Lightnews — Scholar-powered news

PuckerLab publications

@puckerlabpapers.bsky.social

19 followers 11 following 46 posts

Sharing publications of the @puckerlab.bsky.social‬ about #Genomics #Bioinformatics #Evolution #SpecializedMetabolism. Full list: https://www.izmb.uni-bonn.de/en/pbb/publications

www.izmb.uni-bonn.de

Posts Media Videos Starter Packs

Reposted by PuckerLab publications

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.....

Reposted by PuckerLab publications

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...

Reposted by PuckerLab publications

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...

Reposted by PuckerLab publications

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

Reposted by PuckerLab publications

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

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

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

Reposted by PuckerLab publications

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

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

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

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...

Reposted by PuckerLab publications

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...

Reposted by PuckerLab publications

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

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

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

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...

Reposted by PuckerLab publications

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

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

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...

Reposted by PuckerLab publications

PuckerLab @puckerlab.bsky.social · 19d

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

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

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

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

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...

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

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

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

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...

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...

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

Identification of immune response genes of cassava during early phases of cassava brown streak virus infection
doi.org/10.1101/2025...

#PlantSci #Cassava #Viruses #Bioinformatics #BigData #DataScience #OpenAccess #Preprint

Identification of immune response genes of cassava during early phases of cassava brown streak virus infection

Cassava brown streak disease (CBSD) caused by the ipomoviruses CBSV and UCBSV, poses a significant threat to cassava crops and the destruction of tuberous roots leads to substantial yield losses. Viru...

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

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

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

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

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

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

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...

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...

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...

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

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.....

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

Functional Annotation – How to Tackle the Bottleneck in Plant Genomics
www.preprints.org/manuscript/2...

#Genomics #Bioinformatics #FunctionalAnnotation #PlantSci #BigData #DataScience

www.preprints.org

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation
doi.org/10.1101/2024...

#Genomics #Anthocyanins #OrnamentalPlants #MedicinalPlants #LongReadSequencing #ONT

Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation

Digitalis purpurea (foxglove) is a widely distributed ornamental plant and the producer of the biomedical compound digoxin. Here, we present a long read sequencing-based genome sequence of a red flowe...

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

Genome sequence and RNA-seq analysis reveal genetic basis of flower coloration in the giant water lily Victoria cruziana
doi.org/10.1101/2024...

#Genomics #AquaticPlants #Transcriptomics #RNAseq #Coloration #WaterLily #Flavonoids #Anthocyanins

Genome sequence and RNA-seq analysis reveal genetic basis of flower coloration in the giant water lily Victoria cruziana

Victoria cruziana is well known for its huge floating leaves covered with sharp spines and its night blooming. Reports indicate that white flowers open during the first night and turn light pinkish du...

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

Genetic factors explaining anthocyanin pigmentation differences
doi.org/10.1186/s128...

#Evolution #PlantSci #Flavonoids #Anthocyanins #TranscriptionFactors #Mutation #SpecializedMetabolism

Genetic factors explaining anthocyanin pigmentation differences - BMC Plant Biology

Background Anthocyanins are important contributors to coloration across a wide phylogenetic range of plants. Biological functions of anthocyanins span from reproduction to protection against biotic an...

PuckerLab publications @puckerlabpapers.bsky.social · Jul 26

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

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...