiversity and evolution - Nature Reviews Genetics Plant pangenomes have had a transformative impact on crop enhancement, biodiversity conservation and evolutionary research. This Review delves into the application of plant pangenomes for underst...

#PAG32 | #PAG2025
Dr. Wattenburger
Genome Graph vs linear reference
- Genome Graph: Efficient representation of a population of genomes
www.nature.com/articles/s41...

#PAG32 | #PAG2025
Dr. Cassandra J. Wattenburger presents about
"Evaluating Genome Graph Quality for Zea mays with Minigraph-Cactus" in the Application of Genetics and Genomics for Large-scale Breeding Programs workshop

#PAG32 | #PAG2025
Dr. Filiault
BAHAR summary: progress & expansion
Successful field trials to hybrids
Sequencing-based genotype works
- Practical Haplotype graph based genotyping & variant calling
Ambitious plans for 2025 & beyond
- Functional BAHAR-omics (long read haplotype and transcriptomics)

#PAG32 | #PAG2025
Dr. Filiault
BAHAR lines contain ~10% diverse windows
used short read sequencing (~5x coverage)
- Most genomic windows contain diverse material but percent varies among and across chromosomes.
- Does low diverse % truly reflect resistance to introgressions?

#PAG32 | #PAG2025
Dr. Filiault
How to genotype lines without established markers? Sequencing!
Step 1: Optimize variant calling
- Practical haplotype graph of 4 elite parents
Step 2: Identify non-elite regions by divergence
- Non-elite (diverse) regions have high SNP density

#PAG32 | #PAG2025
Dr. Filiault
BAHAR line construction
> 2,500 varieties (1750 were tropical from USDA Plant Germplasm System; remainder from internal open pollinated germplasm)
- Selection for elite lines
- Field trials, Genotyping, GWAS, Pangenome resources

#PAG32 | #PAG2025
Dr. Filiault
BAHAR - a mapping population
- Directly incorporate lines of interest
- Describe new alleles and their phenotypic effects
- Data to explore genetic and GxE interactions

#PAG32 | #PAG2025
Dr. Filiault speaking about "Evaluating and Incorporating Diverse Maize Genomes through the Bayer Haplotype Resource (BAHAR)"

Diverse Germplasm:
Broad source of potential new variation
Select for local important traits
Open pollated populations

Low-pass sequencing: leveraging entire genomes for trait selection WATCH ON DEMAND | This webcast took place on: Wednesday 26 April 2023

#PAG32 | #PAG2025
Dr. Lee
What will this LRLP get us?
- Selection Accuracy
- Large Inserion Capture
nature.com/articles/d44...
Publication has been submitted to bio-archive and should be availble soon.

Khufu Data – HudsonAlpha Institute for Biotechnology

#PAG32 | #PAG2025
Dr. Lee
Khufu from @hudsonalpha
hudsonalpha.org/khufudata/
Blueberry KhufuPan - Preliminary
Over 1 million Variants
- Small indels but variants with 45K

Long-read low Pass (LRLP)
1 sample - coverage 36x
24 samples - ~3.7x
- long-reads covered more area / short reads pile up

PanKmer: k-mer-based and reference-free pangenome analysis AbstractSummary. Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome an

#PAG32 | #PAG2025
Dr. Lee
Search pedigree of blueberries to add to the pan-genomes that would help the breeding program.
PanKmer software:
academic.oup.com/bioinformati...

#PAG32 | #PAG2025
Dr. Lee
Which genomes to sequence and put in pan-genome?
Custom Work:
What is most udeful tool for a breeder?
-Local adaption representation
-Known QTLs of founders will be represented
-Necessary genetic diversity

#PAG32 | #PAG2025
Dr. Lee
Pangenomes are trying to capture everything everywhere all at once

#PAG32 | #PAG2025
Next speaker is Dr. Lee talking about "Utilizing Bespoke Pangenomes in Polyploid Crop Breeding"
--
Benefits of Polyploidy
-Increased Genetic Diversity
-Increase stress resistance
BUT
- Genome recombination between subgenomes
- and many more