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Reposted by Boas Pucker

Nick Desnoyer @nickdesnoyer.bsky.social · 3h

Friday Flower 007: Petunia 💮✨

Petunias carry the active transposon dTph1, which powers mutant screens and paints stripey patterns as it jumps.

Their five petals are fused, with diverse color designs tracing the corolla’s fusion seam.

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Boas Pucker @bpucker.bsky.social · 8h

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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Boas Pucker @bpucker.bsky.social · 8h

Sure. I am always happy to have discussions about our science and I am curious to learn about your plans. Please send me an email to arrange a time: www.izmb.uni-bonn.de/en/pbb/contact

Contact

www.izmb.uni-bonn.de

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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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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

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Boas Pucker @bpucker.bsky.social · 2d

Yes, proanthocyanidin biosynthesis is not affected (LAR and ANR are generally still present) and maybe the force that maintains the genes involved in anthocyanin and PA biosynthesis (DFR, ANS). I would also assume that a non-functional gene would quickly be lost.

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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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Reposted by Boas Pucker

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 by Boas Pucker

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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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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Boas Pucker @bpucker.bsky.social · 4d

Could you explain your idea behind the collinearity maps, please?

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Boas Pucker @bpucker.bsky.social · 4d

of course there are MYBs involved 😂

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Boas Pucker @bpucker.bsky.social · 4d

Well done. Congratulations!

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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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Boas Pucker @bpucker.bsky.social · 5d

Yes, I started with MGSE back in 2018/2019, but the latest version was released weeks ago

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PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

Mapping-based genome size estimation
doi.org/10.1186/s128...

#Genomics #Python #Sequencing #PlantSci #BigData #DataScience

Mapping-based genome size estimation - BMC Genomics

While the size of chromosomes can be measured under a microscope, obtaining the exact size of a genome remains a challenge. Biochemical methods and k-mer distribution-based approaches allow only estim...

doi.org

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Boas Pucker @bpucker.bsky.social · 5d

Thanks for your comments. I am glad to see that you are going through the code. Using fire cli would lead to an additional dependency. We were trying to keep it as simple as possible.

Boas Pucker @bpucker.bsky.social · 6d

Great! If you set it to -70 instead of -80, you could save a lot of energy (approximately 30%)

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Boas Pucker @bpucker.bsky.social · 7d

Anthocyanin biosynthesis in grasses took a divergent evolutionary path, with key gene losses and independent evolutionary innovations #FlavonoidFriday

(details: doi.org/10.1101/2025... & shorturl.at/dprjd)

Grass flowers. Source: https://en.wikipedia.org/wiki/Poaceae#/media/File:Grassflowers.jpg; Hardyplants, Public Domain

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Reposted by Boas Pucker

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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iGEM Bonn @igembonn.bsky.social · 7d

Topic of this week's team discussion: Plum pox virus

Did you know that sharka is the most serious viral disease for the stone fruit industry accounting for €2.4 billion in damage in the last 28 years?🍒🍑

Learn more in this review!
doi.org/10.1111/aab....

#iGEM2026#SynBio#plantsciences#virology

Plum pox virus: An overview of the potyvirus behind sharka, a harmful stone fruit disease

Plum pox virus is a member of the genus Potyvirus in the family Potyviridae. The significance of this virus is underscored by its large strain diversity, wide host range, broad geographical distribut...

doi.org

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Boas Pucker @bpucker.bsky.social · 7d

Yes, free education is very important. Unfortunately, many do not understand and value this enough

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Boas Pucker @bpucker.bsky.social · 7d

Anthocyanin biosynthesis in grasses took a divergent evolutionary path, with key gene losses and independent evolutionary innovations #FlavonoidFriday

(details: doi.org/10.1101/2025... & shorturl.at/dprjd)

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Boas Pucker @bpucker.bsky.social · 7d

Interesting idea. I assume the current models do not cover these cases thus you would not find them with a normal dorado basecalling. @pietzenuk.bsky.social might be able to find out if someone did this before. Good reason to keep the POD5 files ;)

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Boas Pucker @bpucker.bsky.social · 7d

Maybe something for the #synbio experts @nickdesnoyer.bsky.social and @atinygreencell.bsky.social 😉

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