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plantgenomics.bsky.social
@plantgenomics.bsky.social
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plantgenomics.bsky.social
Trait lability as a predictor of diversification dynamics in flowering plants
doi.org/10.1101/2024...

Genetic factors explaining anthocyanin pigmentation differences
doi.org/10.1101/2023...
Trait lability as a predictor of diversification dynamics in flowering plants
Rates of diversification differ between angiosperm lineages. To date, attempts to explain this heterogeneity have focused on the potential correlation between speciation and extinction rates and parti...
doi.org
December 4, 2025 at 1:38 AM
plantgenomics.bsky.social
Spatial Flavonoid Accumulation in Soybean Pericycle Restricts Phytophthora sojae Invasion
doi.org/10.64898/202...

Diversity and Ecological Functions of Anthocyanins
www.preprints.org/manuscript/2...
doi.org
December 3, 2025 at 7:14 AM
plantgenomics.bsky.social
SaVor - A Reproducible Structural Variant Calling and Benchmarking Platform from Short-Read Data
doi.org/10.1101/2025...

Comparison of read mapping and variant calling tools for the analysis of plant NGS data
doi.org/10.1101/2020...
SaVor - A Reproducible Structural Variant Calling and Benchmarking Platform from Short-Read Data
Structural variations (SVs) are differences in genomic regions that are larger than 1 kilobase-pair (Kbp) between individuals, and can arise from errant DNA repair mechanisms, whole genome duplication...
doi.org
December 2, 2025 at 5:51 AM
Reposted
mahenry20.bsky.social
Catching the light - a little geranium from the autumn.😊🩷🌸🤍

#flowers #flowersonfriday #flowerphotography #bloomscrolling #nature #NaturePhotography #gardening #gardens #beauty #hope #peace 🕊
November 28, 2025 at 9:22 AM
Reposted
jbyoder.org
Orchids are famous for specialized flowers that create species isolation by manipulating pollinators— but these ones don't have specialized pollinator relationships. Instead, they're isolated by pollen incompatibilities. 🌿

buff.ly/Ypb77Ir
Flowers of the orchid Anacamptis papilionacea, pink and butterfly-shaped with wide darker wings; photo by Hans Hillewaert via Wikimedia Commons Flowers of the orchid Anacamptis pyramidalis, lighter pink and with big lip-like labellums; photo by Ramin Nakisa via Wikimedia Commons Flowers of the orchid Anacamptis morio hampe, purple with long nectar spurs and big lip-like labellums; photo by Didier Desouens, via Wikimedia Commons
November 28, 2025 at 3:12 PM
Reposted
plantcuttings.bsky.social
An appraisal of a book that will get you thinking about plants (well, gardens actually) and people this week, the intriguingly-named The green fuse.
More at plantcuttings.uk/2025/11/28/w...
Plus, Mr PC’s Black Friday deal – free subscription to the blog is available(!)
Cheers!
#Botany
#PlantScience
What are gardens for..?
The green fuse by Peter Dale explores gardens through a philosophical and cultural lens, emphasizing their connections with literature, music, and art. Challenging yet rewarding, the book enriches …
plantcuttings.uk
November 29, 2025 at 7:55 AM
Reposted
frwildflowers.bsky.social
Tradescantia occidentalis, our Western Spiderwort, blooming in the Boulder foothills #nativeplants

#FallBackFlowers #FallBack to May 28 🌿
Deep purple three petal flower with frilly filaments and yellow bits in the center
November 28, 2025 at 3:20 PM
Reposted
dannyve.bsky.social
Good morning lovely people! Have some flowers to brighten up the last Friday of November!
November 28, 2025 at 8:25 AM
plantgenomics.bsky.social
Is Evolution Predictable? Experiments in an Evolutionary Video Game
doi.org/10.1101/2025...

Evolutionary Rewiring of Anthocyanin Biosynthesis Pathway in Poaceae
doi.org/10.1101/2025...
Is Evolution Predictable? Experiments in an Evolutionary Video Game
The outcome of evolution sometimes appears to be predictable, as in the evolution of the same characteristics independently in convergent evolution. Other times, evolution's path depends on starting c...
doi.org
November 29, 2025 at 6:16 AM
plantgenomics.bsky.social
CHLOROPLAST GENOME AND PHYLOGENETIC ANALYSIS OF KATMON (Dillenia philippinensis Rolfe), A PHILIPPINE ENDEMIC FRUIT
doi.org/10.1101/2025...

Phylogenetic placement of Ceratophyllum submersum based on a complete plastome sequence derived from nanopore long read sequencing data
doi.org/10.1101/2023...
CHLOROPLAST GENOME AND PHYLOGENETIC ANALYSIS OF KATMON (Dillenia philippinensis Rolfe), A PHILIPPINE ENDEMIC FRUIT
Background: Katmon (Dillenia philippinensis Rolfe) is a Philippine endemic fruit species with a relatively well-studied biochemical profile but poor genomic characterization. Studies involving the chl...
doi.org
November 28, 2025 at 8:17 PM
plantgenomics.bsky.social
GWAS for grain and forage quality traits in a subtropical oat germplasm collection adapted to highland regions of Eastern Africa
doi.org/10.1101/2025...

Genomic characterization of a nematode tolerance locus in sugar beet
doi.org/10.1101/2023...
Genome-wide association mapping for grain and forage quality traits in a subtropical oat germplasm collection adapted to highland regions of Eastern Africa
Oat ( Avena sativa L.) is a globally important cereal cultivated for both livestock feed and human nutrition. However, its productivity is increasingly constrained by both biotic and abiotic stresses,...
doi.org
November 28, 2025 at 8:15 PM
Reposted
bpucker.bsky.social
Corinna and I were awarded the “FAIR Software Award Lower Saxony 2025” on Monday at TU Braunschweig!

We are thrilled that our bHLH_annotator tool convinced the jury.

Check it out here: doi.org/10.1186/s128...

#OpenScience #FAIR #Python @puckerlab.bsky.social
Pictures of the award ceremony at TU Braunschweig. Some pictures were taken by Henry Fiebig.
November 28, 2025 at 5:41 AM
Reposted
bpucker.bsky.social
Gave a talk on “Computational Approaches to Unraveling Biosynthetic Pathways in Plants” at the 6th Annual Meeting of the @denbi.bsky.social Industrial Forum 2025.
If you see potential for collaboration or want to discuss ideas, feel free to get in touch!
Event info: www.denbi.de/de-nbi-event...
Title slide of my presentation “Computational Approaches to Unraveling Biosynthetic Pathways in Plants”.
November 27, 2025 at 3:04 PM
plantgenomics.bsky.social
CHALLENGER: Detecting Copy Number Variants in Challenging Regions Using Whole Genome Sequencing Data
doi.org/10.1101/2025...

DupyliCate - mining, classifying, and characterizing gene duplications
doi.org/10.1101/2025...
CHALLENGER: Detecting Copy Number Variants in Challenging Regions Using Whole Genome Sequencing Data
Copy number variation (CNV) detection remains a major challenge in whole-genome sequencing (WGS) data, particularly within repetitive, duplicated, and camouflaged genomic regions where short-read sequ...
doi.org
November 27, 2025 at 5:47 AM
Reposted
jrossibarra.bsky.social
It's been awhile, but I found myself recommending to someone today our groundbreaking code, lead by the inimitable Andy Kern, that magically converts pdfs to... pdfs. This solves the conversion issue so many journals pose to the intrepid scientist. github.com/andrewkern/p...
GitHub - andrewkern/pdf2pdf: does the magical pdf-to-pdf conversion popular in academic journal submission sites and does it faster than they do
does the magical pdf-to-pdf conversion popular in academic journal submission sites and does it faster than they do - andrewkern/pdf2pdf
github.com
November 26, 2025 at 12:29 AM
Reposted
frwildflowers.bsky.social
Acer glabrum, our Rocky Mountain Maple, blooming on the Mesa Trail #nativeplants

#FallBackFlowers #FallBack to May 25 🌿

Nobody notices maple flowers, now you have 😎
Tiny green flowers with creamy anthers
November 26, 2025 at 1:05 AM
Reposted
jrossibarra.bsky.social
corn. paint and crayon by my daughter several years ago. love this, hanging in my office
November 26, 2025 at 1:13 AM
plantgenomics.bsky.social
CLCNet: a contrastive learning and chromosome-aware network for genomic prediction in plants
doi.org/10.1101/2024...

Genomic characterization of a nematode tolerance locus in sugar beet
doi.org/10.1101/2023...
CLCNet: a contrastive learning and chromosome-aware network for genomic prediction in plants
Genomic selection (GS), which integrates genomic markers with phenotypic data, has emerged as a powerful breeding strategy for predicting phenotypes and estimating breeding values in candidate populat...
doi.org
November 26, 2025 at 5:31 AM
plantgenomics.bsky.social
Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation
doi.org/10.1101/2024...
Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation
Digitalis purpurea (foxglove) is a widely distributed ornamental plant and the producer of the biomedical compound digoxin. Here, we present a long read sequencing-based genome sequence of a magenta f...
doi.org
November 26, 2025 at 5:30 AM
Reposted
richardsever.bsky.social
"If the data is accurate...it would call into question the business model of OpenAI and nearly every other general-purpose LLM vendor" www.ft.com/content/fce7...
How high are OpenAI’s compute costs? Possibly a lot higher than we thought
Inference inferred, revenue reconstructed, cash burn quantified
www.ft.com
November 22, 2025 at 2:13 PM
plantgenomics.bsky.social
Genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants
doi.org/10.1101/2025...

Cookbook for Plant Genome Sequences
www.preprints.org/manuscript/2...

#Genomics #PlantSci
A reference genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants
Novel traits frequently evolve by co-opting existing genetic pathways through direct repurposing of existing genes or neofunctionalization of duplicated genes. Parasitism represents a major innovation...
doi.org
November 23, 2025 at 8:41 AM
plantgenomics.bsky.social
AlterNet: Alternative splicing-aware gene regulatory network inference
doi.org/10.1101/2025...

Animal, fungi, and plant genome sequences harbour different non-canonical splice sites
doi.org/10.1101/616565
AlterNet: Alternative splicing-aware gene regulatory network inference
Abstract. Gene regulatory networks (GRNs) help decode biological systems by identifying how genes interact and regulate cellular processes. However, conventional GRN inference methods operate at the g...
doi.org
November 23, 2025 at 8:37 AM
Reposted
puckerlab.bsky.social
Updated our P2 output summary! 📊

Even with strong variation between flow cells, we are seeing an average yield of ~80 Gbp.

Huge thanks to Julie for the sequencing work.

More details: www.izmb.uni-bonn.de/en/pbb/news#...

#Genomics #LongReads #OpenScience
Stacked bar plot showing sequencing output per P2 flow cell. Details: https://www.izmb.uni-bonn.de/en/pbb/news#P2OS
November 22, 2025 at 9:52 AM
Reposted
puckerlab.bsky.social
Yesterday, Nancy shared her Cucurbitaceae anthocyanin loss story with colleagues at our institute. Comprehensive talk highlighting the most striking discoveries. Please find the full story here:

doi.org/10.1101/2025...

#PlantSci #Evolution
Nancy presenting "The World of Cucurbits: No Blues, Just Hues". Details: https://doi.org/10.1101/2025.10.06.680802
November 5, 2025 at 6:05 AM
Reposted
nickdesnoyer.bsky.social
After 10 Fridays, 10 flowers, and 100+ drawings, the Florédex is complete! ✨

Come take a tour of the design and science behind 10 iconic flowers 🌺🧵
November 21, 2025 at 9:59 AM