Biology subjects

Wolff, K.

Publications and source records attributed to Wolff, K..

8 recordsLinked to original sources

bioRxiv2026

Genome sequence of the medicinal plant Urtica dioica reveals the genetic basis of the flavonoid metabolism

BackgroundUrtica dioica, also known as stinging nettle, is a widespread plant that can indicate high nitrogen availability in the soil. It is probably best known for the pain caused by touching it. U. dioica is also recognized as a medicinal plant with reports claiming applicability against numerous diseases. ResultsA highly continuous genome sequence was constructed based on nanopore long read sequencing data. The total assembly size is 1.1 Gbp with an N50 of 40.7 Mbp. RNA-seq data and hints from other species were integrated to produce a high quality annotation of the protein encoding genes. This genomic resource enabled the identification of genes involved in the flavonoid biosynthesis. A particular focus was on anthocyanin biosynthesis genes as these are crucial for high light and nitrogen deprivation stress response, which is revealed by redding of the leaves. ConclusionThis genomic resource provides the basis for future studies unraveling the biosynthesis pathways underlying various medically important compounds produced by stinging nettles.

plant biology↗

bioRxiv2026

Rubus armeniacus genome sequence reveals the secrets of blackberry anthocyanin biosynthesis

Here, we present a comprehensive multiomics analysis of anthocyanin biosynthesis in Rubus armeniacus, known for its dark fruits. A phased genome sequence of the tetraploid blackberry was generated, achieving an N50 of 34 Mb with an assembly size of 1.2 Gbp based on Oxford Nanopore Technology sequencing (ONT). The BUSCO score for the total assembly shows a high completeness of 99.1%. The assembly was separated into 4 pseudohaplophases, with the pseudohaplophase A representing the R. armeniacus genome in 7 chromosome scale contigs, with an N50 of 46 Mbp and 98.8% conserved BUSCO genes. A total of 118,183 protein coding genes were annotated within the genome assembly and all relevant genes encoding enzymes and transcriptional regulators of the anthocyanin biosynthesis pathway were identified within each pseudohaplophase. To further understand the underlying cause of dark pigmentation, the gene expression was analysed during different stages of berry development revealing a strong induction of anthocyanin biosynthesis genes including the anthocyanin activating subgroup 6 MYB transcriptions during the berry ripening process. Further, a quantification of cyanidin-3-O-glucoside in methanolic berry extract, utilizing a UHPLC-HRAM-MS analysis, revealed an approximately 500-fold increase of cyanidin-3-O-glucoside from green to black fruit, indicating that dark pigmentation in R. armeniacus results from high anthocyanin accumulation. Significance statementThis study provides a multiomics analysis of the dark pigmentation of Rubus armeniacus, including a high quality phased assembly and an in-depth analysis of the anthocyanin biosynthesis pathway. A transcriptional and metabolomic analysis revealed that dark berry pigmentation is caused by a high accumulation of cyanidin-3-O-glucoside during fruit ripening.

genomics↗

bioRxiv2026

NanoPlasmiQC: Full plasmid sequencing with ONT long-reads and automatic data analysis

Long-read sequencing has shown a rapid technological development during the last years. It has been established as the standard method for the sequencing of plant genomes and has also gained importance for full plasmid sequencing. As Sanger sequencing has a limited read length of about 1 kb, long read sequencing offers a great advantage, as the full plasmid can be sequenced in one read. Here, we present a cost-effective workflow to sequence full plasmids and compare the results against an expectation. The per plasmid cost of this workflow is determined by the number of plasmids investigated simultaneously, but can be lower than the price of a single Sanger sequencing reaction. We developed a workflow for automatic data processing, which allows us to complete sequencing and data analysis within a day.

genomics↗

bioRxiv2024

Genome sequence of the ornamental plant Aquilegia vulgaris reveals the flavonoid biosynthesis gene repertoire

Aquilegia vulgaris is a widespread ornamental plant. The species is well known for its extensive variation of different flower colors and can even be considered as a model species for the evolution of flower morphology. Anthocyanins are a major pigment group responsible for pigmentation of flowers in A. vulgaris and many plant species. Here, we report a highly continuous genome sequence of an European Aquilegia vulgaris plant displaying purple flowers and a genome sequence of a plant displaying white flowers. The corresponding annotation facilitates research on flower color and morphology evolution. Long-read alignments revealed different structural variants in an anthocyanidin synthase (ANS) gene, crucial for pigment biosynthesis, that could explain the white flower phenotype. Candidate genes for all steps in the core anthocyanidin biosynthesis were identified. The identification of a flavonoid 3,5 hydroxylase (F35H), a gene essential for the biosynthesis of bluish delphinidin derivatives, corroborates previous reports about metabolites and transcripts in A. vulgaris.

plant biology↗

bioRxiv2024

Cacao genome sequence reveals insights into the flavonoid biosynthesis

Theobroma cacao is well known for its role in producing cacao. Many different cacao varieties are cultivated in equatorial regions, each distinguished by unique phenotypic traits. One of these traits is pod color variation, which has been linked to differences in anthocyanin content. Anthocyanins are produced by a branch of the flavonoid biosynthesis pathway. In this study, two high-contiguity T. cacao genomes, BRAU1 and BONN1, were sequenced and assembled and used to investigate genes and structural variants associated with intraspecific variation in flavonoid biosynthesis. Comparative analysis identified structural variations affecting six candidate flavonoid biosynthesis genes, including a 1026 bp deletion at one of the DFR loci in BRAU1, BONN1, and Matina accessions.

plant biology↗

bioRxiv2024

Deficiency of actin depolymerizing factors ADF/Cfl1 in microglia decreases motility and impairs memory

Microglia are highly motile cells that play a crucial role in the central nervous system in health and disease. Here we show that actin depolymerizing factors ADF and Cofilin1 (Cfl1) are key factors of microglia integrity and function. We found a profound morphological phenotype in absence of ADF and Cfl1 in microglia. In vivo two-photon imaging of microglia with ADF/Cfl1-KO revealed reduced microglial fine processes motility and impaired microglia migration towards a laser-induced lesion. We found increased accumulation of stabilized F-actin and altered microtubule dynamics in ADF/Cfl1-KO microglia, indicating that ADF/Cfl1 are necessary for microglial cytoskeleton dynamics. Interestingly, microglial ADF/Cfl1-deficiency decreased learning and memory, suggesting that impaired microglial cytoskeleton dynamics affect neuronal functions relevant for cognition. Our results reveal a fundamental role of ADF/Cfl1 in microglia function and underscore the importance of these innate immune cells for higher cognitive functions.

neuroscience↗

bioRxiv2024

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 during the following day and the second night. Here, we set out to unravel the molecular basis and ecological function of the flower color change in V. cruziana. A high quality genome sequence with a contig N50 of 44.2 Mbp, a scaffold N50 of 300 Mbp, and a total assembly size of 3.5 Gbp was generated as the genetic basis for this study. Comparative transcriptomics revealed the genes required for anthocyanin biosynthesis genes and their transcriptional regulators as differentially expressed between the white and the light pinkish stage of a flower. Structural genes with expression differences between white and light pinkish flower stages include VcrF3H, VcrF35H, VcrDFR, VcrANS, and VcrarGST. The expression pattern of the corresponding transcription factors VcrMYB123, VcrMYB-SG6_a, VcrMYB-SG6_b, VcrTT8, and VcrTTG1 also showed differences that aligned with the flower color.

plant biology↗

bioRxiv2024

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

Digitalis purpurea (foxglove) is a widely distributed ornamental plant. Here, we present a long read sequencing-based genome sequence of a magenta flowering D. purpurea plant and a corresponding prediction of gene models. The high assembly continuity is indicated by the N50 of 4.3 Mbp and the completeness is supported by discovery of about 96% complete BUSCO genes. This genomic resource paves the way for an in-depth investigation of the flower pigmentation of D. purpurea. Structural genes of the anthocyanin biosynthesis and the corresponding transcriptional regulators were identified. The comparison of magenta and white flowering plants revealed a large insertion in the anthocyanidin synthase gene in white flowering plants that most likely renders this gene non-functional and could explain the loss of anthocyanin pigmentation. Furthermore, we found a large insertion in the DpTFL1/CEN gene to be likely responsible for the development of large terminal flowers.

plant biology↗