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plantgenomics.bsky.social @plantgenomics.bsky.social · 15h

Ultra-mild bisulfite outperforms existing methods for 5-methylcytosine detection with low input DNA
doi.org/10.1101/2025...

Ultra-mild bisulfite outperforms existing methods for 5-methylcytosine detection with low input DNA

We present Ultra-Mild Bisulfite Sequencing (UMBS-seq), a method for 5-methylcytosine (5mC) detection that minimizes DNA degradation and background noise. UMBS-seq outperforms conventional bisulfite an...

doi.org

plantgenomics.bsky.social @plantgenomics.bsky.social · 15h

The Spirogyra genome: signatures of shared and divergent division and differentiation
doi.org/10.1101/2025...

The Spirogyra genome: signatures of shared and divergent division and differentiation

Zygnematophytes came as unexpected closest algal relatives to land plants because of their simple body plans, raising questions about the morphogenetic toolkit that was present in the last common ance...

doi.org

Reposted

Stefan A. Rensing @rensingstefan.bsky.social · 1d

Very happy and proud to share the #Spirogyra genome: 50 Mbp small, lacking almost all plastid division proteins and many transcription factors. Kudos to all the many people involved in this multi year project!
@jandevries.bsky.social
@watertoland.bsky.social
www.biorxiv.org/content/10.1...

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Reposted

Journal of Experimental Botany @jxbotany.bsky.social · 1d

🌱 📖 SPECIAL ISSUE REVIEW 📖 🌱

Qi et al. address current challenges in revealing protease roles in biological processes and present systematic methodologies for identifying bona fide protease–substrate pairs in plants 🔬

🔗 doi.org/10.1093/jxb/...

#PlantScience 🧪 @simonstael.bsky.social

Fig. 1.Guidelines for a bona fide protease–substrate pair.

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Reposted

Chenxin Li, PhD @chenxinli2.bsky.social · 1d

Last night I had a dream about looking at whole plasmid sequencing results and saw a transposon landed in my plasmid and had to rebuild the plasmid

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Reposted

PuckerLab @puckerlab.bsky.social · 1d

New preprint from the group:

🧬 Large-scale Phylogenomics Reveals Systematic Loss of Anthocyanin Biosynthesis Genes at the Family Level in Cucurbitaceae

👉 doi.org/10.1101/2025...

@nancy-choudhary.bsky.social @bpucker.bsky.social

Synteny analysis supporting anthocyanin biosynthesis gene loss in the Cucurbitaceae. Reference: https://doi.org/10.1101/2025.10.06.680802

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Reposted

Mike Grillo @mikegrillo.bsky.social · 2d

I am hiring a postdoc to examine the genomic and evolutionary basis of plant microbiome variation in legumes. There are opportunities to gain teaching experience. Chicago is a great city to live in! Please help spread the word.
share.google/gukbzS1zdIx6...

Postdoctoral Researcher in Plant Evolutionary Genomics

The postdoctoral researcher will work in Dr. Michael Grillo’s plant evolutionary genetics lab. The goal of this research project is to understand the genomic basis of plant-microbiome variation in leg...

share.google

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Reposted

PlantEvolution 🌱🌾 @plantevolution.bsky.social · 2d

Congrats, Joe Ecker @salkinstitute.bsky.social, to receiving the McClintock Prize! Joe has been a visionary leader of the field of genetics and genomics – not only for plants – for decades
www.salk.edu/news-release...

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Reposted

Plant & Cell Physiology @plantcellphysiol.bsky.social · 3d

The same but different... ♊

Wu et al. have performed comparative genomics analyses in legumes & other species to reveal the similarities & unique features of gene regulatory networks operating in nitrogen-fixing & arbuscular mycorrhizal symbioses

🔗 doi.org/10.1093/pcp/...

#PlantScience

Figure 1 (split into panels a-g) of the paper by Wu et al. showing Transcriptomic change in arbusculated and nodulated roots across different species. (a) bar chart showing DEGs in arbusculated roots of six plant species. (b) bar chart showing DEGs in nodulated roots of three legume species. (c) GO enrichment analysis showing words/phrases related to DEGs in arbusculated roots across six plant species. (d−f) Venn diagrams illustrating shared and unique DEGs between arbusculated and nodulated roots in three legume species. (g) 3 scatter plots comparing gene expression changes between AMS and NFS in M. trunculata, G. max and L. japonicus.

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Reposted

Nancy Choudhary @nancy-choudhary.bsky.social · 2d

Have you ever wondered why pumpkins are never purple or blue like other plants? 🎃🌈

While most plants can produce pink, blue, and purple pigments (thanks to anthocyanins), the Cucurbitaceae family 🍈 🍉 🥒have lost all the pathway genes to produce these pigments.
🔗 doi.org/10.1101/2025...

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plantgenomics.bsky.social @plantgenomics.bsky.social · 1d

Uncertainty in joint Ancestral State Reconstruction: Improving accuracy and biological interpretability of ancestral state prediction
doi.org/10.1101/2025...

Uncertainty in joint Ancestral State Reconstruction: Improving accuracy and biological interpretability of ancestral state prediction

Ancestral state reconstruction (ASR) is a foundational tool in comparative biology, offering insights into the evolutionary history of lineages. With each new evolutionary model, our ability to estima...

doi.org

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plantgenomics.bsky.social @plantgenomics.bsky.social · 1d

Mapping the Telomeric 3D Interactome with Telomere-C Reveals Repetitive Element Hubs Associated with Telomere Maintenance
doi.org/10.1101/2025...

Mapping the Telomeric 3D Interactome with Telomere-C Reveals Repetitive Element Hubs Associated with Telomere Maintenance

Telomeres are essential for genome integrity, but the accurate, high-resolution mapping of their three-dimensional (3D) chromatin interactions, a process thought to mediate gene regulation and telomer...

doi.org

Reposted

Boas Pucker @bpucker.bsky.social · 2d

Soybean flavonol 3-O-glucosyltransferase (UFGT78D2) makes plants more susceptible to leaf-chewing insects, while its loss confers resistance #FlavonoidFriday
(details: rb.gy/h21hpi) @puckerlab.bsky.social

Soy beans. Author: Wikideas1. CC0. https://en.wikipedia.org/wiki/File:Soy_beans.jpg

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plantgenomics.bsky.social @plantgenomics.bsky.social · 2d

Split or spread - A spatio-temporal framework for the evolution of annual Arabis (Brassicaceae) in Eurasia
doi.org/10.1101/2025...

Split or spread - A spatio-temporal framework for the evolution of annual Arabis (Brassicaceae) in Eurasia

Life history in plants appears to be an important determining factor for the capacity to cope with major environmental change. Consequently, the evolutionary history of life form may have constrained ...

doi.org

plantgenomics.bsky.social @plantgenomics.bsky.social · 2d

Convergence, stability, and thermal adaptation in the rubisco enzyme in plants
doi.org/10.1101/2025...

Convergence, stability, and thermal adaptation in the rubisco enzyme in plants

Enzymes are thought to be tuned to perform similarly in different thermal regimes. Whether the photosynthetic enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) follows similar rules, es...

doi.org

plantgenomics.bsky.social @plantgenomics.bsky.social · 3d

An improved epigenetic age estimation with TFMethyl Clock reveals DNA methylation changes during aging in transcription factor binding sites
doi.org/10.1101/2025...

An improved epigenetic age estimation with TFMethyl Clock reveals DNA methylation changes during aging in transcription factor binding sites

Methylation-based epigenetic clocks are among the most accurate tools for predicting chronological age. Although DNA methylation (DNAm) at genomic CpG sites is linked to various regulatory mechanisms,...

doi.org

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Reposted

Boas Pucker @bpucker.bsky.social · 3d

Excited to share our new preprint!

🧬 Large-scale Phylogenomics Reveals Systematic Loss of Anthocyanin Biosynthesis Genes at the Family Level in Cucurbitaceae

👉 doi.org/10.1101/2025...

A deep dive into the genomic evolution of color in cucurbits 🎃🍉 — feedback welcome!
@puckerlab.bsky.social

Synteny plots supporting loss of DFR, ANS, and arGST in Cucurbitaceae. Reference: https://doi.org/10.1101/2025.10.06.680802

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plantgenomics.bsky.social @plantgenomics.bsky.social · 4d

Plastid genome of non-photosynthetic plant Rhopalocnemis phalloides is one of the most polymorphic genomes known
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...

The plastid genome of the non-photosynthetic plant Rhopalocnemis phalloides is one of the most polymorphic genomes known

The common ancestor of plants in the Balanophoraceae family lost the ability to photosynthesize, and all several dozen extant species of this family feed exclusively by parasitizing other plants. Prev...

doi.org

plantgenomics.bsky.social @plantgenomics.bsky.social · 4d

Diploid origins and early genome stabilization in the allotetraploid Arabidopsis suecica
doi.org/10.1101/2024...

Diploid origins and early genome stabilization in the allotetraploid Arabidopsis suecica

Polyploidization, followed by genome downsizing, is a recurrent evolutionary cycle that dramatically reshapes genome structure. Newly formed polyploids must quickly adjust their cell division machiner...

doi.org

plantgenomics.bsky.social @plantgenomics.bsky.social · 4d

Taming the reference genome jungle: the refget sequence collection standard
doi.org/10.1101/2025...

Taming the reference genome jungle: the refget sequence collection standard

Reference genomes are foundational to genomics but suffer from widespread ambiguity and incompatibility due to inconsistent naming, undocumented differences, and lack of formal mechanisms for comparis...

doi.org

plantgenomics.bsky.social @plantgenomics.bsky.social · 4d

ceQTL: A co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation
doi.org/10.1101/2025...

ceQTL: A co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation

Expression quantitative trait locus (eQTL) mapping is used to identify a functional link between a genomic variant, such as single nucleotide polymorphism (SNP), and gene expression (often close-by pa...

doi.org

plantgenomics.bsky.social @plantgenomics.bsky.social · 4d

A Fully Automated, Data-Driven Approach for Dimensionality Reduction and Clustering in Single-Cell RNA-seq Analysis
doi.org/10.1101/2025...

raxtax: A k-mer-based non-Bayesian Taxonomic Classifier
doi.org/10.1101/2025...

A Fully Automated, Data-Driven Approach for Dimensionality Reduction and Clustering in Single-Cell RNA-seq Analysis

Single-cell RNA sequencing (scRNA-seq) provides deep insights into cellular heterogeneity but demands robust dimensionality reduction (DR) and clustering to handle high-dimensional, noisy data. Many D...

doi.org

Reposted

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

Multiple mechanisms explain loss of anthocyanins from betalain-pigmented Caryophyllales, including repeated wholesale loss of a key anthocyanidin synthesis enzyme
doi.org/10.1111/nph....

#Anthocyanins #Flavonoids #Betalains #Caryophyllales #Evolution #Biosynthesis #TranscriptionFactor #Evolution

Multiple mechanisms explain loss of anthocyanins from betalain‐pigmented Caryophyllales, including repeated wholesale loss of a key anthocyanidin synthesis enzyme

In this study, we investigate the genetic mechanisms responsible for the loss of anthocyanins in betalain-pigmented Caryophyllales, considering our hypothesis of multiple transitions to betalain pig.....

doi.org

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plantgenomics.bsky.social @plantgenomics.bsky.social · 5d

A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures
doi.org/10.1101/2025...

A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures

Somatic mosaicism is essential in human biology and disease, yet robust benchmarks are scarce. The SMaHT Consortium mixed six HapMap cell lines to create artificial somatic variants spanning 0.25% to ...

doi.org

plantgenomics.bsky.social @plantgenomics.bsky.social · 5d

In-depth phenotyping reveals unexpected floral trait variation in Mimulus cardinalis across a range-wide latitudinal gradient
doi.org/10.1101/2025...

In-depth phenotyping reveals unexpected floral trait variation in Mimulus cardinalis across a range-wide latitudinal gradient

Background & Aims: Pollinators play a crucial role in the evolution and diversification of flowering plants. Intraspecific variation in floral traits occurs frequently and likely reflects variable bio...

doi.org