We address biological questions by combining molecular biology and computational methods. Our focus is on the genetic basis of plant specialized metabolism and the evolution of biosynthetic capabilities. To elucidate biosynthetic networks, we combine data from our own sequencing with public datasets. Bioinformatics tools are developed to answer specific questions through the analysis of large datasets, often employing methods of artificial intelligence. We investigate the regulation of biosynthetic networks through transcriptomics. Phylogenetic analyses assist in selecting candidate genes for specific molecular functions. Identified genes and biosynthetic pathways serve as a basis for experiments using synthetic biology methods. The results from the various approaches culminate in biotechnological applications.
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1 to 10 of 13 Results
Aug 29, 2026
Natarajan, Shakunthala; Sterling, Claudia; Choudhary, Nancy; Khatun, Najnin; Brieske, Mia-Sophie; Busch, Hannah Elisa; Pucker, Boas, 2026, "PanXpresso - comprehensive collection of gene expression data across domains of life", https://doi.org/10.60507/FK2/OBIGQH, bonndata, V1
This is a comprehensive collection of gene expression count tables in transcripts per million (TPMs) encompassing species from five domains of life - plants, fungi, animals, bacteria and archaea. This data publication is referenced and discussed in detail in the manuscript - “XpBrew and PanXpresso - automatic RNA-seq processing workflow and compreh...
Aug 25, 2026
Marín Recinos, María Fernanda; Ajayi, Blessing; Wolff, Katharina; Choudhary, Nancy; Vieira Salgado de Oliveira, Julie Anne; Pucker, Boas, 2026, "Theobroma cacao: Genome Sequences and Annotations", https://doi.org/10.60507/FK2/YQDFT4, bonndata, V1
The genomes of two Theobroma cacao plants were sequenced with Nanopore long reads. The genome sequence was assembled with hifiasm and the gene models were predicted by GeMoMa. The functional annotation was predicted based on sequence similarity to well characterized Arabidopsis thaliana sequences.
Aug 18, 2026
Vieira Salgado de Oliveira, Julie Anne; Baez, Mariana Alejandra; Pucker, Boas, 2026, "Valeriana officinalis genome sequence and annotation V1", https://doi.org/10.60507/FK2/TQZVWU, bonndata, V1
Here we present the first genome sequence and annotation of Valeriana officinalis (commonly known as valerian), a widespread perennial plant widely used as a herbal remedy. Using ONT long-read sequencing data, a highly continuous genome assembly was generated for V. officinalis. This study uncovers the flavonoid biosynthesis gene repertoire and num...
Jun 24, 2026
Meckoni, Samuel Nestor; Vieira Salgado de Oliveira, Julie Anne; Pucker, Boas, 2026, "Utricularia gibba genome sequence and annotation", https://doi.org/10.60507/FK2/JJ5QZX, bonndata, V1
The genome of an Utricularia gibba plant was sequenced with nanopore long reads. The genome sequence was assembled with hifiasm and the gene models were predicted by Helixer, BRAKER3 and GeMoMa. The functional annotation was predicted based on sequence similarity to well characterized Arabidopsis thaliana sequences.
May 12, 2026
Pucker, Boas; Wolff, Katharina; Vieira Salgado de Oliveira, Julie Anne, 2026, "Genome sequence and annotation of Urtica dioica", https://doi.org/10.60507/FK2/1XHSZ3, bonndata, V1
The Urtica dioica genome was sequenced with ONT long-reads. The genome sequence was assembled with Hifiasm and annotated with GeMoMa.
May 5, 2026
Pucker, Boas; Wolff, Katharina, 2026, "Rubus armeniacus genome sequence and annotation", https://doi.org/10.60507/FK2/L7LG2L, bonndata, V1
Here, we present the genome sequence and annotation of Rubus armeniacus. Oxford Nanopore Technologies (ONT) long-read sequencing data were assembled to generate the genome sequence. Protein-coding genes were predicted and functionally annotated.
Feb 21, 2026
Fischer, Victoria; Dassow, Chiara Marie; Pucker, Boas, 2026, "Begonia manicata genome sequence and annotation", https://doi.org/10.60507/FK2/MOR7FZ, bonndata, V2
Here, we present the genome sequence and annotation of Begonia manicata. Oxford Nanopore Technologies (ONT) long-read sequencing data were assembled to generate the genome sequence. Protein-encoding genes were predicted and functionally annotated.
Feb 15, 2026
Horz, Jakob; Wolff, Katharina; Friedhoff, Ronja; Pucker, Boas, 2025, "Digitalis purpurea genome sequence and annotation V2", https://doi.org/10.60507/FK2/4KUKXI, bonndata, V2
Here we present a high-quality genome sequence and annotation of Digitalis purpurea (commonly known as foxglove), a plant valued both for its ornamental flowers and for producing the cardiac drug digoxin. The study aims to uncover the genetic basis of flower color variation in this species. Using ONT long-read sequencing data, we assembled the geno...
Jan 20, 2026
Vieira Salgado de Oliveira, Julie Anne; Friedhoff, Ronja; Katharina Wolff; Pucker, Boas, 2026, "Purple and White Aquilegia vulgaris genome sequence and annotation V2", https://doi.org/10.60507/FK2/GKLMOG, bonndata, V1
Here we present high-quality genome sequences and annotations of Aquilegia vulgaris (commonly known as columbine), a widespread ornamental plant renowned for its extensive flower color variation. The study uncovers the flavonoid biosynthesis gene repertoire underlying anthocyanin pigmentation in this species. Using ONT long-read sequencing data, hi...
Jan 20, 2026
Vieira Salgado de Oliveira, Julie Anne; Pucker, Boas, 2026, "Tacca chantrieri genome sequence and annotation", https://doi.org/10.60507/FK2/6SOMER, bonndata, V1
Here we present high-quality genome sequence and annotation of Tacca chantrieri (commonly known as black bat flower), famous for its dark, bat-shaped flowers with long filaments, making it an exotic and unusual ornamental plant. Using ONT long-read sequencing data, highly continuous genome assemblies were generated. This data publication contains t...
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