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plantgenomics.bsky.social @plantgenomics.bsky.social · 23h

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

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 · 1d

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 · 1d

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 · 1d

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 · 1d

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

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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 · 3d

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 · 3d

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

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

Natural variation in IBF1 disrupts its interaction with CHS1 and affects metabolism of hulls in rice
doi.org/10.1101/2025...

Natural variation in IBF1 disrupts its interaction with CHS1 and affects metabolism of hulls in rice

Secondary metabolites in plants have various physiological functions, including antioxidant and antibacterial activities. Previous studies have suggested genes and associated molecular mechanisms invo...

doi.org

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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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iGEM Bonn @igembonn.bsky.social · 3d

The gut microbiome is substantially remodelled in colorectal cancer (CRC). Several microorganisms, as seen in this review, are of particular interest.🦠

In the future, synthetic biology can be a useful tool in CRC therapy and diagnostics!

doi.org/10.1038/s415...

#iGEM2026#SynBio#cancer

The microbial landscape of colorectal cancer - Nature Reviews Microbiology

In this Review, White and Sears examine recent evidence showing the link between the gut microbiota and colorectal cancer (CRC) and discuss the roles and mechanisms of specific microorganisms as well as of complex microbial communities in the pathogenesis of CRC.

doi.org

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Nature @nature.com · 3d

BREAKING: The Nobel Prize in Physiology or Medicine has been awarded jointly to Mary E. Brunkow, Fred Ramsdell, and Shimon Sakaguchi "for their discoveries concerning peripheral immune tolerance"

Stay tuned for more.
#NobelPrize

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Pixels&AlchemyPhotography @pixelsandalchemy.bsky.social · 3d

Bright Pink CrepeMyrtle AKA CrapeMyrtle
Seen on my #DailyWalk, Friday
I could not believe this tree was so robust and laden with blossoms in fall!
#PinkMon #Photography #Blossoms

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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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David L. Stern @gallseeker.bsky.social · 9d

It's official! We are moving to Stowers!
Very exciting opportunity to expand our studies of insect-plant interactions. We have many opportunities available in biochemistry, development, behavior, genetics, evolution, genomics, AI, and even pest control. Interested in any of these things? Reach out!

Stowers Institute @stowersinstitute.bsky.social · 9d

NEWS🎉 We’re excited to announce @hhmijanelia.bsky.social Investigator David Stern will join the Institute from Janelia Research Campus. His lab studies how aphids transform plants at the genetic level, uncovering secrets of #evolution & new strategies for pest control. @hhmi.org bit.ly/4np96Fb

Stowers Institute recruits renowned developmental and evolutionary…

David Stern, Ph.D., brings groundbreaking research on insect–plant interactions for next-generation pest control to the Institute.

bit.ly

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Journal of Experimental Botany @jxbotany.bsky.social · 16d

🌸 FLOWERING NEWSLETTER REVIEW 🌸

🧬 Since the discovery of the first plant sex-determining gene, more than 20 other genes have been identified. Here Marais et al. review what this tells us about the evolution of separate sexes (dioecy) in angiosperms 🌸

🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪

Fig. 1 (shortened, full legend in paper): Advances in characterizing plant sex chromosomes using genomics in the last 15 years. Most of the systems have been characterized using non-standard methods (see text). References to this work are: Silene latifolia (Bergero and Charlesworth, 2011; Chibalina and Filatov, 2011; Muyle et al., 2012), Carica papaya (Wang et al., 2012), Diospyros lotus (Akagi et al., 2014), Rumex hastatulus (Hough et al., 2014), Asparagus officinalis (Harkess et al., 2017), Rumex rothschildianus (Crowson et al., 2017), Actinidia chinensis (Akagi et al., 2018), Fragaria species (Tennessen et al., 2018), Phoenix dactylifera (Torres et al., 2018), Mercurialis annua (Veltsos et al., 2019), Silene otites and Silene colpophylla (Balounova et al., 2019; Martin et al., 2019), Cannabis sativa (Prentout et al., 2020), Coccinia grandis (Fruchard et al., 2020), Populus and Salix species (Müller et al., 2020; Zhou et al., 2020a, b)...

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Oregon 🕎🎲 @oregonthedm.bsky.social · 4d

Pink empress Mantis

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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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PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

Data Reuse in Agricultural Genomics Research: Present Challenges and Future Solutions
doi.org/10.1093/giga...

#DataScience #OpenScience #Genomics #Agriculture #DataReuse #Bioinformatics #ComputationalBiology #OpenData #BigData

Data reuse in agricultural genomics research: challenges and recommendations

Abstract. The scientific community has long benefited from the opportunities provided by data reuse. Recognizing the need to identify the challenges and bo

doi.org

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FrontRangeWildflowers @frwildflowers.bsky.social · 5d

Tulips are some of the first spring flowers to bloom in my yard. 🌿

#FallBackFlowers #FallBack to April 4

Instead of setting the clock back just an hour I’ll be setting it back six months so we can enjoy Spring & Summer again.

Bright yellow tulip with red spots in the center

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WA Orchids @wa-orchids.bsky.social · 7d

I love exploring granite outcrops, they can be a haven for a variety of native plants. Albany has many, including Kardarup/Mt Melville near the city

🌿 Drummond’s Sundew
🍄 Golden-eye Lichen
🌱 Lemon-scented Sun Orchid
🌸 Plumed Featherflower

#ozplants #lichen #wildoz #orchids #nativeplants #nature

Drosera drummondii - a scrambling carnivorous sundew with deep pinky/purple flowers

Teloschistes chrysophthalmus - an orange lichen growing on a dry twig

Thelymitra antennifera - close up of two bright yellow orchid flowers in the sunshine.

Verticordia plumosa - a shrub with small leaves and rounded groups of pink flowers with a feathered appearance to them.

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petuniaplatform.org @petuniaplatform.bsky.social · 7d

#Petunia in the library! <3

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

Do y'all like this bloom style? I like the clamshell shape but its quite different from conventional snapdragons.

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