When morphology stands still: constrained floral evolution in a mega diverse legume genus · Changes in floral morphology are key for the evolutionary success of flowering plants. However, many species-rich and ecologically diverse groups show low variation in floral traits. Low morphologic...

When morphology stands still: constrained floral evolution in a mega diverse legume genus
doi.org/10.1101/2025...

Genetic factors explaining anthocyanin pigmentation differences
doi.org/10.1101/2023...

#Evolution #PlantSci

Friday Flower 009: Nigella arvensis ✨

Nigella’s flowers form a morphologically complex display with ornate bracts and blue sepals.

The true petals have diverse patterning with intricate, nectar-bearing structures that look alien.

This is based on a talk I gave to the Crop Trust, before we conserve we need to understand the standing variation in the genebanks we have -- #ConservationGenomics kamounlab.medium.com/crispr-gene-...

Espalier fig tree against a brick wall with branches splayed out

🌿🍇🍎 Espalier fruit trees are space-saving, beautiful, and productive! Train apples, pears, or figs flat against a wall or trellis for stunning architectural interest and easy harvesting. A perfect blend of art and horticulture! #Espalier #Gardening #FruitTrees

Svirlpool: structural variant detection from long read sequencing by local assembly Motivation: Long-Read Sequencing (LRS) promises great improvements in the detection of structural genome variants (SVs). However, existing methods are lacking in key areas such as the reliable detecti...

Svirlpool: structural variant detection from long read sequencing by local assembly
doi.org/10.1101/2025...

Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis
doi.org/10.1101/2021...

#Genomics #Bioinformatics

Nanoclustering of a plant transcription factor enables strong yet specific DNA binding Transcription factors (TFs) are traditionally depicted as monomeric, or oligomeric, units that recognize and bind specific DNA sequences to regulate transcription. Emerging evidence suggests that many TFs can undergo liquid phase separation, resulting in condensates that bind DNA through a different mechanism. For the Auxin Response Factors (ARFs), canonical plant TFs, evidence for both scenarios exists. But which of these scenarios is operational in the plant nucleus is unclear. Here, we demonstrate using MpARF2 of Marchantia polymorpha that a third scenario is operational: MpARF2 forms nanoscopic clusters under physiological conditions. Nanoclusters combine DNA-binding features that cannot be accessed by the other two scenarios: high-affinity, switch-like, and sequence-specific. Our results suggest nanoclustering as a mechanism that equips TFs with the DNA-binding properties necessary for transcriptional regulation. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, Catch 101000981 European Research Council, DIRNDL 833867 Human Frontiers Science Program, RGP0015/2022 Marie Skłodowska-Curie Individual Fellowship 2020, REOX 101026004 NWO, 184.036.012

Nanoclustering of a plant transcription factor enables strong yet specific DNA binding
doi.org/10.1101/2025...

Automatic identification and annotation of MYB gene family members in plants
doi.org/10.1101/2021...

Dynamic epigenetic and transcriptional regulatory network in pepper fruit development and ripening Pepper (Capsicum) is among the most widely cultivated and consumed vegetable crops worldwide. Although extensive studies in model fruit crops such as tomato have provided insights into the genetic and...

Dynamic epigenetic and transcriptional regulatory network in pepper fruit development and ripening
doi.org/10.1101/2025...

Genome sequence and RNA-seq analysis reveal genetic basis of flower coloration in the giant water lily Victoria cruziana
doi.org/10.1101/2024...

Genomics course announcement. Please find details here: https://www.izmb.uni-bonn.de/en/pbb/news#denbi2025

Curious about plant genomics? 🌿

Join our upcoming training courses to explore how plant genomes are assembled and annotated.

Details 👉 www.izmb.uni-bonn.de/en/pbb/news#...
#Genomics #Bioinformatics #DeNBI #PlantScience
@denbi.bsky.social @puckerlab.bsky.social

Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae The flowering plant order Asterales exhibits a striking disparity in species richness, with >30,000 species in Asteraceae compared to <50 in its sister family Calyceraceae. To investigate the genomic ...

Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae
doi.org/10.1101/2025...

DupyliCate - mining, classifying, and characterizing gene duplications
doi.org/10.1101/2025...

#Genomics #Bioinformatics #Evolution

Scaling up orphan crop research: A global genetic perspective of cowpea (Vigna unguiculata) diversity from 10,617 accessions Cowpea (Vigna unguiculata L. Walp) is a dryland legume crop, providing essential food and nutritional security for millions of people across the semi-arid tropics, in Africa, Asia, and Latin America. ...

Scaling up orphan crop research: A global genetic perspective of cowpea (Vigna unguiculata) diversity from 10,617 accessions
doi.org/10.1101/2025...

Reference-based QUantification Of gene Dispensability (QUOD)
doi.org/10.1101/2020...

#Genomics #Bioinformatics

ProteoCast: a web server to predict, validate, and interpret missense variant effects Understanding how mutations affect protein function remains critical yet challenging, particularly for variants in clinical databases lacking experimental characterisation and for intrinsically disord...

ProteoCast: a web server to predict, validate, and interpret missense variant effects
doi.org/10.1101/2025...

NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
doi.org/10.1101/596718

annoSnake: a Snakemake workflow for taxonomic and functional annotation of metagenomes and metagenome-assembled genomes (MAGs) Omic technologies revolutionised research in microbiomics and helped decipher the complex community structure of gut microbiota, each comprising hundreds of species of bacteria, archaea, and protists. Even as sequencing costs decrease, understanding these communities remains a challenge. Here, we introduce annoSnake, a Snakemake workflow that facilitates taxonomic and functional annotation of metagenomes and metagenomic-assembled genomes (MAGs). This user-friendly and highly flexible workflow integrates state-of-the-art software packages, taking raw sequencing reads, assembling them into contigs, assigning taxonomies and annotating them using various popular protein databases. The workflow handles paired-end as well as interleaved read data, and provides publication-ready figures and tables for downstream analysis. annoSnake, as all Snakemake workflows, is highly scalable, reproducible, and portable, enabling execution across diverse high-performance computing environments with remarkable efficiency. ### Competing Interest Statement The authors have declared no competing interest.

annoSnake: a Snakemake workflow for taxonomic and functional annotation of metagenomes and metagenome-assembled genomes (MAGs)
doi.org/10.1101/2025...

Image: The plant species that produce iridoids and possess a gene copy of the cyclase include (top row from left to right) icepac Carapichea ipecacuanha, fever tree (Cinchona pubescens), golden trumpet (Allamanda cathartica), princess tree (Paulownia tomentosa), (bottom row, from left to right) Carolina jessamine (Gelsemium sempervirens), Madagascar periwinkle (Catharanthus roseus), strychnine tree (Strychnos nux-vomica), and devil pepper (Rauvolfia tetraphylla). Credit: Eva Rothe, greenhouse of the MPI f. Chemical Ecology (ipecac plant: Maite Colinas)

Final step in the biosynthesis of iridoids elucidated

Iridoid-producing plants use a cyclase to synthesize the characteristic double-ring structure of this important class of defense compounds and medically relevant substances

buff.ly/kqtPHl2 via @maxplanck.de #PlantScience #Plants #Science

🚀 de.NBI & ELIXIR-DE on tour at EOSC Symposium 2025 in Brussels!
Björn Grüning showcased the power of @galaxyproject.bsky.social Europe (usegalaxy.eu) and the de.NBI Cloud in the EOSC ecosystem.
#EOSC2025 #Bioinformatics #usegalaxy #ELIXIRDE #deNBI

Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting

I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:

🎉 We are excited to join this year's #Biohackathon Europe in Bad Saarow!
Looking forward to a week of fruitful projects, networking, & fun—thanks to the @elixir-europe.org Hub & everyone joining onsite or online!
🚀 @sneumann.bsky.social, Michael Crusoe, Nils Hoffmann & many more from across Europe.

🐢💙 Big win for sea turtle conservation!
Genome-informed conservation is helping keep these icons in our seas. 🌊
📄 Explore the 2025 publication: bit.ly/4ogC36B
🌊 Dive deeper into how these and other EBP-affiliated reference genomes are benefiting marine life in our latest newsletter: bit.ly/4qhJdZK

Symbiotic diversification relies on an ancestral gene network in plants Symbioses have been fundamental to colonization of terrestrial ecosystems by plants and their evolution. Emergence of the ancient arbuscular mycorrhizal symbiosis was followed by the diversification o...

Symbiotic diversification relies on an ancestral gene network in plants
doi.org/10.1101/2025...

Thanks! Is it free to use?

Spatiotemporal regulation of arbuscular mycorrhizal symbiosis at cellular resolution Arbuscular mycorrhizal (AM) symbiosis develops through successive colonization of root epidermal and cortical cells, culminating in the formation of arbuscules, tree-like intracellular structures that...

Spatiotemporal regulation of arbuscular mycorrhizal symbiosis at cellular resolution
doi.org/10.1101/2025...

A mycorrhiza-associated receptor-like kinase with an ancient origin in the green lineage
doi.org/10.1073/pnas...

Establishing benchmarks for quantitative mapping of m6A by Nanopore Direct RNA Sequencing Nanopore direct RNA sequencing (DRS) coupled with Dorado modification-aware basecalling enables mapping of epitranscriptomic modifications including N6-methyladenosine (m6A) at the level of individual...

Establishing benchmarks for quantitative mapping of m6A by Nanopore Direct RNA Sequencing
doi.org/10.1101/2025...

Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis Background Experimental proof of gene function assignments in plants is based on mutant analyses. T-DNA insertion lines provided an invaluable resource of mutants and enabled systematic reverse geneti...

Compound-specific DNA adduct profiling with nanopore sequencing and IonStats
doi.org/10.1101/2025...

Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis
doi.org/10.1101/2021...

#Genomics #LongReads

Effects of carbon dioxide enrichment and environmental factors on photosynthesis, growth and yield and their interaction in cucumber: a meta-analysis Despite the ongoing increase in atmospheric carbon dioxide concentrations, these levels remain well below the optimal threshold for cucumber growth and development. In addressing the challenges posed ...

Effects of CO2 enrichment and environmental factors on photosynthesis, growth and yield and their interaction in cucumber
doi.org/10.1101/2025...

Large-scale Phylogenomics Reveals Systematic Loss of Anthocyanin Biosynthesis Genes at the Family Level in Cucurbitaceae
doi.org/10.1101/2025...

Diverse haplotypes at a complex Solanum americanum locus confer resistance to Phytophthora infestans and P. capsici Plants encounter diverse pathogens and have evolved a two-layered innate immune system to detect pathogen molecules and activate defense mechanisms that restrict infection. Most cloned plant Resistanc...

Diverse haplotypes at a complex Solanum americanum locus confer resistance to Phytophthora infestans and P. capsici
doi.org/10.1101/2025...

Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis
doi.org/10.1101/2024...

@igemhq.bsky.social and SB8 was unforgettable.

Would love to supervise a team on flower design for the new art/design village 🎨🌹🧬

ONT P2 sequencing output per flow cell. Will be updated over time. Details: https://www.izmb.uni-bonn.de/en/pbb/news#P2OS

Interested in long-read plant genomics? 🌱

We are sharing our ONT P2 Solo sequencing outputs per flowcell — explore our real data and experience here:

👉 www.izmb.uni-bonn.de/en/pbb/news#...

#Genomics #LongReads #PlantSci @puckerlab.bsky.social

igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review We present igv-reports, a command-line tool to create standalone HTML pages embedding interactive genomic visualizations of read alignments and associated annotations to support variant inspection wor...

igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review
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...

Autopolyploid establishment under gametophytic self-incompatibility: the impact of self-fertilization and pollen limitation Polyploidy is widespread in plants, yet the establishment of neo-polyploids is limited by minority cytotype exclusion (MCE). As polyploidy has been associated with higher selfing rates in empirical st...

Autopolyploid establishment under gametophytic self-incompatibility: the impact of self-fertilization and pollen limitation
doi.org/10.1101/2025...

Fig 3C from the linked article, showing three rows of 12 panels, each with a graph of cell density over time for 7-day competition experiments with coevolved E coli and yeast plus competitor bacteria. Different competitor strains are in each column of the 3x12 grid, and each row gives results for experiments with ancestral, 1000-generation coevolved, or 4000-generation coevolved E coli. The ancestral E coli fails to resist invasion of many competitors, but the coevolved strains resist most of the competitors.

Experimentally co-evolved E. coli and yeast achieve stable coexistence — and the coevolved E. coli, but not the yeast, is able to resist invasion by other bacterial strains

buff.ly/jowWRLN

Researchers Prof. Boas Pucker, Nancy Choudhary, and Marie Hagedorn in the lab. They hold colorful pumpkins (blue, pink, purple) in their hands and look frightened. Around them are spiders and spider webs. A “spooky” photo montage withthe researchers, made for Halloween.

🎃 Why are (Halloween) pumpkins orange – and not pink or blue? This secret is explored by @bpucker.bsky.social, @nancy-choudhary.bsky.social and Marie Hagedorn. Their research examines how carotenoids took over, making Jack O’Lanterns forever orange: www.uni-bonn.de/en/news/colo.... Happy Halloween!