Lightnews — Scholar-powered news

Reposted

Boas Pucker @bpucker.bsky.social · 13h

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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dnarnaresearch.bsky.social @dnarnaresearch.bsky.social · 13h

Darwin's entangled bank through deep time: Structural stability of mutualistic networks over evolutionary timescales
doi.org/10.1101/2025...

Darwin's entangled bank through deep time: Structural stability of mutualistic networks over evolutionary timescales

Mutualistic interactions form species-rich, complex networks that play essential roles for ecosystem function. Over macroevolutionary time scales, these networks change as species emerge and go extinc...

doi.org

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dnarnaresearch.bsky.social @dnarnaresearch.bsky.social · 1d

The plastid genome of the non-photosynthetic plant Rhopalocnemis phalloides is one of the most polymorphic genomes known
doi.org/10.1101/2025...

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

Reposted

Boas Pucker @bpucker.bsky.social · 1d

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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dnarnaresearch.bsky.social @dnarnaresearch.bsky.social · 2d

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

Adaptive Disruption of Carotenoid Metabolism in Cavefish via Loss of Beta-carotene oxygenase 2a (Bco2a)
doi.org/10.1101/2025...

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

Plant pigmentation secrets are among the oldest interests of plant scientists, with pigments such as chlorophyll, carotenoids, flavonoids, and betalains contributing to the diversity of hues in higher...

doi.org

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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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dnarnaresearch.bsky.social @dnarnaresearch.bsky.social · 3d

Arms races between selfish genetic elements and their host defence
doi.org/10.1101/2023...

Arms races between selfish genetic elements and their host defence

Arms races between parasites and hosts are key drivers of evolution. Selfishly replicating transposable elements (TEs) are thought to follow similar dynamics, but strong evidence is missing. We tested...

doi.org

dnarnaresearch.bsky.social @dnarnaresearch.bsky.social · 3d

RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques
doi.org/10.1101/2025...

RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques

Nanopore sequencing technologies continue to advance rapidly, offering critical benefits such as real-time analysis, the ability to sequence extremely long DNA fragments (up to millions of bases in a ...

doi.org

dnarnaresearch.bsky.social @dnarnaresearch.bsky.social · 3d

Ragnarok: a flexible and RApid GeNe Annotation (ROcKs) pipeline deployed through Nextflow
doi.org/10.1101/2025...

KIPEs3: Automatic annotation of biosynthesis pathways
doi.org/10.1101/2022...

Ragnarok: a flexible and RApid GeNe Annotation (ROcKs) pipeline deployed through Nextflow

High-quality genome assemblies and pangenomes are increasingly accessible and achievable due to advances in third-generation sequencing and assembly algorithms, but genome annotation remains a critica...

doi.org

dnarnaresearch.bsky.social @dnarnaresearch.bsky.social · 3d

The genomic response to drought across spatiotemporal scales in Amaranthus tuberculatus
doi.org/10.1101/2025...

The genomic response to drought across spatiotemporal scales in Amaranthus tuberculatus

How genetic diversity responds to environmental change across spatiotemporal scales remains poorly understood despite its importance for species persistence in changing landscapes. Agricultural weeds ...

doi.org

Reposted

PuckerLab @puckerlab.bsky.social · 3d

Hard to believe — it has already been one semester of @puckerlab.bsky.social at @unibonn.bsky.social 🎉
New discoveries 🌿, great teaching 👩‍🏫, international visitors 🌍, and a growing team 🔬 — it has been an incredible start.
Huge thanks to everyone who has been part of the journey! 💚
#Science #Genomics

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Reposted

Nick Desnoyer @nickdesnoyer.bsky.social · 4d

Fantastical flowers, synthetic biology, and storytelling.

Giving an accessible science talk tomorrow at 10:40 UK time... come join!

Register here for the link 👉 jic.link/NBIAST2025

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Reposted

Plantae.org @plantaeofficial.bsky.social · 3d

#ASPBPlantPhysMonday #ICYMI

Plant Physiology @plantphys.bsky.social · Jul 21

Call for Papers: 2026 Focus Issue on Early Land Plant Evolution – Phylogenetics, Paleobotany, and Evo-devo Physiology. Submission Deadline: 03/2026. academic.oup.com/plphys/pages...

#plantscience

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Reposted

VegPlotter: Online Vegetable Garden and Allotment Planner @vegplotter.bsky.social · 5d

October is perfect for planting broad beans (fava beans) for an early crop next spring! 🍂
Top tips:
1️⃣ Choose a hardy, overwintering variety like 'Aquadulce Claudia'.
2️⃣ Plant seeds 5cm deep in a sunny, well-drained spot to protect them from frost and mice.
#Gardening #GrowYourOwn #BroadBeans

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Reposted

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

Genome sequence of the blue flowering Centaurea cyanus
doi.org/10.1101/2025...

#Genomics #PlantSci #FlowerColors #Bioinformatics #BigData #DataScience #OpenData #OrnamentalPlants

Genome sequence of the blue flowering Centaurea cyanus

The genome of the cornflower (Centaurea cyanus ) was sequenced with long reads (ONT) to reveal the full sequences of genes in the flavonoid biosynthesis. Of particular interest are genes responsible f...

doi.org

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Reposted

plantpostdocs.bsky.social @plantpostdocs.bsky.social · 14d

Dr. Erika Moore-Pollard is currently a postdoctoral researcher at the University of Connecticut whose research focuses on photosynthetic metabolism and functional trait tradeoffs in Bromeliaceae. @erikarmoore11.bsky.social

I am Erika Moore-Pollard, a postdoctoral researcher at the University of
Connecticut. My current research focuses on photosynthetic metabolism and functional trait tradeoffs in Bromeliaceae. I earned my PhD at the University of Memphis, where I investigated the phylogenomics, genomics, and systematics of Asteraceae, with a particular focus on the complex genus Packera. My overall research goal is to uncover the molecular drivers of plant diversification, with an emphasis on how polyploidy, hybridization, and convergent evolution shape trait innovation and ecological success across angiosperms.

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Reposted

Jason Stajich @hyphaltip.bsky.social · 13d

Assistant Professor Plant or Fungal
Genomics. Univ of Wyoming. eeik.fa.us2.oraclecloud.com/hcmUI/Candid...

Asst Professor - Plant or Fungal Genomics

The Department of Botany and the School of Computing at the University of Wyoming invites applications for a tenure-track position in Plant or Fungal Genomics at the rank of Assistant Professor. We in...

eeik.fa.us2.oraclecloud.com

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Reposted

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
doi.org/10.1371/jour...

#Bioinformatics #VariantCalling #VariantAnnotation #FunctionalGenomics #Genomics #PlantSci #DataScience #OpenData #OpenAccess #BigData #Python #100DaysOfCode

NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction

Once a suitable reference sequence has been generated, intra-species variation is often assessed by re-sequencing. Variant calling processes can reveal all differences between strains, accessions, gen...

doi.org

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Reposted

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

CoExpPhylo - A Novel Pipeline for Biosynthesis Gene Discovery
doi.org/10.1101/2025...

#Bioinformatics #GeneExpression #PathwayDiscovery #BigData #Python #SpecializedMetabolism #OpenAccess

CoExpPhylo – A Novel Pipeline for Biosynthesis Gene Discovery

Background The rapid advancement of sequencing technologies has drastically increased the availability of plant genomic and transcriptomic data, shifting the challenge from data generation to function...

doi.org

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dnarnaresearch.bsky.social @dnarnaresearch.bsky.social · 5d

Accuracy and Scalability of Machine Learning Methods for Genotype-Phenotype Association Data
doi.org/10.1101/2025...

Accuracy and Scalability of Machine Learning Methods for Genotype-Phenotype Association Data

Many machine learning methods can be applied to predicting phenotypes from genetic data. Which of these methods work best remains an open question, however. To answer this question, we propose to comp...

doi.org

dnarnaresearch.bsky.social @dnarnaresearch.bsky.social · 6d

EasyFigAssembler: Enhance Omics Data Storytelling through Effective Figure Assembly
doi.org/10.1101/2025...

EasyFigAssembler: Enhance Omics Data Storytelling through Effective Figure Assembly

Motivation: An effective figure helps communicate the data and findings clearly. The assembly of multi-panel omics-based figures for scientific publications is a time-consuming and error-prone process...

doi.org

Reposted

Boyce Thompson Institute @btiscience.bsky.social · 8d

Shape the future of #PlantScience! BTI, affiliated with Cornell, seeks a tenure-track Assistant Professor to drive discovery in plant biology. Review of applications begins November. Apply: recruiting.paylocity.com/Recruiting/J...

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Reposted

Sebastian S. Cocioba @atinygreencell.bsky.social · 7d

Does anyone know if nanopores can read cyclobutane bonded thymines? The kind that UVC causes. Would love to send some in-vitro zapped plasmids to @plasmidsaurus.bsky.social and see if it can detect the TT, TC, and rarer CC dimers. Could be a fun way to mutagenize if transformed in darkness.

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Reposted

Nick Desnoyer @nickdesnoyer.bsky.social · 7d

Friday Flower 006: Aquilegia 🌸🦋

Columbines vary in stamen number, making them a powerful model for how floral whorls expand.

Darwin marveled at their long nectar spurs, which co-evolve with hawkmoth tongues to reward pollinators that brush the stamens ✨

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Reposted

Sebastian S. Cocioba @atinygreencell.bsky.social · 7d

Evolution be like:

franz @franzanth.bsky.social · Aug 12

just make it exist first
you can make it crab later

a comic in two parts.
part one. text says, just make it exist first. image is a drawing of a circle.
part two. text says, you can make it crab later, but the word crab is scribbled as if it replaced something. image is a drawing of a crab.

footer says: by joabaldwin, based on the comic by growthbyvisuals, then carcinized by franzanth.

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