Pangenome coordinates can be complex... Shredtools offers a new approach using exact matches to query pangenome data efficiently. Its tools can extract syntenic regions across hundreds of genomes, making pangenome-scale exploration more accessible. pubmed.ncbi.nlm.nih.gov/42465356/

Navigating the pangenome coordinate system with Shredtools - PubMed

Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and represent conserved stretches of columns in the underlying MSA. We introduce Shredtools, which uses mul …

pubmed.ncbi.nlm.nih.gov

The sorghum pangenome, available on the JGI’s Phytozome portal, opens more possibilities to breed sorghum and other crops for biofuels and bioproducts. Learn more in the latest episode of Genome Insider: 🖥️ 🧬🌱 @danforthcenter.bsky.social

A Spectrum of Sorghum | Joint Genome Institute

Hear from Nadia Shakoor (Donald Danforth Plant Science Center), John Lovell (HudsonAlpha Institute for Biotechnology), and Jeremy Schmutz (head of the JGI’s Plant Program, HudsonAlpha) about how a sor...

jgi.doe.gov

Looking forward to #Evolution2026! If you're there, come say hi! Or better yet, come here my talk on Tuesday in collaboration with the phenomenal @avril-m-harder.bsky.social on why pangenome graphs are a lifesaver for evolutionarily important structural variation!

We are often asked whether pangenomes are worth the hassle. The files can be large and methods to explore them are much more challenging than linear references. Earlier this week, we preprinted a clear example of how and why pan-genome graphs are so important for trait discovery.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 4mo ago

Dissecting the regulatory and genomic drivers of the dichogamy determining G-locus in pecan https://www.biorxiv.org/content/10.64898/2026.05.14.725045v1

✨ Paper spotlight ✨ (🧵 1/7) Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome nph.onlinelibrary.wiley.com/doi/10.1111/...

Very excited to announce that the final version of this is live now at @nature.com!! www.nature.com/articles/s41...

A sorghum pangenome reference improves global crop trait discovery - Nature

A pangenome reference for the phenotypically diverse crop sorghum aims to help accelerate future efforts to breed crops that are better adapted to changing environments.

nature.com

John Lovell@jotlovell.bsky.social · last yr.

This began as a @jgi.doe.gov Community Science Program (CSP) project in 2017 with the goal of uniting the diverse sorghum breeding and mapping populations in the framework of a 'pangenome'. Thanks to a huge efforts across many stakeholders, the article was preprinted today. A 🧵 w/ what we found:

We’re excited to share the Pan-genomes Doorstep Meeting @ #PEQG26! Join this 3-hour workshop on evolutionary applications of pangenomics, covering construction, analysis, phylogenetics, annotation & graph QC. Register separately or as an add-on to PEQG: genetics-gsa.org/peqg-2026/do...

Pan-genomes Meeting - 2026 Population, Evolutionary, and Quantitative Genetics Conference

Visit our website to learn more.

genetics-gsa.org

"Sure, bedtools is great and happily used by literally everyone, but, it could be bedder" That takes some serious courage. Kudos Brent and @aaronquinlan.bsky.social !

Aaron Quinlan (he/him)@aaronquinlan.bsky.social · 10mo ago

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

1/2 #NearLab @chasedbrownstein.bsky.social described Birmingham Darter Etheostoma birminghamesnse in April 2025 It is under threat from a mega data center. A petition was filed yesterday by the @biologicaldiversity.org to review the species for protection under the ESA www.wbrc.com/2025/11/14/n...

National conservation group joining fight against proposed data center

A national conservation group is joining their fight, saying the center will have a major impact on a fish population found only in this area of Alabama.

wbrc.com

New — with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social, and many more — we created seven new high-quality genomes and explored pangenomic variation in the emerging oilseed crop pennycress (Thlaspi arvense). 1/

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome

Summary · Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biod...

biorxiv.org

Another hit from @alabamarivers.bsky.social and Southern Exposure

John P. Friel, Ph.D.@friel.bsky.social · 12mo ago

Meet Alabama’s salamanders like you’ve never seen them before and fall for their undeniable charm. vimeo.com/1114098611/8...

🌿Plant pangenomes🌿 have a LOT of genomic presence-absence-variation. Or do they??? A new @jgi.doe.gov preprint by @tomasbruna.bsky.social @jotlovell.bsky.social @avril-m-harder.bsky.social Avinash Sreedasyam takes a closer look www.biorxiv.org/content/10.1...

'Hoods are out!!! Big thank you to @plantevolution.bsky.social for the support throughout. Luisa, @kdm9.bsky.social , @aconga.bsky.social , @hajkdrost.bsky.social it was intellectually stimulating ride with you, so congratulations!!!! #diversity #NLR #immune #pan-genome #graphs #networktheory

K.D. Murray@kdm9.bsky.social · last yr.

Happy to be able to finally share our NLR pangenome paper, out now in CHM. "Pangenomic context reveals the extent of intraspecific plant NLR evolution" www.cell.com/cell-host-mi... #plantscience #plantimmunity #pangenomes #science #nlr

my new idea is to look at runs of homozygosity (ROH) only for mutations that are restricted to heterozygous state in other pops, suggesting they are low freq. and enriched for deleterious stuff. a good measure of inbreeding. I call my new statistic

This began as a @jgi.doe.gov Community Science Program (CSP) project in 2017 with the goal of uniting the diverse sorghum breeding and mapping populations in the framework of a 'pangenome'. Thanks to a huge efforts across many stakeholders, the article was preprinted today. A 🧵 w/ what we found:

bioRxiv Genomics@biorxiv-genomic.bsky.social · last yr.

Developing future resilience from signatures of adaptation across the sorghum pangenome https://www.biorxiv.org/content/10.1101/2025.08.01.667986v1

🚨 We're looking for a #postdoc to join our team at the Center for Bioenergy Innovation at Oak Ridge National Labs, TN 🚨 Project: Advance poplar bioenergy by understanding adaptive trait/genomic variation — breeding/pop gen/bioinformatics Apply by 18-Aug Apply here: jobs.ornl.gov/job/Oak-Ridg...

Ok, fine I'm willing to admit it now: Mimulus is interesting www.authorea.com/doi/full/10....

That time in 2013 when this crabeater seal decided to see what this noisy orange menace was doing in its territory....In 2013 near Peter I Island in #Antarctica on our research cruise (LMG 13-12). Bonus (the 'wait for it' at the end): amazing sunset/sunrise around 1am that night :) 🧪🌎🦑🐧🇦🇶

Wow, the cover looks great! Nice work Patrice and @roederlab.bsky.social The GENESPACE plot uses our new @jgi.doe.gov Pennycress and Brassica rapa genomes built in collaboration with @spicybotrytis.bsky.social & Katie Greenham, hosted on phytozome

Adrienne Roeder Lab@roederlab.bsky.social · last yr.

Check out the beautiful cover to our focus issue on Translational research from Arabidopsis to crop plants and beyond. More articles coming shortly. Congrats Patrice Salome and @jotlovell.bsky.social. @theplantcell.bsky.social academic.oup.com/plcell/issue...

Clever new BUSCO-like method to evaluate the quality of pangenome graphs www.biorxiv.org/content/10.1...

PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers

Motivation Pangenome graphs integrate multiple assemblies to represent non-redundant genetic diversity. However, current evaluations of pangenome graph quality rely primarily on technical parameters (...

biorxiv.org

Quick break from the doom and gloom for science! We're really proud of this one. We found that two major effect loci on duplicated versions of the same ancestral chromosome play a major role in run timing diversity across four species of salmon (pink, chum, sockeye, coho) shorturl.at/GISX2

Diversification of large-effect loci in a duplicated genomic region leads to complex phenotypes

Whole genome duplication provides evolutionary opportunities to increase biological complexity and phenotypic diversity by selective retention of duplicated genes. We identify a small genomic region a...

shorturl.at

longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/lon...

GitHub - yangao07/longcallD: A local-haplotagging-based small and structural variant caller

A local-haplotagging-based small and structural variant caller - yangao07/longcallD

github.com

Post a warning.

John P. Friel, Ph.D.@friel.bsky.social · 2y ago

Post a warning.

"Our results reveal substantial differences between pipelines, with many inversions either misrepresented or lost. Most notably, recovery rates remain strikingly low, even with the most simple simulated genome sets, highlighting major challenges in analyzing inversions in pangenomic approaches."

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 2y ago

Investigating the topological motifs of inversions in pangenome graphs https://www.biorxiv.org/content/10.1101/2025.03.14.643331v1

Our paper on the past, present, and genomics-enabled future of American chestnut (Castanea dentata) tree breeding for resistance to invasive pathogens is on BioRxiv. 🧵with some background and a few things we found 👇 bsky.app/profile/bior...

bioRxiv Genomics@biorxiv-genomic.bsky.social · 2y ago

Improving American chestnut resistance to two invasive pathogens through genome-enabled breeding https://www.biorxiv.org/content/10.1101/2025.01.30.635736v1

A new version of our variation graphs (vg) tool, "Boccaleone," is now available! Updates include: 🔵 HiFi and Oxford Nanopore read support to the Giraffe read mapper 🔵 Faster read sorting 🔵 New Unix manual page Link: github.com/vgteam/vg/re...

Welcome to Day 2 of #PAG32 | #PAG2025. Today's cant miss session is Comparative Genomics hosted by Vijay Tiwari and John Lovell. It is 10:30 - 12:40 in Pacific A. pag.confex.com/pag/32/meeti...

Are you headed to #PAG32 and interested in plant reproduction? 🌼 Come check out my talk in the “Sex Chromosomes and Sex Determination” session on Saturday! I’ll be talking about ancient ZW sex chromosomes, the impact of polyploidy on sexual system evolution, “leaky” dioecy, and much more.

What's better than one polyploid genome? Twelve polyploid genomes! We report a pangenome of the hexaploid oilseed crop Camelina sativa and investigate pangenomic variation and genome evolution in a complex allopolyploid genome. www.biorxiv.org/content/10.1...