Biology subjects

Friedhoff, R.

Publications and source records attributed to Friedhoff, R..

8 recordsLinked to original sources

bioRxiv2025

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 for the striking blue pigmentation of the flower. Through basecalling, read correction and assembling the sequenced DNA strands, we were able to generate a genome sequence with 98.8% BUSCO completeness, N50 of 16 Mbp, and an accuracy of 72 reported by Merqury. HERRO-based correction of the R10 nanopore sequencing reads resulted in a substantially improved assembly compared to uncorrected reads. The gene prediction revealed structural genes of the flavonoid biosynthesis and associated MYB and bHLH transcription factors. A tandem duplication of F3H was discovered. Additionally, a putative tandem duplication resulting in three copies of the anthocyanin biosynthesis activating MYB was observed.

plant biology↗

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

Genome sequence of the medicinal plant Tropaeolum majus provides insights into flavonoid biosynthesis

Tropaeolum majus is a very popular species around the world with an enormous number of commercially available varieties displaying various flower color patterns and growth characteristics. It is rich in phytochemicals such as glucotropaeolin, hydroxycinnamic acid derivatives, and flavonol glycosides. Here, we report a highly continuous genome sequence of T. majus and a comprehensive annotation of protein encoding genes suitable for comparative genomics. The potential for the exploration of individual gene functions in this valuable plant is demonstrated by an analysis of the flavonoid biosynthesis genes and their transcriptional regulators. Important players of the flavonol biosynthesis, including structural genes and a transcription factor, were identified that are required to produce precursors of phytomedically relevant flavonol glycosides. The genome sequence does not reveal an ortholog of the leucoanthocyanidin reductase encoding gene (LAR), which aligns with previous reports about the absence of this gene in many Brassicales species.

plant biology↗

bioRxiv2024

Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis

Withanolides are steroidal lactones from nightshade (Solanaceae) plants. Of the over 1,200 known representatives, many possess potent biological activities, but their drug potential has not been fully realised up until now. A central obstacle is the limited availability of minor withanolides, caused by a lack of knowledge about the underlying biosynthetic pathways. Here, we combine phylogenomics with metabolic engineering to overcome this limitation. By sequencing the genome of the medicinal plant and archetypical withanolide producer ashwagandha (Withania somnifera) and comparing the genome sequences of nine Solanaceae species, we discovered a conserved gene cluster for withanolide biosynthesis, consisting of two sub-gene clusters which differ in their expression patterns. To investigate the functions of the encoded enzymes, we established metabolic engineering platforms in yeast (Saccharomyces cerevisiae) and the model plant Nicotiana benthamiana. This allowed us to reconstitute the first three oxidative steps of withanolide biosynthesis, catalysed by the cytochrome P450 monooxygenases CYP87G1, CYP88C7, and CYP749B2, leading to the aglycone of the known compound withanoside V. Our work sets the basis for the biotechnological production of withanolides in heterologous hosts and will therefore help to fully harness the drug potential of these plant steroids in the future.

plant biology↗

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

T7 RNA polymerase-independent expression of reporter genes from a T7 promoter-driven SARS-CoV-2 replicon-encoding DNA in human cells

Replicons, derived from RNA viruses, are genetic constructs retaining essential viral enzyme genes while lacking key structural protein genes. Upon introduction into cells, the genes carried by the replicon RNA are expressed, and the RNA self-replicates, yet viral particle production does not take place. Typically, RNA replicons are transcribed in vitro and are then electroporated in cells. However, it would be advantageous for the replicon to be generated in cells following DNA transfection instead of RNA. In this study, a bacterial artificial chromosome (BAC) DNA encoding a SARS-CoV-2 replicon under control of a T7 promoter was transfected into HEK293T cells engineered to functionally express the T7 RNA polymerase (T7 RNAP). Upon transfection of the BAC DNA, we observed low, but reproducible expression of reporter proteins GFP and luciferase carried by this replicon. Expression of the reporter proteins required linearization of the BAC DNA prior to transfection. Surprisingly, however, expression occurred independently of T7 RNAP. Gene expression was also insensitive to remdesivir treatment, suggesting that it did not involve self-replication of replicon RNA. Similar results were obtained in highly SARS-CoV-2 infection-permissive Calu-3 cells. Strikingly, prior expression of the SARS-CoV-2 N protein boosted expression from transfected SARS-CoV-2 RNA replicon but not from the replicon BAC DNA. In conclusion, transfection of a large DNA encoding a coronaviral replicon led to reproducible replicon gene expression through an unidentified mechanism. These findings highlight a novel pathway toward replicon gene expression from transfected replicon cDNA, offering valuable insights for the development of methods for DNA-based RNA replicon applications.

microbiology↗

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↗