Biology subjects

Pucker, B.

Publications and source records attributed to Pucker, B..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Expansion of the DFR Gene Family in Fagopyrum

BackgroundGene duplication is a fundamental evolutionary mechanism that contributes to genetic innovation, such as in the diversification of plant metabolic pathways. This study investigates the duplication of dihydroflavonol-4-reductase (DFR) genes in Fagopyrum, focusing on their evolutionary origin and implications for flavonoid biosynthesis. DFR is a key enzyme in the flavonoid pathway, specifically involved in the biosynthesis of anthocyanins and proanthocyanidins. DFR can accept three main substrates: dihydrokaempferol (DHK), dihydroquercetin (DHQ), and dihydromyricetin (DHM), and they exhibit variable substrate preferences. ResultThrough comparative genomic analysis, this study identified three unique DFR gene copies in Fagopyrum, designated DFR1, DFR2a, and DFR2b. DFR2a and DFR2b show unique mutations affecting the 26-amino acid substrate-binding region, including substitution of the conserved asparagine at position 3 with valine or isoleucine, and an insertion between positions 5 and 6 involving glycine, arginine, or lysine. Synteny analysis reveals that DFR1 is located in a conserved region across related species, while DFR2a and DFR2b lie at distinct genomic loci. Gene expression analysis shows DFR1 is universally expressed, whereas DFR2a and DFR2b expression is primarily restricted to seeds and roots. Promoter analysis supports this, revealing the absence of MYB recognition elements in DFR2a and DFR2b that are present in the DFR1 promoter. Selective pressure analysis indicates that DFR2 copies are under strong purifying selection relative to ancestral DFR1 but appear slightly relaxed between DFR2a and DFR2b in a way suggesting functional differentiation, particularly in conserved regions. ConclusionBased on multiple lines of evidence, we propose DNA duplication associated with inversion (DDAI) as a mechanism to explain the emergence of the DFR2 copies, involving a staggered single-strand break, followed by inversion and non-homologous end joining repair mechanism.

plant biology↗

bioRxiv2025

Evolutionary Rewiring of Anthocyanin Biosynthesis Pathway in Poaceae

Poaceae is a species-rich family of plants in the monocots harboring many important crop species. As grasses, these plants lack striking flowers that are typically pigmented by anthocyanins. Here, we investigated the anthocyanin biosynthesis genes in Poaceae and characterized several striking patterns. (1) An independently evolved MYB lineage (ncaMYB) is responsible for the regulation of the anthocyanin biosynthesis in Poaceae. (2) The independently evolved BZ2 lineage replaced the otherwise widespread TT19/An9 lineage as anthocyanin-related glutathione S-transferase in Poaceae. (3) The anthocyanin biosynthesis genes ANS, arGST (BZ2), and the anthocyanin biosynthesis activating MYB (ncaMYB) appear to be absent from the genus Brachypodium. These observations could be explained by a loss of the anthocyanin biosynthesis at the basis of the Poaceae, followed by an evolutionarily independent regain and again a loss of the anthocyanin biosynthesis in Brachypodium.

plant biology↗

bioRxiv2025

PHO2 suppresses arbuscular mycorrhizal symbiosis in high phosphate conditions

Arbuscular mycorrhizal (AM) symbiosis is an ancient relationship formed between most plants and Glomeromycotina fungi, typically in response to phosphate (Pi) limitation in soils. By hosting these fungi in their roots, plants extend their access to essential mineral nutrients and water beyond the rhizosphere, while providing the fungus with carbon in return. This mutualistic symbiosis presents a promising tool for enhancing sustainability in agriculture, as it not only supports plant nutrition but also immunity and wider soil health. However, achieving high crop yields currently relies on supplementing plants with excess Pi, which suppresses AM symbiosis. We found that this suppression is mediated by a key negative regulator of the Pi starvation response (PSR) in rice (Oryza sativa), Phosphate overaccumulator 2 (PHO2). PHO2 encodes an E2 ubiquitin-conjugating enzyme which targets various proteins involved in the PSR in Pi-sufficient conditions for protein degradation. Here we report that pho2 mutants of rice and Nicotiana benthamiana retained high AM fungal colonisation even in high Pi conditions. Our transcriptomic analysis of uninoculated rice roots revealed that pho2 mutants are less sensitive to Pi treatment and retain susceptibility to AM symbiosis by maintaining expression of a core set of AM-related genes gating the early stage AM fungal entry, such as genes involved in strigolactone biosynthesis, LysM-containing plant receptors for fungal molecules, and components of the common symbiosis signalling pathway (CSSP). Furthermore, isotope tracing using 33P and phosphate transporter (PHT1) gene expression patterns collectively suggest enhanced direct and symbiotic Pi overaccumulation in pho2 mutant leaves. Together, our data reveal a new role for PHO2, as a negative regulator of AM colonisation and symbiotic Pi accumulation in shoots.

plant biology↗

bioRxiv2025

Evolutionary Dynamics of the Proanthocyanidin Biosynthesis Gene LAR

BackgroundLeucoanthocyanidin reductase (LAR) is a key enzyme in proanthocyanidin (PAs) biosynthesis, catalyzing the conversion of leucoanthocyanidins to catechins. While early steps in the flavonoid pathway are broadly conserved across plant lineages, increasing evidence demonstrates lineage-specific evolutionary trajectories and functional diversification in its terminal branches, particularly in the case of LAR. To explore the evolutionary dynamics and functional divergence of LAR genes, we conducted a large-scale comparative and phylogenetic analyses across major plant clades. ResultsPhylogenetic analysis revealed multiple independent duplication events and lineage-specific expansions of LAR lineages, particularly among dicots and gymnosperms. In dicots, LAR1 and LAR2 were differentially retained and diversified, whereas gymnosperm LAR homologs formed early-diverging clades, suggesting an ancient duplication and potential neofunctionalization. Coexpression analyses across species and tissues indicate paralog-specific expression patterns. Sequence analysis identified both conserved and clade-specific protein domains, supporting functional divergence. Promoter analyses showed differences in transcription factor binding site composition between LAR1 and LAR2, pointing to regulatory sub- or neofunctionalization. Lastly, synteny analyses supports the potential absence of LAR in multiple Brassicacea genomes. ConclusionsLAR shows evidence of evolutionary diversification, shaped by both coding and regulatory changes. These patterns of diversification help explain variation in flavonoid profiles in gymnosperms and angiosperms. Understanding the evolutionary dynamics of LAR not only deepens our knowledge of metabolic pathway evolution but also provides insights relevant to the breeding and metabolic engineering of plant traits related to pigmentation, stress resilience, and nutritional quality.

evolutionary biology↗

bioRxiv2025

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. Virus resistance identified in some South American cassava germplasm lines inhibits virus replication and movement and, is a complete immunity of some lines or, a restriction of the virus replication to phloem companion cells and root infection in others. To further explore the resistance responses and identify potential resistance genes, a time-course RNA-Seq study was conducted comparing gene expression of a virus-susceptible cassava TMS 96/0304 with a cassava line restricting CBSV to the roots and a cassava DSC 167 (COL2182), immune to the virus. Differential gene expression patterns across leaves, stems, and roots revealed substantial differences between susceptible and resistant genotypes. Temporal analysis highlighted significant variations in the number of differentially expressed genes (DEGs), particularly in stem tissues at one day after inoculation (DAI), with notable overexpression observed in the resistant lines DSC 167 (436 DEGs) and DSC 260 (335 DEGs). In contrast, significant expression changes were noted only at 10 DAI in the virus infected TMS 96/0304 (737 DEGs). Several DEGs in resistant genotypes were associated with proteins involved in hormonal regulation, defense and immunity, transcriptional regulation, stress response, cell structure, and signal transduction. The analysis indicates that virus resistance in the studied lines is driven by early-stage regulation of genes for which specific functions remain to be elucidated.

plant biology↗

bioRxiv2025

CoExpPhylo - A Novel Pipeline for Biosynthesis Gene Discovery

BackgroundThe rapid advancement of sequencing technologies has drastically increased the availability of plant genomic and transcriptomic data, shifting the challenge from data generation to functional interpretation. Identifying genes involved in specialized metabolism remains difficult. While coexpression analysis is a widely used approach to identify genes acting in the same pathway or process, it has limitations, particularly in distinguishing genes coexpressed due to shared regulatory triggers from those directly involved in the same pathway. To enhance functional predictions, integrating phylogenetic analysis provides an additional layer of confidence by considering evolutionary conservation. Here, we introduce CoExpPhylo, a computational pipeline that systematically combines coexpression analysis and phylogenetics to identify candidate genes involved in specialized biosynthetic pathways across multiple species based on one to multiple bait gene candidates. ResultsCoExpPhylo systematically integrates coexpression information and phylogenetic signals to identify candidate genes involved in specialized biosynthetic pathways. The pipeline consists of multiple computational steps: (1) species-specific coexpression analysis, (2) local sequence alignment to identify orthologs, (3) clustering of candidate genes into Orthologous Coexpressed Groups (OCGs), (4) functional annotation, (5) global sequence alignment, (6) phylogenetic tree generation, and optionally (7) visualization. The workflow is highly customizable, allowing users to adjust correlation thresholds, filtering parameters, and annotation sources. Benchmarking CoExpPhylo on multiple pathways, including the biosynthesis of anthocyanins, proanthocyanidins, and flavonols, as well as lutein and zeaxanthin, confirmed its ability to recover known genes while also suggesting novel candidates. ConclusionCoExpPhylo provides a systematic framework for identifying candidate genes involved in the specialized metabolism. By integrating coexpression data with phylogenetic clustering, it facilitates the discovery of both conserved and lineage-specific genes. The resulting OCGs offer a strong foundation for further experimental validation, bridging the gap between computational predictions and functional characterization. Future improvements, such as incorporating multi-species reference databases and refining clustering for large gene families, could further enhance its resolution. Overall, CoExpPhylo represents a valuable tool for accelerating pathway elucidation and advancing our understanding of specialized metabolism in plants.

bioinformatics↗

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

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

Cassava (Manihot esculenta Grantz) is a vital staple crop for millions of people, particularly in Sub-Saharan Africa, where it is a primary source of food and income. However, cassava production is threatened by several viral diseases, including cassava brown streak disease, which causes severe damage to the edible storage roots. Current cassava varieties in Africa lack effective resistance to this disease, leading to significant crop losses. We investigated the genetic diversity of cassava and identifed new sources of resistance to the viruses causing cassava brown streak disease. The cassava line, COL40, from a South American germplasm collection showed broad-spectrum resistance against all known strains of the viruses that cause this disease. To further understand the genetic basis of this resistance, we sequenced the genome of COL40 and produced a high-quality, haplotype-resolved genome assembly. This genomic resource provides new insights into cassavas genetic architecture, particularly in regions associated with disease resistance. The sequence reveals significant structural variation, including transposable elements, inversions, and deletions, which may contribute to the resistance phenotype. The reference genome assembly presented here will provide a valuable genomic resource for studying the cassava brown streak resistance and will help in accelerating breeding efforts to introduce virus resistance into African cassava varieties. By identifying genetic variants linked to resistance, future breeding programs can develop cassava cultivars that are more resilient to viral threats, enhancing food security and livelihoods for smallholder farmers across regions affected by the disease.

genomics↗

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

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↗

bioRxiv2024

Metabolic fingerprinting reveals roles of Arabidopsis thaliana BGLU1, BGLU3 and BGLU4 in glycosylation of various flavonoids

Flavonoids are specialized metabolites that play important roles in plants, including interactions with the environment. The high structural diversity of this metabolite group is largely due to enzyme-mediated modifications of flavonoid core skeletons. In particular, glycosylation with different sugars is very common. In this study, the functions of the Arabidopsis thaliana glycoside hydrolase family 1-type glycosyltransferase proteins BGLU1, BGLU3 and BGLU4 were investigated, using a reverse genetics approach and untargeted metabolic fingerprinting. We screened for metabolic differences between A. thaliana wild type, loss-of-function mutants and overexpression lines and partially identified differentially accumulating metabolites, which are putative products and/or substrates of the BGLU enzymes. Our study revealed that the investigated BGLU proteins are glycosyltransferases involved in the glycosylation of already glycosylated flavonoids using different substrates. While BGLU1 appears to be involved in the rhamnosylation of a kaempferol diglycoside in leaves, BGLU3 and BGLU4 are likely involved in the glycosylation of quercetin glycosides in A. thaliana seeds. In addition, we present evidence that BGLU3 is a multifunctional enzyme that catalyzes other metabolic reactions with more complex substrates. This study deepens our understanding of the metabolic pathways and enzymes that contribute to the high structural diversity of flavonoids. HighlightThe proteins BGLU1, BGLU3 and BGLU4 are involved in glycosylations of different, already glycosylated flavonoids in Arabidopsis thaliana. BGLU3 appears to be multifunctional, acting on several complex substrates.

plant biology↗

bioRxiv2023

Conserved amino acid residues and gene expression patterns associated with the substrate preferences of the competing enzymes FLS and DFR

BackgroundFlavonoids, an important class of specialized metabolites, are synthesized from phenylalanine and present in almost all plant species. Different branches of flavonoid biosynthesis lead to products like flavones, flavonols, anthocyanins, and proanthocyanidins. Dihydroflavonols form the branching point towards the production of non-colored flavonols via flavonol synthase (FLS) and colored anthocyanins via dihydroflavonol 4-reductase (DFR). Despite the wealth of publicly accessible data, there remains a gap in understanding the mechanisms that mitigate competition between FLS and DFR for the shared substrate, dihydroflavonols. ResultsAn angiosperm-wide comparison of FLS and DFR sequences revealed the amino acids at positions associated with the substrate specificity in both enzymes. A global analysis of the phylogenetic distribution of these amino acid residues revealed that monocots generally possess FLS with Y132 (FLSY) and DFR with N133 (DFRN). In contrast, dicots generally possess FLSH and DFRN, DFRD, and DFRA. DFRA, which restricts substrate preference to dihydrokaempferol, previously believed to be unique to strawberry species, is found to be more widespread in angiosperms and has evolved independently multiple times. Generally, angiosperm FLS appears to prefer dihydrokaempferol, whereas DFR appears to favor dihydroquercetin or dihydromyricetin. Moreover, in the FLS-DFR competition, the dominance of one over the other is observed, with typically only one gene being expressed at any given time. ConclusionThis study illustrates how almost mutually exclusive gene expression and substrate-preference determining residues could mitigate competition between FLS and DFR, delineates the evolution of these enzymes, and provides insights into mechanisms directing the metabolic flux of the flavonoid biosynthesis, with potential implications for ornamental plants and molecular breeding strategies.

plant biology↗

bioRxiv2023

Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets

BackgroundSugar beet (Beta vulgaris subsp. vulgaris) and its crop wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNA sequences represent the fastest evolving parts of the genome, they likely impact genomic variability and contribute to the separation of beet gene pools. Hence, we investigated if innovations and losses in the repeatome can be linked to chromosomal differentiation and speciation. ResultsWe traced genome- and chromosome-wide evolution across sugar beet and twelve wild beets comprising all sections of the beet genera Beta and Patellifolia. For this, we combined data from short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive data framework for our beet panel that spans the complete scale from DNA sequence to chromosome up to the genome. Genome sizes and repeat profiles reflect the separation of the beet species into three gene pools. These gene pools harbor repeats with contrasting evolutionary patterns: We identified section- and species-specific repeat emergences and losses, e.g. of the retrotransposons causal for genome expansions in the section Corollinae/Nanae. Since most genomic variability was found in the satellite DNAs, we focused on tracing the 19 beetSat families across the three beet sections/genera. These taxa harbor evidence for contrasting strategies in repeat evolution, leading to contrasting satellite DNA profiles and fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia species to the formation of patchwork chromosomes in Corollinae/Nanae species. ConclusionsWe show that repetitive DNA sequences are causal for genome size expansion and contraction across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably among beet taxa, leading to the evolution of distinct chromosomal setups. These differences likely contribute to the barriers in beet breeding between the three gene pools. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genome variability, and chromosomal differentiation/evolution and provide a theoretical basis for understanding barriers in crop breeding.

genomics↗

bioRxiv2023

Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet

Most crop plants, including sugar beet (Beta vulgaris subsp. vulgaris), suffer from domestication bottlenecks and low genetic diversity caused by extensive selection for few traits. However, crop wild relatives (CWRs) harbour useful traits relevant for crop improvement, including enhanced adaptation to biotic and abiotic stresses. Especially polyploids are interesting from an evolutionary perspective as genes undergo reorganisation after the polyploidisation event. Through neo-and subfunctionalisation, novel functions emerge, which enable plants to cope with changing environments and extreme/harsh conditions. Particularly in the face of climate change, specific stress and pathogen resistances or tolerances gain importance. To introduce such traits into breeding material, CWRs have already been identified as an important source for sustainable breeding. The identification of genes underlying traits of interest is crucial for crop improvement. For beets, the section Corollinae contains the tetraploid species Beta corolliflora (2n=4x=36) that harbours salt and frost tolerances as well as a wealth of pathogen resistances. The number of beneficial traits of B. corolliflora is increased compared to those of the known diploids in this section (all 2n=2x=18). Nevertheless, neither the parental relationships of B. corolliflora have been resolved, nor are genomic resources available to steer sustainable, genomics-informed breeding. To benefit from the resources offered by polyploid beet wild relatives, we generated a comprehensive pangenome dataset including B. corolliflora, Beta lomatogona, and Beta macrorhiza, as well as a more distant wild beet Patellifolia procumbens (2n=2x=18). Joined analyses with publicly available genome sequences of two additional wild beets allowed the identification of genomic regions absent from cultivated beet, providing a sequence database harbouring traits relevant for future breeding endeavours. In addition, we present strong evidence for the parental relationship of the B. corolliflora wild beet as an autotetraploid emerging from B. macrorhiza.

genomics↗