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
Very excited to announce that the final version of this is live now at @nature.com!!
www.nature.com/articles/s41...
There are a bunch of ways ... here is one:
```
ggplot()+ggtitle(expression(paste("Reference: ", italic("Quercus rubra"), " is the best")))
```
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.
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...
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)
We added this analysis to the published version (table 1). Short answer, it solves some problem, but creates others!
Thanks again to @tomasbruna.bsky.social and @jgi.doe.gov for making this work possible!
Second, we re-annotated all the genomes with the popular ML tool, Helixer. Helixer solves some PAV methodological artifacts, but it also produces implausible gene models at a high rate.
For example, 1 in 5 Helixer gene models have non-canonical splice sites or very short internal introns/exons.
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.
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!
This work would not have been possible without Jill M. Farrant, @jleebensmack.bsky.social, @bobvanburen.bsky.social, Alex Harkess, many other coauthors, and the HudsonAlpha Genome Sequencing Center assembly and sequencing team
Find the genomes on phytozome phytozome-next.jgi.doe.gov/info/Mflabel...
@tomasbruna.bsky.social annotated the genome with deep RNA-sequencing support collected across a dehydration time course. Differential expression analyses revealed expected reduced activity of photosynthesis-related genes but also previously unobserved reductions in cell division-related processes.
The @jgi.doe.gov assembled a haplotype-resolved genome of a male (XY) Myrothanus flabellifolia with @pacbio.bsky.social HiFi reads. Analysis led by @scarey.bsky.social uncovered a ~700kb sex determining region (SDR) - one of the smallest observed in any plant.
We started working on Myrothamnus because of its adaptation to extreme drought conditions. The cover photo is its ‘resurrected’ state, but Myrothamnus survives long and severe droughts in its native south Africa by entering a physiologically quiescent state and tolerating internal desiccation.
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)
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.
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/
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)!
I haven’t slept for seven days either … that would be too long
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...
Very nice! Thanks for the link.
This is something you find when you dig deep enough. We've been looking for ways to harmonize annotations since we saw a similar pattern among pecan genomes in 2021 (buried in the SI tho). www.nature.com/articles/s41...
We can try it, but my guess is way worse. So many false positives.
So, tl;dr: gene PAV and CDS variation is highly dependent on annotation method. Carefully choose, re-annotate, and integrate your pangenome if you want to trust the results
Preprint led by @tomasbruna.bsky.social, Avinash Sreedasyam, and @avril-m-harder.bsky.social. Support from @jgi.doe.gov.
Furthermore, even within fully present ('core') gene families we noticed a disturbing trend — identical sequence was not annotated with identical gene structures 20-50% of the time w/in annotation methods and 40-70% of the time btw methods
IGC-reannotation is not perfect, but reduces this to 5-15%
But what about within methods? Is using the same method enough to trust PAV? The answer here is less obvious, but method clearly matters.
Within two groups that annotated 7 and 23 soybean genomes there were 3x & 2x more PAVs than IGC — these pangenomes are not as 'open' as reported.
These results clearly show that 'naive' integration of existing annotations is not a good idea, especially among genomes that were annotated with similar but not identical methods.
