Arun Seetharam

First slide of the maize meeting.

Travel permits of all US government employees (USDA, NSF) have been revoked shortly before the the maize meeting affecting:
- The chair of the meeting
- The winner of the most prestigious McClintock award
- A plenary speaker
- Two short talk presenters
- 22 scientists presenting posters.
#MGM2025

Maize and wild relatives show distinct patterns of genome downsizing following polyploidy Plant genomes are smaller than expected despite the ubiquity of polyploidy due to the process of genome downsizing called fractionation. This process causes loss of DNA sequences, including genes, unt...

New preprint from @sjsnodgrass.bsky.social and our colleagues showing variable fractionation in Zea and Tripsacum post-polyploidy. We welcome your thoughts as we work toward submission to a journal.

www.biorxiv.org/content/10.1...

The latest preprint from the PanAnd project, led by @mcstitzer.bsky.social is out today. We look at genome evolution in the Andropogoneae tribe of grasses. Interesting to see how processes occurring in #maize after #polyploidy may not be a general phenomenon.
www.biorxiv.org/content/10.1...

I totally forgot that in addition to the radical genomics, Michelle put together a website where you can learn about the biology of all the species we looked worked with: mcstitzer.github.io/panand_assem...

On top, five Andropogoneae grass species, from left to right Zea mays subsp. mays, Hemarthria uncinata, Miscanthus sinensis, Sorghum bicolor, Andropogon gerardi. On bottom, a map of the world, with collection sites of Andropogoneae grasses in points. A green background shows the distribution of Andropogoneae grasses throughout tropical and temperate latitudes

On left, a phylogeny of Andropogoneae species, with 14 independent polyploidy origins noted. On right, genome size and repeat content of each assembly. Across all assemblies, average assembly size is 1.9 Gb, and average repeat size is 1.5 Gb.

New preprint featuring my favorite maize-relatives, the Andropogoneae! We sequenced the genomes of 27 species, including lemongrass, kangaroo grass, little and big bluestem, and more -- key species that shape grasslands and prairies worldwide. www.biorxiv.org/content/10.1...

There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...

I have written a couple of threads 🧵 on "classic" #PlantScience papers. I always tag them with #PlantScienceClassics , but will also compile them here in this thread: 👇

🎉I am really excited to share that our paper is out. We present PHILO ChIP-seq, a user-friendly and cost-effective platform for high-throughput, low-input chromatin profiling in plants!

From Mark Zander group

academic.oup.com/nar/advance-...

By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12

Polaris: Polarization of ancestral and derived polymorphic alleles for inferences of extended haplotype homozygosity in human populations. https://www.biorxiv.org/content/10.1101/2024.12.06.627098v1

Chromosome-level Assemblies of Three Candidatus Liberibacter solanacearum Vectors: Dyspersa apicalis, Dyspersa pallida, and Trioza urticae (Hemiptera: Psylloidea) Psyllids are major vectors of plant diseases, including Candidatus Liberibacter solanacearum (CLso), the bacterial agent associated with 'zebra chip' disease in potatoes and 'carrot yellows' disease i...

New insect genomes just dropped. Very happy to have been a (small) part of this cool project 😁

www.biorxiv.org/content/10.1...

Hey educators, tidyplots.org is great for teaching students data visualization because it is

🕊️ Free and open-source
🚀 Easy, intuitive and fast
💾 Loaded with demo datasets
🏆 Embracing best practices
🌈 Beautiful

#rstats #phd #dataviz #education

Cool preprint! How do polyploids lose genes during fractionation/diploidization? Old work in maize pointed to recombination-driven deletions (journals.plos.org/plosbiology/...) but generality was unclear. New evidence this is the more common deletion mechanism! www.researchsquare.com/article/rs-4...

Hybrid adaptation is hampered by Haldane’s sieve - Nature Communications Hybrids have complex genomes that influence their adaptive potential. This study reveals that yeast hybrids adapt slower than their parental species in a new environment, primarily due to a reduced ra...

For her PhD work, Carla Bautista in our group discovered that yeast hybrids adapted slower to stressful conditions, and she figured out why. See what she found here. #evolution www.nature.com/articles/s41...

Pod5Viewer: a GUI for inspecting raw nanopore sequencing data academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/dietvin/pod5...

Source: https://www.biorxiv.org/content/10.1101/2024.12.02.625113v1.full High throughput nanopore sequencing of synthetic xeno-nucleic acids (XNAs)

Direct high-throughput deconvolution of unnatural bases via nanopore sequencing and bootstrapped learning. #Nanopore #Sequencing #XenoNucleicAcids #XNAs #genomics #bioinformatics @nanoporetech.com 🧬🖥️
www.biorxiv.org/content/10.1...

🚨 Summer '25 Paid Internships! Join Purdue’s Anvil Research Experience for Undergraduates for hands-on experience in AI, bioinformatics, & data centers. $680/week + housing. Apply now: purdue.ca1.qualtrics.com/jfe/form/SV_... 🌟

Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate …

Want to learn about the evolution of brown algae as derived from 60 new genomes? Exciting results of the Phaeoexplorer project:
www.sciencedirect.com/science/arti...

Thrilled to see this paper out! 🎉

We analyzed 470 (!) angiosperm genomes and identified and dated 132 whole-genome duplication events. Importantly, we observed that WGD occurrence dates are not randomly distributed, but clustered at times of major environmental upheaval.

Release Hifiasm-0.21.0-r686 · chhylp123/hifiasm Since Hifiasm-0.20.0 (r639): New Feature: Introduced a beta module for ONT assembly using ONT simplex R10 reads. To enable this feature, add the --ont option as shown below: hifiasm -t64 --ont -o...

Exciting news! The latest hifiasm release from Haoyu Cheng and Heng Li adds beta support for @nanoporetech.com simplex R10 reads. Initial results look very promising. 🚀

Check it out: github.com/chhylp123/hi...

If you've missed hyper-k-mers, this joint work with Lucas who's presenting, @imartayan.bsky.social Antoine Limasset and Yoshihiro Shibuya.
They propose a new way to compact k-mers as super-k-mers or unitigs do, but that improves the bit per k-mer level in the representation and storage.

We are proud to announce a collaboration with UK Biobank to create the world’s first large-scale #epigenetic dataset of 50k participants. The dataset will unlock crucial insights into how #epigenetics drives disease & the breakthroughs to treat them.

Read more: nanoporetech.com/news/oxford-...

bamSliceR: a Bioconductor package for rapid, cross-cohort variant analysis https://www.biorxiv.org/content/10.1101/2023.09.15.558026v2 🧬🖥️🧪 #rstats https://github.com/trichelab/bamSliceR from @timtriche.bsky.social lab

annoy a bioinformatician with these simple phrases:
"Can't you just use Excel?"
"Isn't BLAST basically Google for DNA?"
"But did you annotate it?"

A photo of the Sonoran Desert at night with a saguaro cactus in the foreground with the top glowing from the moonlight. A field of stars is visible in the sky behind the cactus.

Come join us in Tucson!! I am excited to announce a tenure track faculty position on the genomics of resilience
@uofa-eeb.bsky.social! Read more about the position in the updated link below! We will begin reviewing applications on December 9! arizona.csod.com/ux/ats/caree...

By popular request, here's how to add Bluesky replies as your blog's comment section!

This requires some technical know-how for now, but I'm hoping that we see some no-code solutions for this pop up soon, like Ghost or Wordpress plugins.

emilyliu.me/blog/comments

Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1 Mapping enhancers and their target genes in specific cell types is crucial for understanding gene re

Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1

The Rise of Polyploids During Environmental Catastrophes https://www.biorxiv.org/content/10.1101/2024.11.22.624806v1 Polyploidy, or whole-genome duplication (WGD), both a strong evolutionary and ecological force and a

The Rise of Polyploids During Environmental Catastrophes https://www.biorxiv.org/content/10.1101/2024.11.22.624806v1

Release v1.25.2 · MultiQC/MultiQC MultiQC v1.25.2 - 2024-11-20 Multiple bug fixes and minor updates. Updates Add natural sort for sample sorting (#2959) Custom content: for plot_type: image, support custom_data config with section...

Just out: @multiqc.info v1.25.2 🎉

This patch release fixes a whole host of bugs, the most important one being for #bcl2fastq 🐛

There are also a host of small additions sneaking in for #ngsbits, #picard, #Nanostat, #Samtools and more - so well worth the update!

github.com/MultiQC/Mult...

Hello! I've made it to bluesky. I never liked Twitter but we'll give this a go!

Starting with Sarcodes sanguinea, aka Snow Plant fungal parasite associated with conifers.

Recorded in UVIVF, I hypothesize that the blue fluorescence is intended to attract bees!

#botany #photography #uvivf