iiinova — where your digital self keeps evolving

Reposted by John Lovell

Joe Hanly @hanliconius.bsky.social · 22/09/2026

I hate to do this with real data, but this is a persistent data vis issue in chromosome synteny riparian plots that we Need to get better at. Left, a synteny plot published today. Right, a rearranged version with exactly the same gross arrangement but with reordered chromosomes:

chromosome synteny riparian plot in which every chromosome has crossing lines

chromosome synteny plot in which no chromosomes have crossing lines. The underlying structure is identical.

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John Lovell @jotlovell.bsky.social · 19/05/2026

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.

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John Lovell @jotlovell.bsky.social · 12/02/2026

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.

science.org

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...

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John Lovell @jotlovell.bsky.social · 06/02/2026

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...

genetics-gsa.org

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

Visit our website to learn more.

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Reposted by John Lovell

Maddy Seale @maddyseale.bsky.social · 06/02/2026

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)

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John Lovell @jotlovell.bsky.social · 30/01/2026

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.

academic.oup.com

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

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Reposted by John Lovell

Rebecca Mosher @rm0sher.bsky.social · 26/01/2026

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. :-)

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John Lovell @jotlovell.bsky.social · 21/01/2026

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

Synteny map and chromosome squashes showing gene and repeat density.

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John Lovell @jotlovell.bsky.social · 20/12/2025

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)

doi.org

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...

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Reposted by John Lovell

Heng Li @lh3lh3.bsky.social · 30/09/2025

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

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John Lovell @jotlovell.bsky.social · 29/09/2025

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

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Reposted by John Lovell

Matt Rockman @wormsrock.bsky.social · 24/09/2025

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 🧵]

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Carrie Wessinger @carriewessi.bsky.social · 24/09/2025

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)!

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Reposted by John Lovell

C. Brandon Ogbunu @cbo.bsky.social · 11/09/2025

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...

undark.org

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.

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John Lovell @jotlovell.bsky.social · 18/08/2025

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...

pangenome 'expansion' curves for cotton and soybean

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Carl T. Bergstrom @carlbergstrom.com · 14/08/2025

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.

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John Lovell @jotlovell.bsky.social · 06/08/2025

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:

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John Lovell @jotlovell.bsky.social · 21/07/2025

🚨 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...

jobs.ornl.gov

Postdoctoral Research Associate - Plant Systems Biology & The Center for Bioenergy Innovation (CBI)

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John Lovell @jotlovell.bsky.social · 14/05/2025

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

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Reposted by John Lovell

Karolina Heyduk @kheyduk.bsky.social · 13/05/2025

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.

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Seema Sheth @seemasheth.bsky.social · 29/04/2025

We begin reviewing applications next week!

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John Lovell @jotlovell.bsky.social · 03/02/2025

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...

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Reposted by John Lovell

Mike Schatz @mikeschatz.bsky.social · 15/01/2025

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

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Reposted by John Lovell

Kevin Bird @stairwaytokevin.bsky.social · 15/11/2024

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.

doi.org

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

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John Lovell @jotlovell.bsky.social · 12/11/2024

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....

academic.oup.com

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

The genome sequence for the drought tolerant peanut variety

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Reposted by John Lovell

🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 10/11/2024

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

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John Lovell @jotlovell.bsky.social · 12/11/2024

@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

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John Lovell @jotlovell.bsky.social · 29/03/2024

Our groups' goal is to produce genomes that are useful; this does not always mean 'telomere-to-telomere' assemblies. The hybrid sugarcane genome is a nice example of this. The article is out this week in Nature: www.nature.com/articles/s41...

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Reposted by John Lovell

Graham Coop @gcbias.bsky.social · 21/02/2024

The All of Us paper is rightly being criticized for its UMAP figure, which suggests an overly discrete view of human variation—a problem that is compounded by colouring the plot with self-identified race and then omitting the “self-identified” from the title & legend. 1/n

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Matt Johnson, PhD @mossmatters.bsky.social · 15/02/2024

I can confirm the appalling news that Duke intends to close its 800K specimen herbarium as part of an embarrassing plan to delete its position as a leader in biodiversity research. This is despite successful fundraising efforts with a donor secured to save the herbarium.

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John Lovell @jotlovell.bsky.social · 14/02/2024

Excellent postdoc right at the cutting edge of genomics; the Harkess lab is great! “collab w/ Loren Honaas (USDA) & Stephen Ficklin (WSU) labs to sequence 1000s of apple/pear RNAs to develop biomarker assays for maturity and post-harvest traits. $60,000.” hudsonalpha.applicantpro.com/jobs/3238779

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John Lovell @jotlovell.bsky.social · 30/01/2024

🚨We're hiring🚨 We are looking for a scientist to bridge the gap between genomics and breeding, focusing on traditionally under-invested crops and regions. It's physically located at Colorado State University in beautiful Ft. Collins, CO. Pls share! hudsonalpha.applicantpro.com/jobs/3211389

hudsonalpha.applicantpro.com

HudsonAlpha - Staff Scientist - Genome Sequencing Center - Huntsville, AL

Position: STAFF-SCIENTIST: Evolutionary gen

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John Lovell @jotlovell.bsky.social · 18/01/2024

We are trying to come up with subgenome IDs for a new genome. Need to be single uppercase character for each of two subgenomes. Any suggestions of characters to NOT USE? Right now we are avoiding: ABCDEIOPQUVWXYZ

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Reposted by John Lovell

Kevin Bird @stairwaytokevin.bsky.social · 12/01/2024

I'm pulling double duty this year at #PAG31. On Sunday, check out the Polyploid session for some amazing talks on the biological & evolutionary impacts of polyploidy across plants & animals. On Monday evening I'm presenting our work on a pangenome of hexaploid Camelina sativa in the DOE-BER session

screenshot of a session schedule:
Location Pacific E
Date: Sundary, Jan 14 1:30PM
Duration 2 hours 10 minutes

1:30 PM Identification of Xenopus Subtelomers Illustrates Allopolyploids As Ideals Models for Genome Evolution
Presenting Author: Adam Session

1:50 PM Exploring and Exploiting Genomic Regions of Interest in Complex Polyploid Crops
Presenting Author: John Lovell
2:10 PM Delayed Rediploidization Following Genome Duplication in Teleost Fishes
Presenting Author: Elise Parey

2:30 PM Subgenome Bias in Lineage Assembly Following Fractionation in the Tribe Brassiceae
Presenting Author: R. Shawn Abrahams

2:50 PM Fertility Based Selection across Three Generations of a Segregating Allohexaploid Brassica Population for Improved Genomic Stability

3:10 PM Landrace and Bred Accessions of Allotetraploid Sour Cherry (Prunus cerasus L.) Reveal Variation in Subgenome Dosage and Subgenome Expression Bias
Presenting Author: Kathleen E.B. Rhoades

Details
Session: BER Plant Genomic Science
Location: Palm 3-4
Date: Monday, Jan 15 6:38 PM

Presenting Author
Kevin Bird
Pangenomic Analyses Reveal Structural and Gene-Content Variation in the Allohexaploid Biofuel Crop Camelina sativa

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Jill Wegrzyn @jillwegrzyn.bsky.social · 07/01/2024

The 2nd biennial meeting of the North American Forest Genetics Society (June 10-14th 2024) will take place in Oaxaca, Mexico! Researchers at all levels are encouraged to attend - nafgs24.org for info on confirmed speakers, preliminary schedule, & training workshops. Registration opens Jan 19th! 🌲🌳

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Matt Hufford @mbhufford.bsky.social · 07/12/2023

Inaugural Bluesky post (👋 Everyone!): The Ecology, Evolution, and Organismal Biology Dept. at Iowa State U. (my dept!) is conducting an open search at the rank of Professor for a new Dept. Chair! isu.wd1.myworkdayjobs.com/en-US/IowaSt...

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Jesse Lasky @laskyjr.bsky.social · 07/12/2023

I am recruiting a manager/tech for our plant evolutionary genetics lab, looking for someone interested in learning ancient DNA techniques psu.wd1.myworkdayjobs.com/PSU_Staff/jo...

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Jill Wegrzyn @jillwegrzyn.bsky.social · 05/12/2023

@cbcuconn.bsky.social is offering 2 virtual #bioinformatics training workshops in Jan! Genome Assembly (Jan 8-11) and Genome Annotation (Jan 22-25). 1/2 days, real instructors, real data examples! Learn more & register here: bioinformatics.uconn.edu/cbc-workshops/

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John Lovell @jotlovell.bsky.social · 05/12/2023

If you review a genome paper and state that the major flaw is that it is not "T2T" ... please justify why a couple gaps in highly repetitive regions is such a problem. For the same $$ we can learn so much more from multiple nearly gapless genomes than a single gap-patched reference.

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John Lovell @jotlovell.bsky.social · 30/11/2023

We're working on a viz tool to show differences btw genome assemblies, both due to biology and assembly quality. Currently, the output looks like this for Human Hg38 vs. CHM13-T2T: orange = gene density, blue = repeats, red = gaps, grey ribbons = GENESPACE synteny any thoughts for improvements?

upcoming GENESPACE::plot_2genomes output. Here a map of two human genomes showing gaps in the older that are filled in with repetitive sequence in the new genome.

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Dan Koenig @evogen.bsky.social · 24/10/2023

So excited to announce our search for an Assistant Professor focused on understanding plant response to climate change! Come join us at UC Riverside aprecruit.ucr.edu/JPF01827

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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 11/10/2023

SMBE 2024 Puerto Vallarta website is live! The call for symposia opens soon! www.smbe2024.org

smbe2024.org

SMBE 2024

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John Lovell @jotlovell.bsky.social · 29/09/2023

Great integration of genomics, quant gen and breeding. Great story too. doi.org/10.1038/s414...

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John Lovell @jotlovell.bsky.social · 20/09/2023

Question for the #genomics hive mind: I want to test whether a transcription factor binds better to one of two sequences … is there a tool that can do this statistical test?

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