Nancy Choudhary

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).