PuckerLab publications

Begonia manicata plant with red, soft outgrowths emerging from the leaf and stems. Photo credit: Jakob Maximilian Horz. Source: https://doi.org/10.64898/2026.02.26.708300

🌿 New preprint: Genome sequence of Begonia manicata and genes responsible for striking red color of its leaf/stem outgrowths. Pigmentation appears linked to anthocyanin biosynthesis genes that are strongly expressed in the red tissues

📄 doi.org/10.64898/202...
#PlantGenomics @puckerlab.bsky.social

Genome sequence annotation workflow. Source: https://doi.org/10.1186/s12864-026-12623-z

How to complete your plant genomics project with a comprehensive annotation?

"Cookbook for Plant Genome Sequences"

doi.org/10.1186/s128...

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

Genome sequence annotation workflow. Source: https://doi.org/10.1186/s12864-026-12623-z

How to complete your plant genomics project with a comprehensive annotation?

"Cookbook for Plant Genome Sequences"

doi.org/10.1186/s128...

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

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

Jakob celebrating https://doi.org/10.1186/s12870-025-08006-3 with his new paper mug.

New paper + new mug = official celebration 🎉☕

Here is Jakob with our review:

“Diversity and ecological functions of anthocyanins”
doi.org/10.1186/s128...

Paper mugs are a tradition in our group — and this one is well earned. Congrats! 🌸🔬

#Anthocyanins #Pigments #Flavonoids #Evolution

Digitalis purpurea genome sequence data publication in bonndata. Details: https://doi.org/10.60507/FK2/4KUKXI

Looking for genome sequences, annotations, or expression data from @puckerlabpapers.bsky.social ?

Access large datasets on bonndata:
🔗 www.izmb.uni-bonn.de/en/pbb/resea...

#OpenScience #Genomics #ResearchData #Bioinformatics #GenomeData @bpucker.bsky.social @opensciene-unibonn.bsky.social

MoeA tree showing the postulated evolution involving independent domain fusion events. Details: https://doi.org/10.64898/2025.12.12.693926

Our first preprint of 2026 is online:

Phylogenetic based dissection of eukaryotic Mo-insertase functionality: From mechanism to complex assembly
doi.org/10.64898/202...

#Evolution #Phylogenetics @puckerlab.bsky.social

Tree showing relationships of LAR genes. Details: https://doi.org/10.1186/s12864-025-12429-5

Excited to share that Maria's work on the evolution of the LAR gene has been published in BMC Genomics:

Evolutionary dynamics of the proanthocyanidin biosynthesis gene LAR
doi.org/10.1186/s128...

#Evolution #FlavonoidBiosynthesis #PlantSciences
@bpucker.bsky.social @maferrecinos.bsky.social

Selection of ecological functions of anthocyanins: Aposematism, Pathogens, Camouflage, Batesian mimicry, Anti-camouflage. Details: https://doi.org/10.1186/s12870-025-08006-3

What is the major role of anthocyanins—painting flowers, acting as sunscreens, responding to stress, or defending against pathogens?

Our latest paper dives into the diversity and ecological functions of anthocyanins 🌈🌿

doi.org/10.1186/s128...

#PlantSciences #Anthocyanins @bpucker.bsky.social

Overview figure of our plant genome sequencing workflow. Details and reference: https://www.preprints.org/manuscript/202508.1176/v2

🚀 Exciting update: "Cookbook for Plant Genome Sequences" now includes an updated overview figure! 🌱🔬
Check out how to run a plant genome sequencing project:
www.preprints.org/manuscript/2...
#Genomics #LongReads #Bioinformatics
@puckerlab.bsky.social

Our review article got published in 'Biotechnology Advances':

"Decoding bioprocesses with transcriptomics: current status and future potential"
doi.org/10.1016/j.bi...

#Biotech #ScaleUp #ScaleDown #Transcriptomics
@puckerlab.bsky.social

DupyliCate - mining, classifying, and characterizing gene duplications Paralogs, copies of a gene, form an important basis for novelty during evolution. Analysis of such gene duplications is important to understand the emergence of novel traits during evolution. DupyliCa...

Excited to share DupyliCate - our new tool for discovery and characterization of gene duplications:

"DupyliCate - mining, classifying, and characterizing gene duplications"

doi.org/10.1101/2025...

#Bioinformatics #Python #Genomics #Evolution
@puckerlab.bsky.social

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 estimations. An alternative approach to estimate the genome size based on high contiguity assemblies and read mappings is presented here. Analyses of Arabidopsis thaliana and Beta vulgaris data sets are presented to show the impact of different parameters. Oryza sativa, Brachypodium distachyon, Solanum lycopersicum, Vitis vinifera, and Zea mays were also analyzed to demonstrate the broad applicability of this approach. Further, MGSE was also used to analyze Escherichia coli, Saccharomyces cerevisiae, and Caenorhabditis elegans datasets to show its utility beyond plants. Mapping-based Genome Size Estimation (MGSE) and additional scripts are available on GitHub: https://github.com/bpucker/MGSE . MGSE predicts genome sizes based on short reads or long reads requiring a minimal coverage of 5-fold.

New tool alert: MGSE estimates genome size from read mappings — works with short & long reads, even at low coverage. A mapping-based alternative to k-mer methods. 🧬
🔗 doi.org/10.1186/s128...

#Genomics #Bioinformatics

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

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

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.....

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

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...

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

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

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...

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

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

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

The haplotype-resolved assembly of COL40 a cassava (Manihot esculenta) line with broad-spectrum resistance against viruses causing Cassava brown streak disease unveils a region of highly repeated elem... Abstract. Cassava (Manihot esculenta Grantz) is a vital staple crop for millions of people, particularly in Sub-Saharan Africa, where it is a primary sourc

The haplotype-resolved assembly of COL40 a cassava (Manihot esculenta) line with broad-spectrum resistance against viruses causing Cassava brown streak disease unveils a region of highly repeated elements on chromosome 12
doi.org/10.1093/g3jo...
#Genomics #Cassava #Bioinformatics #LongReadSequencing

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...

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

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

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...

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

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

Dark side of anthocyanin pigmentation This review examines dark anthocyanin pigmentation in plants by outlining its distribution, exploring the genetic mechanisms behind its development, and discussing its ecological role together with i...

Dark side of anthocyanin pigmentation
doi.org/10.1111/plb....

#Anthocyanins #Ecology #Biochemistry #Pigmentation #Flavonoids #FlowerColor #Review

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

Plant genome sequencing workflow. Reference and description: https://www.doi.org/10.20944/preprints202508.1176.v2

How long does it take to sequence a plant genome?

The most decisive factor is the genome size, but with an efficient workflow, an annotated genome sequence can be available within days to weeks. Read the full story:

www.doi.org/10.20944/pre...

#Genomics #SciComm #SciArt #Bioinformatics #PlantSci

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

Dark side of anthocyanin pigmentation This review examines dark anthocyanin pigmentation in plants by outlining its distribution, exploring the genetic mechanisms behind its development, and discussing its ecological role together with i...

Dark side of anthocyanin pigmentation
doi.org/10.1111/plb....

#Anthocyanins #Ecology #Biochemistry #Pigmentation #Flavonoids #FlowerColor #Review

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...

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

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