Boas Pucker

Boas Pucker
Technische Universität Braunschweig · Institute of plant biology

Dr. rer. nat.
Unlocking the specialized metabolism of plants with genomics, transcriptomics, and bioinformatics

About

133
Publications
66,844
Reads
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698
Citations
Introduction
Evolution of specialised metabolism in plants, Flavonoid and betalain biosynthesis, R2R3 MYB transcription factors in plants, Long read sequencing of plant genomes, Bioinformatics with focus on genomics and transcriptomics; Molecular Biology; Synthetic Biology (iGEM)
Additional affiliations
October 2021 - present
Technische Universität Braunschweig
Position
  • Professor (Assistant)
Description
  • Plant Biotechnology and Bioinformatics: https://www.tu-braunschweig.de/en/ifp/pbb
April 2020 - September 2021
University of Cambridge
Position
  • PostDoc Position
Description
  • https://www.cebitec.uni-bielefeld.de/~bpucker
November 2019 - present
Ruhr-Universität Bochum
Position
  • Research Associate
Education
July 2017 - March 2020
Bielefeld University
Field of study
  • Bioinformatics
February 2016 - September 2019
Bielefeld University
Field of study
  • Biology
October 2013 - September 2015
Bielefeld University
Field of study
  • Genome-based Systems Biology (GBSB)

Publications

Publications (133)
Preprint
Full-text available
Combined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing demand for scientists with a combined background in both fields, the education in dry lab and wet lab is often separated. This work describes an example of integrated education wit...
Preprint
Full-text available
The flavonoid biosynthesis is a well characterised model system for specialised metabolism and transcriptional regulation in plants. Flavonoids have numerous biological functions like UV protection and pollinator attraction, but also biotechnological potential. Here, we present Knowledge-based Identification of Pathway Enzymes (KIPEs) as an automat...
Article
Full-text available
High-throughput sequencing technologies have rapidly developed during the past years and have become an essential tool in plant sciences. However, the analysis of genomic data remains challenging and relies mostly on the performance of automatic pipelines. Frequently applied pipelines involve the alignment of sequence reads against a reference sequ...
Preprint
Full-text available
Background: MYBs are among the largest transcription factor families in plants. Consequently, members of this family are involved in a plethora of processes including development and specialized metabolism. The MYB families of many plant species were investigated in the last two decades since the first investigation looked at Arabidopsis thaliana....
Preprint
Full-text available
The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, defense responses and metabolite accumulation. To date MYB family genes have not yet been comprehensively identified in the major staple fruit crop banana. In this study, we present a compr...
Preprint
Flavonols are structurally and functionally diverse molecules playing roles in plant biotic and abiotic stress tolerance, auxin transport inhibition, pollen development, etc. Despite their ubiquitous occurrence in land plants and multifunctionality, the effect of perturbation of flavonol biosynthesis over global gene expression and pathways other t...
Article
Full-text available
It is critical to develop plant isoprenoid production when dealing with human-demanded industries such as flavoring, aroma, pigment, pharmaceuticals, and biomass used for biofuels. The methylerythritol phosphate (MEP) and mevalonic acid (MVA) plant pathways contribute to the dynamic production of isoprenoid compounds. Still, the cross-talk between...
Poster
Full-text available
Most SARS-CoV-2 neutralizing antibodies were generated against the Receptor-Binding-Domain (RBD). As a result of frequent mutations within the RBD, upcoming variants lead to immune escape. Here, we describe an ORFeome phage display approach to identify immunogenic targets of SARS-CoV-2 using our own genome library. A major immunogenic epitope could...
Article
Full-text available
Main conclusion We identified 119 typical CaMYB encoding genes and reveal the major components of the proanthocyanidin regulatory network. CaPARs emerged as promising targets for genetic engineering toward improved agronomic traits in C. arietinum. Abstract Chickpea (Cicer arietinum) is among the eight oldest crops and has two main types, i.e., de...
Preprint
Full-text available
Bananas are among the most popular fruits in the world and provide food security and employment opportunities in several developing countries. An increased anthocyanin content could enhance the health promoting properties of banana fruits. The biosynthesis of anthocyanins is largely regulated at the transcriptional level. However, little is known a...
Preprint
Full-text available
Background Flavonoids and carotenoids are pigments involved in stress mitigation and numerous other processes. Both pigment classes can contribute to flower and fruit coloration. Carotenoids and flavonoid aglycons are produced by a pathway that is largely conserved across land plants. Glycosylations, acylations, and methylations of the flavonoid ag...
Article
Full-text available
Rapeseed (Brassica napus L.) is an important oil crop and has the potential to serve as a highly productive source of protein. This protein exhibits an excellent amino acid composition and has high nutritional value for humans. Seed protein content (SPC) and seed oil content (SOC) are two complex quantitative and polygenic traits which are negative...
Article
Full-text available
The development of antibody therapies against SARS-CoV-2 remains a challenging task during the ongoing COVID-19 pandemic. All approved therapeutic antibodies are directed against the receptor binding domain (RBD) of the spike, and therefore lose neutralization efficacy against emerging SARS-CoV-2 variants, which frequently mutate in the RBD region....
Preprint
Full-text available
Rapeseed ( Brassica napus L.) is an important oil crop and harbours the potential to serve as a highly productive source of protein. This protein exhibits an excellent amino acid composition and has a high nutritional value for humans. Seed protein content (SPC) and seed oil content (SOC) are two complex quantitative and polygenic traits which are...
Preprint
The development of antibody therapies against SARS-CoV-2 remains a challenging task during the ongoing COVID-19 pandemic. All approved therapeutic antibodies are directed against the receptor binding domain (RBD) of Spike and lost neutralization efficacy against continuously emerging SARS-CoV-2 variants, which especially mutate in the RBD region. P...
Article
Full-text available
Flavonoids are a biochemically diverse group of specialized metabolites in plants that are derived from phenylalanine. While the biosynthesis of the flavonoid aglycone is highly conserved across species and well characterized, numerous species-specific decoration steps and their relevance remained largely unexplored. The flavonoid biosynthesis take...
Article
Full-text available
Resulting from impaired collagen turnover, fibrosis is a hallmark of adipose tissue (AT) dysfunction and obesity-associated insulin resistance (IR). Prolidase, also known as peptidase D (PEPD), plays a vital role in collagen turnover by degrading proline-containing dipeptides but its specific functional relevance in AT is unknown. Here we show that...
Preprint
Flavonoids are a biochemically diverse group of specialized metabolites in plants that are derived from phenylalanine. While the biosynthesis of the flavonoid aglycone is highly conserved across species and well characterized, numerous species-specific decoration steps and their relevance remained largely unexplored. The flavonoid biosynthesis take...
Article
Full-text available
Background MYBs are among the largest transcription factor families in plants. Consequently, members of this family are involved in a plethora of processes including development and specialized metabolism. The MYB families of many plant species were investigated in the last two decades since the first investigation looked at Arabidopsis thaliana. T...
Preprint
Flavonoids are a biochemically diverse group of specialized metabolites in plants that are derived from phenylalanine. While the biosynthesis of the flavonoid aglycone is highly conserved across species and well characterized, numerous species-specific decoration steps and their relevance remained largely unexplored. The flavonoid biosynthesis take...
Preprint
Background Flavonoids are specialized metabolites with numerous biological functions in stress response and reproduction of plants. Flavones are one subgroup that is produced by the flavone synthase (FNS). Two distinct enzyme families evolved that can catalyze the biosynthesis of flavones. While the membrane-bound FNS II is widely distributed in se...
Article
Full-text available
Background As the major source of sugar in moderate climates, sugar-producing beets ( Beta vulgaris subsp. vulgaris ) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes – traits that often reside in the crop wil...
Article
Full-text available
Third-generation long-read sequencing is transforming plant genomics. Oxford Nanopore Technologies and Pacific Biosciences are offering competing long-read sequencing technologies and enable plant scientists to investigate even large and complex plant genomes. Sequencing projects can be conducted by single research groups and sequences of smaller p...
Article
Full-text available
Here we respond to the paper entitled “ Contribution of anthocyanin pathways to fruit flesh coloration in pitayas ” (Fan et al., BMC Plant Biol 20:361, 2020). In this paper Fan et al. 2020 propose that the anthocyanins can be detected in the betalain-pigmented genus Hylocereus , and suggest they are responsible for the colouration of the fruit fles...
Preprint
Full-text available
Here we respond to Zhou et al., 2020 'Combined Transcriptome and Metabolome analysis of Pitaya fruit unveiled the mechanisms underlying Peel and pulp color formation' published in BMC Genomics. Given the evolutionary conserved anthocyanin biosynthesis pathway in betalain-pigmented species, we are open to the idea that species with both anthocyanins...
Preprint
Full-text available
Background As the major source of sugar in moderate climates, sugar-producing beets ( Beta vulgaris subsp. vulgaris ) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes – traits that often reside in the crop wil...
Article
Full-text available
Thioredoxins (TRXs), a large subclass of ubiquitous oxidoreductases, are involved in thiol redox regulation. Here, we performed a comprehensive analysis of TRXs in the Arabidopsis thaliana genome, revealing 41 genes encoding 18 typical and 23 atypical TRXs, and 6 genes encoding thioredoxin reductases (TRs). The high number of atypical TRXs indicate...
Article
Full-text available
Background Experimental proof of gene function assignments in plants is based on mutant analyses. T-DNA insertion lines provided an invaluable resource of mutants and enabled systematic reverse genetics-based investigation of the functions of Arabidopsis thaliana genes during the last decades. Results We sequenced the genomes of 14 A. thaliana GAB...
Article
Full-text available
Receptor-like kinases (RLKs) are key cell signaling components. The rice ARBUSCULAR RECEPTOR-LIKE KINASE 1 (OsARK1) regulates the arbuscular mycorrhizal (AM) association postarbuscule development and belongs to an undefined subfamily of RLKs. Our phylogenetic analysis revealed that ARK1 has an ancient paralogue in spermatophytes, ARK2 . Single ark2...
Article
Full-text available
Key message Our results provide insights into the flavonol biosynthesis regulation of M. truncatula. The R2R3-MYB transcription factor MtMYB134 emerged as tool to improve the flavonol biosynthesis. Abstract Flavonols are plant specialized metabolites with vital roles in plant development and defense and are known as diet compound beneficial to hum...
Preprint
Full-text available
Background Experimental prove of gene function assignments in plants is heavily based on mutant analyses. T-DNA insertion lines provided an invaluable resource of mutants and enabled systematic reverse genetics-based investigation of the functions of Arabidopsis thaliana genes during the last decades. Results We sequenced the genomes of 14 A. thali...
Article
Full-text available
Background Dispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level. Most analyses classify genes as core genes, which are present in all investigated individual genomes, and dispensable genes, which only occur in a single or a...
Article
Full-text available
Plants display sophisticated mechanisms to tolerate challenging environmental conditions and need to manage their ontogenesis in parallel. Here, we set out to generate an RNA-Seq time series dataset throughout grapevine (Vitis vinifera) early bud development. The expression of the developmental regulator VviAP1 served as an indicator of the progres...
Preprint
Full-text available
Plants display sophisticated mechanisms to tolerate challenging environmental conditions 20 and need to manage their ontogenesis in parallel. Here, we set out to generate an RNA-Seq time 21 series dataset throughout grapevine (Vitis vinifera) early bud development. The expression of the 22 developmental regulator VviAP1 served as an indicator for p...
Article
Full-text available
The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, defense responses and metabolite accumulation. To date MYB family genes have not yet been comprehensively identified in the major staple fruit crop banana. In this study, we present a compr...
Article
Full-text available
The evolution of a lipid‐based cuticle on aerial plant surfaces that protects against dehydration is considered a fundamental innovation in the colonization of the land by the green plants. However, key evolutionary steps in the early regulation of cuticle synthesis are still poorly understood due to limited studies in early diverging land plant li...
Article
Full-text available
The ‘big data’ revolution has enabled novel types of analyses in the life sciences, facilitated by public sharing and reuse of datasets. Here, we review the prodigious potential of reusing publicly available datasets and the associated challenges, limitations and risks. Possible solutions to issues and research integrity considerations are also dis...
Article
Full-text available
The flavonoid biosynthesis is a well-characterised model system for specialised metabolism and transcriptional regulation in plants. Flavonoids have numerous biological functions such as UV protection and pollinator attraction, but also biotechnological potential. Here, we present Knowledge-based Identification of Pathway Enzymes (KIPEs) as an auto...
Preprint
Full-text available
Fibrosis is a hallmark of adipose tissue (AT) dysfunction and obesity-associated insulin resistance that results from an impaired collagen turnover. Peptidase D (PEPD) plays a vital role in collagen turnover by degrading proline-containing dipeptides. Nevertheless, its specific function and importance in AT is unknown. GWAS identified the rs731839...
Article
Full-text available
Most plants associate with beneficial arbuscular mycorrhizal (AM) fungi that facilitate soil nutrient acquisition. Prior to contact, partner recognition triggers reciprocal genetic remodelling to enable colonisation. The plant Dwarf14-Like (D14L) receptor conditions pre-symbiotic perception of AM fungi, and also detects the smoke constituent karrik...
Preprint
Full-text available
Background Dispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level. Most analyses classify genes as core genes, which are present in all investigated individual genomes, and dispensable genes, which only occur in a single or a...
Preprint
Full-text available
High-throughput sequencing technologies have rapidly developed during the past years and became an essential tool in plant sciences. However, the analysis of genomic data remains challenging and relies mostly on the performance of automatic pipelines. Frequently applied pipelines involve the alignment of sequence reads against a reference sequence...
Article
Full-text available
Trifoliate yam (Dioscorea dumetorum) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 h after harvesting and renders the tubers inedible. Genomic resources are required for D. dumetorum to improve breeding for non-hardening varieties as well as for other traits. We s...
Article
Full-text available
Grapevine breeding has become highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Viti...
Preprint
Plant DNA extraction and preparation for ONT sequencing This CTAB-based protocol is suitable for extraction of genomic DNA from a wide range of plant species. The DNA quality is sufficient for ONT sequencing after SRE enrichment of long fragments and removal of short fragments. Quality control steps are described as part of this protocol. Successfu...
Article
Full-text available
Most protein-encoding genes in eukaryotes contain introns, which are interwoven with exons. Introns need to be removed from initial transcripts in order to generate the final messenger RNA (mRNA), which can be translated into an amino acid sequence. Precise excision of introns by the spliceosome requires conserved dinucleotides, which mark the spli...
Preprint
Full-text available
The 'big data revolution' has enabled novel types of analyses in the life sciences, facilitated by public sharing and reuse of datasets. Here, we review the prodigious potential of reusing publicly available datasets and the challenges, limitations and risks associated with it. Due to the prominence, abundance and wide distribution of sequencing re...
Preprint
Full-text available
The yam species Dioscorea dumetorum is one example of an orphan crop, not traded internationally. Post-harvest hardening starts within 24 hours after harvesting and renders the tubers inedible. Genomic resources are required for trifoliate yam to improve breeding for non-hardening varieties and for other traits. Here, we describe the sequencing of...
Preprint
Full-text available
Grapevine breeding becomes highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis v...
Article
Full-text available
Different Musa species, subspecies, and cultivars are currently investigated to reveal their genomic diversity. Here, we compare the genome sequence of one of the commercially most important cultivars, Musa acuminata Dwarf Cavendish, against the Pahang reference genome assembly. Numerous small sequence variants were detected and the ploidy of the c...
Chapter
Full-text available
Recent progress in sequencing technologies facilitates plant science experiments through the availability of genome and transcriptome sequences. Genome assemblies provide details about genes, transposable elements, and the general genome structure. The availability of a reference genome sequence for a species enables and supports numerous wet lab a...
Article
Full-text available
Arabidopsis thaliana is one of the best studied plant model organisms. Besides cultivation in greenhouses, cells of this plant can also be propagated in suspension cell culture. At7 is one such cell line that was established about 25 years ago. Here, we report the sequencing and the analysis of the At7 genome. Large scale duplications and deletions...
Article
Full-text available
The evolution of L‐DOPA 4,5‐dioxygenase activity, encoded by the gene DODA, was a key step in the origin of betalain biosynthesis in Caryophyllales. We previously proposed that L‐DOPA 4,5‐dioxygenase activity evolved via a single Caryophyllales‐specific neofunctionalisation event within the DODA gene lineage. However, this neofunctionalisation even...
Preprint
Full-text available
Arabidopsis thaliana is one of the best studied plant model organisms. Besides cultivation in greenhouses, cells of this plant can also be propagated in suspension cell culture. At7 is one such cell line that has been established about 25 years ago. Here we report the sequencing and the analysis of the At7 genome. Large scale duplications and delet...
Poster
Full-text available
The Poster describes this year's iGEM Bielefeld-CeBiTec project. We are developing a M13 phage-based protein coat to fight against pathogenic eukaryotes like crop-damaging fungi. To induce cell death in the target organisms we use the properties of Cas13a which starts collateral RNA cleavage after detecting its specific target RNA. This makes our p...
Poster
Full-text available
The Poster describes this year's iGEM Bielefeld-CeBiTec project. We are developing a M13 phage-based protein coat to fight against pathogenic eukaryotes like crop-damaging fungi. To induce cell death in the target organisms we use the properties of Cas13a which starts collateral RNA cleavage after detecting its specific target RNA. This makes our p...
Preprint
Full-text available
Different Musa species, subspecies, and cultivars are currently investigated to reveal their genomic diversity. Here, we compare the Musa acuminata cultivar Dwarf Cavendish against the previously released Pahang assembly. Numerous small sequence variants were detected and the ploidy of the cultivar presented here was determined as triploid based on...
Article
Full-text available
Within the angiosperm order Caryophyllales, an unusual class of pigments known as betalains can replace the otherwise ubiquitous anthocyanins. In contrast to the phenylalanine-derived anthocyanins, betalains are tyrosine-derived pigments which contain the chromophore betalamic acid. The origin of betalain pigments within Caryophyllales and their mu...
Article
Full-text available
Combined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing demand of scientists with a combined background in both fields, the education of dry and wet lab subjects are often still separated. This work describes an example of integrated ed...