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 · 3mo 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

Plant Science Research Weekly --  Genomic studies offer new hope for restoring the dwindling American chestnut (Science) @jotlovell.bsky.social @jholliday.bsky.social (Summary by Sonal Sachdev sci3ntyst.bsky.social) buff.ly/9AuuGUY #PlantaePSRW

Genomic studies offer new hope for restoring the dwindling American chestnut | Plantae

Deadly blight caused by the fungal pathogen (Cryphonectria parasitica) and root rot caused by an oomycete pathogen have pushed the American chestnuts toward extinction. In this study by Westbrook et…

buff.ly

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 · 12mo ago

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:

I'm super excited to share that this article was published today in Science! www.science.org/doi/10.1126/... All made possible by the fantastic group of donors, volunteers and scientists at The American Chestnut Foundation (tacf.org), HudsonAlpha Institute for Biotechnology, and our collaborators.

Genomic approaches to accelerate American chestnut restoration

More than a century after two introduced pathogens killed billions of American chestnut trees, introgression of resistance alleles from Chinese chestnuts has contributed to the recovery of self-sustai...

science.org

John Lovell@jotlovell.bsky.social · 2y ago

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...

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

This week in @science.org, a celebration of plant pangenomes. A pangenome analysis for massively polyploid sugarcane species, and one for Brassica rapa giving insight into subspeciation. What's all the fuss about pangenomes? Pamela and Douglas Soltis explore this in an insightful Perspective(1/4)

This article is now published! academic.oup.com/nargab/artic... We’ve added a few new analyses. First off, we show that, while gene presence absence variation (PAV) scales with evolutionary distance in both plants and animals, the base level and rate of accrual are both twice as high in plants.

Evolutionary and methodological considerations when interpreting gene presence–absence variation in pangenomes

Abstract. While graph-based pangenomes have become a standard and interoperable foundation for comparisons across multiple reference genomes, integrating p

academic.oup.com

John Lovell@jotlovell.bsky.social · 12mo ago

Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts. We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...

I am excited to offer a postdoctoral research position in my lab in Oxford studying the distribution of small RNAs during plant sexual reproduction. shorturl.at/7Goxt Reposts appreciated! Obligatory cat video to brighten your day. :-)

@amarques.bsky.social really knows how to tell a story graphically. Maybe the most information dense but visually appealing figure I've seen recently!

André Marques@amarques.bsky.social · 7mo ago

2️⃣ A holocentric pangenome links karyotype evolution to meiotic recombination 🔄 Structural variation and recombination landscapes are tightly intertwined in holocentric systems. 🔗 doi.org/10.64898/202...

The January issue of New Phytologist is online now, featuring on the cover @roseamarks.bsky.social’s article on the physiology and genomics of the resurrection plant, Myrothanus flabellifolia. doi.org/10.1111/nph.... (I’m posting here for Dr. Marks, who is currently doing field work off the grid)

The architecture of resilience: a genome assembly of Myrothamnus flabellifolia sheds light on desiccation tolerance and sex determination

Myrothamnus flabellifolia is a dioecious resurrection plant endemic to southern Africa that has become an important model for understanding desiccation tolerance. Despite its ecological and medicina...

doi.org

Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin

Just an outrageous amount of structural variation in pennycress. While not yet reproductively isolated, its likely these shredded pericentromeres contribute to some reproductive incompatibilities.

Kevin Bird@stairwaytokevin.bsky.social · 10mo ago

Whole-genome alignments revealed pennycress has nearly dichotomous genome compartmentalization: huge gene-poor pericentromeric regions (~300Mb; <1% genic) with frequent rearrangements and highly syntenic gene-rich chromosome arms (~150Mb; ~20% genic). What we call a "two-speed" genome structure. 3/

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

C. elegans is a real animal and we set out to understand how it comes to have its distinctive biogeography. Its ancestral center of diversity is in the higher elevation forests of Hawaii. Its closest relatives are spread across east Asia. Did they travel from Asia? [Preprint 🧵]

Don't forget to apply to our position in Evolutionary Genetics at U of South Carolina! In my experience it is a fantastic place to start a new lab, with friendly and supportive colleagues and many junior faculty in EEB! Review starts in 1 week (Oct 1)!

Carrie Wessinger@carriewessi.bsky.social · 12mo ago

Please repost and amplify ! We are hiring a faculty position in Evolutionary Genetics in the Biology Department at U of South Carolina! Check us out and come be our colleague! sc.edu/study/colleg... Deadline for applications is Oct 1 #AcademicJobs #EvoBio

And yes, now is the right time. New for @undark.org "The fundamental problem with the tenure process is that it has struggled to recognize that knowledge is curated, created, and consumed differently today than even a decade ago." undark.org/2025/09/11/o...

It’s Time to Rethink the Academic Tenure Process

Opinion | To fight the war on science, higher education needs to reimagine the most important career milestone for faculty.

undark.org

Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts. We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...

Motherfucker wrote one sloppy paper in April 2020 and instead of being like oops, shit, my bad, he has kept doubling down until now he's killing most promising medical technology of the past quarter century rather than going to therapy.

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 · 12mo ago

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...

@jrossibarra.bsky.social your kind of street art

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...

The PLANTS program (funded by NSF) at @botsocamerica.bsky.social was a cornerstone of the conference each year, bringing together new-to-science scholars with more experienced mentors. It helped provide community, support, and connection to new scientists. The grant was terminated last week.

We begin reviewing applications next week!

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

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

My work on a pangenome for the hexaploid oilseed crop Camelina sativa is now out early access in Genetics! This young polyploid genome has a small pangenome to match it's low SNP diversity, but regained lost diversity by packing in all the unique genes from its 3 diploid progenitors.

Allopolyploidy expanded gene content but not pangenomic variation in the hexaploid oilseed Camelina sativa

Abstract. Ancient whole-genome duplications (WGDs) are believed to facilitate novelty and adaptation by providing the raw fuel for new genes. However, it i

doi.org

Last week we published a peanut genome that was much more complex than it originally appeared. A 🧵 about 🥜 genomes and what we found ... Find the article as a ‘featured’ genome report in G3: academic.oup.com/g3journal/ar....

Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar

The genome sequence for the drought tolerant peanut variety

academic.oup.com

Genomics, evolution, and more starter pack! Help build community with this starter pack. This list is currently incomplete. Want to be included? Reply and I will remedy that! go.bsky.app/JjvzkWU

@carlbergstrom.com you had a post about making 🐦‍⬛ friends a while back - mind linking it here? We’re gonna try it out with the magpies on our street. Got the 🥜 ready to go