Nancy Choudhary

Plant genome sequencing workflow. Details: https://doi.org/10.1186/s12864-026-12623-z

Need a genome sequence of your favourite plant? We laid out instructions for a complete workflow based on ONT sequencing:

"Cookbook for plant genome sequences"
doi.org/10.1186/s128...

#Genomics #LongReads #PlantSciences #Bioinformatics
@puckerlab.bsky.social @unibonn.bsky.social

Microsynteny analysis around the DFR, ANS, and arGST loci in Cucurbitaceae and closely related lineages. Details: https://doi.org/10.1101/2025.10.06.680802

Updated preprint:

"Out of the blue: Family-wide loss of anthocyanin biosynthesis in Cucurbitaceae"

doi.org/10.1101/2025...

#Evolution #Pigments #Genomics #Bioinformatics
@nancy-choudhary.bsky.social @bpucker.bsky.social @unibonn.bsky.social

Impressions from “Plant Genome Sequence Assembly and Annotation” course 🌱. Details: https://www.izmb.uni-bonn.de/en/pbb/news#d2025c1

Just wrapped up “Plant Genome Sequence Assembly and Annotation” 🌱
Processing long-reads, genome sequence assembly, assembly QC, and predicting genes. Thanks to everyone involved!

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

#Genomics #PlantScience #Bioinformatics
@puckerlab.bsky.social @denbi.bsky.social

Impressions from our "From Gene Models to Biological Insights - Functional Annotation" course. More details: https://www.izmb.uni-bonn.de/en/pbb/news#d2025c2

Our course “From Gene Models to Biological Insights – Functional Annotation” just finished! We loved teaching 20+ young researchers new skills in plant genomics. Excited to see how they will apply these tools to uncover biological insights. 🌿🧬
#PlantSci #Genomics
www.izmb.uni-bonn.de/en/pbb/news#...

Impressions from our "From Gene Models to Biological Insights - Functional Annotation" course. More details: https://www.izmb.uni-bonn.de/en/pbb/news#d2025c2

From Gene Models to Biological Insights course done! Over 20 young scientists dove into functional annotation and plant genomics with incredible energy 🌿🧬
#PlantSci #FunctionalAnnotation
www.izmb.uni-bonn.de/en/pbb/news#...
@nancy-choudhary.bsky.social @shakunthalan.bsky.social @bpucker.bsky.social

Undergrads visiting @PuckerLab during the summer of 2025. Details: https://www.pbb.uni-bonn.de

We are looking for undergrads to visit us over the next summer!

If you study in the UK, USA, or Canada, you might be eligible for the DAAD-RISE program 🇩🇪🧬

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

Do excellent science in Bonn next summer!

@puckerlab.bsky.social @unibonn.bsky.social

Nancy presenting "The World of Cucurbits: No Blues, Just Hues". Details: https://doi.org/10.1101/2025.10.06.680802

Yesterday, Nancy shared her Cucurbitaceae anthocyanin loss story with colleagues at our institute. Comprehensive talk highlighting the most striking discoveries. Please find the full story here:

doi.org/10.1101/2025...

#PlantSci #Evolution

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!

Graphical overview of PuckerLab’s 2026 DAAD-RISE research projects: exploring gene duplications, harnessing aquatic plants for biotechnology, producing dark plant pigments, and studying the evolution of plant coloration. More details at https://www.izmb.uni-bonn.de/en/pbb/news#DR

We are looking for curious undergrads to join our research team next summer!

If you study in the UK, USA, or Canada, you might be eligible for the DAAD-RISE program 🇩🇪🧬

Learn more 👉 www.izmb.uni-bonn.de/en/pbb/news#DR
Come do science in Bonn next summer!
@puckerlab.bsky.social @unibonn.bsky.social

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

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

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...

Check out our new preprint to know more about this loss: doi.org/10.1101/2025...

Let's just say the Spookley crew are scientifically exceptional icons! 🎃✨

Great eye! Chlorophyll-rich rind might be responsible for the bluish/blackish appearance

I'm on board with that campaign! 💪🟣

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...

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

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

Evolutionary Rewiring of Anthocyanin Biosynthesis Pathway in Poaceae Poaceae is a species-rich family of plants in the monocots harboring many important crop species. As grasses, these plants lack striking flowers that are typically pigmented by anthocyanins. Here, we ...

"Evolutionary Rewiring of Anthocyanin Biosynthesis Pathway in Poaceae" 🎨
We describe how grasses have reorganized the anthocyanin biosynthesis pathway through gene loss, regulatory shifts, and independent evolution:
🔗 doi.org/10.1101/2025...
@bpucker.bsky.social @nancy-choudhary.bsky.social

Evolutionary Rewiring of Anthocyanin Biosynthesis Pathway in Poaceae Poaceae is a species-rich family of plants in the monocots harboring many important crop species. As grasses, these plants lack striking flowers that are typically pigmented by anthocyanins. Here, we ...

Evolutionary Rewiring of Anthocyanin Biosynthesis Pathway in Poaceae www.biorxiv.org/content/10.1...

If you're new to plant genomics research, don't miss the supplementary hands-on manual we included - it walks you through the major data analysis steps in a typical plant genomics project! ☘️ 🧬

#PlantScience #GenomeAssembly #OpenScience

Thinking of starting a plant genome sequencing project?

Check out this step-by-step guide:

Cookbook for Plant Genome Sequences
📖 www.preprints.org/manuscript/2...

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

KIPEs3: Automatic annotation of biosynthesis pathways Flavonoids and carotenoids are pigments involved in stress mitigation and numerous other processes. Both pigment classes can contribute to flower and fruit coloration. Flavonoid aglycones and caroteno...

KIPEs3: Automatic annotation of biosynthesis pathways
doi.org/10.1371/jour...

#PlantSci #Bioinformatics #Genomics #DataScience #AI

Conserved amino acid residues and gene expression patterns associated with the substrate preferences of the competing enzymes FLS and DFR Background Flavonoids, an important class of specialized metabolites, are synthesized from phenylalanine and present in almost all plant species. Different branches of flavonoid biosynthesis lead to p...

Conserved amino acid residues and gene expression patterns associated with the substrate preferences of the competing enzymes FLS and DFR
doi.org/10.1371/jour...

#Metabolism #PlantSci #GeneExpression #Flavonoids #Flavonols #Anthocyanins #Evolution #Bioinformatics #BigData

Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis - Nature Communications Withanolides are plant steroids with potent bioactivities found in many medicinal plants including Withania somnifera, but their biosynthetic pathway is largely unknown. Here, the authors report the g...

Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis
doi.org/10.1038/s414...

#Genomics #Withanolides #SpecializedMetabolism #BiosyntheticGeneCluster #LongReadSequencing #MetabolicEngineering #OpenAccess #OpenData

Picture of Withania somnifera next to a MinION. Source: https://www.uni-bonn.de/en/news/130-2025

ICYMI: We explored the biosynthesis of withanolides 🧪

Here’s the official press release by @unihannover.bsky.social & @unibonn.bsky.social:
🔗 www.uni-bonn.de/en/news/130-...

📄 Original research: doi.org/10.1038/s414...

#Science #NaturalProducts
@frankelab.bsky.social @puckerlab.bsky.social

Withanolide #biosynthesis from nightshade plants decoded. Withanolide steroids are used as a basis for medications for centuries.

Now published by a team around @frankelab.bsky.social + @puckerlab.bsky.social in @natcomms.nature.com (DOI: 10.1038/s41467-025-61686-1).