Fate of a supergene in the shift from diploidy to polyploidy

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Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results Fate of a supergene in the shift from diploidy to polyploidy View ORCID Profile Emiliano Mora-Carrera , Narjes Yousefi , View ORCID Profile Giacomo Potente , View ORCID Profile Rebecca Lynn Stubbs , View ORCID Profile Barbara Keller , Étienne Léveillé-Bourret , View ORCID Profile Grob Stefan , Ferhat Celep , Giorgi Tedoradze , View ORCID Profile Elena Conti doi: https://doi.org/10.1101/2025.01.18.633704 Emiliano Mora-Carrera 1 Department of Systematic and Evolutionary Botany, University of Zurich , Zurich, Switzerland Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Emiliano Mora-Carrera For correspondence: emiliano.mora{at}systbot.uzh.ch elena.conti{at}systbot.uzh.ch Narjes Yousefi 1 Department of Systematic and Evolutionary Botany, University of Zurich , Zurich, Switzerland 2 Department of Evolutionary Biology and Environmental Studies, University of Zurich , Zurich, Switzerland Find this author on Google Scholar Find this author on PubMed Search for this author on this site Giacomo Potente 1 Department of Systematic and Evolutionary Botany, University of Zurich , Zurich, Switzerland Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Giacomo Potente Rebecca Lynn Stubbs 1 Department of Systematic and Evolutionary Botany, University of Zurich , Zurich, Switzerland Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Rebecca Lynn Stubbs Barbara Keller 1 Department of Systematic and Evolutionary Botany, University of Zurich , Zurich, Switzerland Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Barbara Keller Étienne Léveillé-Bourret 3 Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal , Québec H1X 2B2, Canada Find this author on Google Scholar Find this author on PubMed Search for this author on this site Grob Stefan 4 Université de Strasbourg, CNRS GMGM UMR 7156 , Strasbourg, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Grob Stefan Ferhat Celep 5 Department of Biology, Faculty of Engineering and Natural Sciences, Kırıkkale University , Kırıkkale, Turkey Find this author on Google Scholar Find this author on PubMed Search for this author on this site Giorgi Tedoradze 6 Department of Plant Systematics and Geography, Institute of Botany, Ilia State University , Tbilisi 0105, Georgia Find this author on Google Scholar Find this author on PubMed Search for this author on this site Elena Conti 1 Department of Systematic and Evolutionary Botany, University of Zurich , Zurich, Switzerland Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Elena Conti For correspondence: emiliano.mora{at}systbot.uzh.ch elena.conti{at}systbot.uzh.ch Abstract Full Text Info/History Metrics Preview PDF ABSTRACT Despite the evolutionary importance of supergenes, their properties in polyploids remain unexplored. Polyploid genomes are expected to undergo chromosomal rearrangements and gene losses over time, potentially affecting supergene architecture. The iconic distyly supergene ( S -locus), controlling a floral heteromorphism with two self-incompatible morphs, has been well-documented in diploids, but remains unknown in polyploids. Primula , the classic model for distyly since Darwin, is ancestrally diploid and distylous, yet polyploid, homostylous species with a single, self-compatible floral morph evolved repeatedly. The intraspecific loss of distyly is associated with small loss-of-function mutations in the S -locus CYP T gene controlling style length and female self-incompatibility. Over longer timescales, relaxed selection on CYP T should generate greater accumulation of larger mutations, including exon and gene loss. By analyzing the first assembled genome of an allotetraploid, homostylous species ( Primula grandis ) in a comparative framework, we discovered two, nearly identical S -locus alleles in the same subgenome, suggesting it originated via inter-specific hybridization between a homostylous and a distylous progenitor. Conformant to predictions from theory, the macroevolutionary loss of distyly coincided with considerable degeneration of CYP T , while other S -locus genes remained largely unaffected, suggesting the shift to homostyly preceded and facilitated polyploid establishment. At the whole-genome level, we found minimal subgenome dominance — as expected, given the inferred recent origin of P. grandis — and highly reduced genetic diversity, congruently with its narrow distribution and self-compatibility. This study provides the first comparison of a supergene across ploidy levels and reproductive systems, contributing new knowledge on the previously unknown fate of supergenes in polyploids. SIGNIFICANCE This study advances knowledge on genome evolution by elucidating how supergenes (clusters of tightly linked genes) evolve across species with different sets of chromosomes and reproductive systems. By analyzing the newly assembled genome of the polyploid, self-compatible Primula grandis in a broad framework, we provide the first comparison of the distyly supergene between diploid outcrossers and polyploid self-fertilizers. We discovered one pair of identical supergene alleles in the same subgenome, rather than one pair per subgenome, revealing the species originated via a cross between a self-compatible and a self-incompatible progenitor. Conformant to theory, the gene controlling female self-incompatibility and style length ( CYP T ) was considerably degenerated, because of relaxed selection over time, with the rest of the supergene largely unaffected. INTRODUCTION Transitions from diploidy to polyploidy and from outcrossing to selfing frequently co-occur in plants, attracting considerable attention from researchers across evolutionary biology and agronomy ( Soltis & Soltis, 1999 , 2000 ; Wendel & Cronn, 2003 ; Adams & Wendel, 2005 ; Igic et al ., 2006 ; Flagel & Wendel, 2009 ; Robertson et al ., 2011 ; Jiao et al ., 2011 ; Paterson et al ., 2012 ; van de Peer et al ., 2017 ; Nieto Feliner et al ., 2020 ; Yuan & Song, 2023 ). Selfing facilitates reproduction when mates are scarce, favoring the establishment of new polyploids and likely explaining why polyploids are often self-compatible ( Otto & Whitton, 2000 ; Barringer, 2007 ; Bachmann et al ., 2021 ; Novikova et al ., 2023 ). Primula L. (primroses) is an ideal system to study the above-mentioned transitions because it includes both diploid species that are typically self-incompatible outcrossers and polyploid species that can self-fertilize ( Richards, 2003 ). Primroses have served as a classic evolutionary model since Darwin’s ( Darwin, 1877 ) seminal studies on heterostyly, a floral heteromorphism characterized in Primula by two self-incompatible floral morphs: short-styled flowers (thrums) with short style and high anthers and long-styled flowers (pins) with long style and low anthers (i.e., distyly; Fig. 1a ). An adaptation for efficient cross-pollination and outcrossing, heterostyly evolved repeatedly in angiosperms ( Lloyd & Webb, 1992 ; Barrett, 2002 ; Naiki, 2012 ; Keller et al ., 2014 ; Armbruster et al ., 2017 ; Simón-Porcar et al ., 2024 ). This trait increases genetic variation and species resilience ( de Vos et al ., 2014a ) but requires mates and pollinators for reproduction. Conversely, homostyly — characterized by self-compatible, monomorphic flowers with anthers and stigma at the same level — enables selfing, thus decreasing genetic variation but affording reproduction when mates or pollinators are scarce ( de Vos et al ., 2012 , 2014b , 2018 ), for instance after long-distance dispersal or range expansion into uncolonized habitats ( Baker, 1955 ; Husband & Barrett, 1991 ). In Primula , homostyles typically have long style and high anthers ( Fig. 1a ). Phylogenetic analyses inferred the ancestor of the Primula clade (500+ spp.) to be distyslous and diploid ( de Vos et al ., 2014a ), while homostylous, likely allopolyploid taxa evolved repeatedly via secondary contact following Pleistocene glacial retreat ( Guggisberg et al ., 2006 , 2008 , 2009 ). Conversely, the autopolyploid origin of homostyles has rarely been proposed ( Dowrick, 1956 ). Download figure Open in new tab Fig. 1. Shift from diploid distyly to polyploid homostyly in Primula . a) Distylous and homostylous phenotypes and S -locus genotypes in diploid P. vulgaris . Top, from left to right: Short-styled (thrum) and long-styled (pin) flowers: reciprocal positioning of male and female sexual organs in the two floral morphs promotes cross-pollination (solid arrows), while self-incompatibility (SI) prevents selfing, thus heterostyly favors outcrossing. In Primula sect. Primula , the heterostyly S -locus is hemizygous and present exclusively in short-styled ( S /0) individuals, with CYP T determining short styles and female incompatibility; the S -locus is absent from long-styled ( 0 / 0 ) individuals. Bottom: Long-homostylous flower with high stigma and anthers in close proximity, favoring self-pollination; long-homostyles typically have two copies of the S -locus with a disrupted CYP T ( S* / S* ), enabling self-fertilization ( Mora-Carrera et al., 2023 ); b) Inflorescence and single flower of polyploid, homostylous P. grandis (pictures courtesy of Pam Eveleigh © 2011); c) Distribution map of P. grandis , endemic (dark green square) to the Caucasus mountain range (outlined in lighter green): two populations were sampled; d) Models for the expected number of S-loci in the presumably allotetraploid P. grandis: under Model-1 (inter-specific cross between a homostyle and a long-styled plant) only two alleles of the S -locus are expected in the same subgenome; under Model-2 (inter-specific cross between two homostyles) four alleles of the S -locus are expected, two per subgenome, with different (marked in red and blue for Species A and B, respectively) mutations between subgenomes; Model-1 is hypothesized to be more likely due to less stigma clogging by self-pollen in the long-styled flower. Arrows indicate the direction of pollination from anthers to stigma. Distyly is typically controlled by a hemizygous supergene present only in thrums but absent from pins ( Li et al ., 2016 ; Gutiérrez-Valencia et al ., 2022 ; Raimondeau et al ., 2024 ). Supergenes are groups of tightly linked genes inherited as a single unit due to suppressed recombination; they control multi-trait, balanced polymorphisms that are central to key evolutionary processes such as adaptation and reproduction ( Schwander et al ., 2014 ; Berdan et al ., 2022 ). The heterostyly (or distyly) supergene, also known as the S -locus, has been most thoroughly studied in Primula , where it comprises 4-5 genes called S -genes hereafter ( Li et al ., 2016 ; Huu et al ., 2020 ; Potente et al ., 2022a , 2024 ). Function has been experimentally characterized for only two of these genes: CYP T determines short style and female incompatibility, while GLO T determines high anthers in thrums of distylous primroses ( Fig. 1a ; Huu et al ., 2016 , 2020 ). Within the ancestrally distylous, diploid Primula vulgaris Huds., homostylous, self-compatible plants evolved repeatedly from self-incompatible thrums via different loss-of-function mutations in CYP T ( Mora-Carrera et al ., 2023 ). Primula vulgaris homostyles co-occurring with pins and thrums have either nonsynonymous mutations or small deletions in CYP T ; a large deletion comprising exon-1 was found only in homostyles from the single known monomorphic population. Due to self-fertilization, most homostyles of P. vulgaris have two, rather than one, disrupted CYP T copies ( Mora-Carrera et al ., 2024 ). Despite the above-mentioned infraspecific studies, the fate of CYP T and the heterostyly supergene in interspecific shifts to polyploid homostyly remains unknown. Theory predicts that, over macroevolutionary timescales, relaxed selection on genes associated with lost traits leads to the accumulation of extensive mutations, including large insertions and/or deletions, exon loss, or entire gene loss ( Collin & Miglietta, 2008 ; Lahti et al ., 2009 ). Once a gene loses its function, it becomes a pseudogene, a nonfunctional remnant of a gene that was once active ( Cheetham et al ., 2020 ). The fate of pseudogenes over time, including their potential loss, depends on environmental pressures, selection, pleiotropic effects, and the possibility of being repurposed for similar or other functions ( Cheetham et al ., 2020 ). Does extensive degradation and even loss of CYP T occur in interspecific shifts to homostyly, as predicted? Furthermore, theory predicts that polyploid genomes rediploidize over time, a process involving extensive chromosomal rearrangements and gene losses that could also affect the S -locus ( Li et al ., 2021 ). Does the transition from diploidy to polyploidy affect the organization and copy number of the heterostyly supergene? Overall, the impact of polyploidy on supergenes remains unknown. To fill these gaps of knowledge, we focus on the tetraploid Primula grandis Trautv. (2n=4x=22) because its biological characteristics and available resources are ideal to clarify the macroevolutionary consequences of shifts to polyploidy on supergenes ( Fig. 1b,c ). Primula grandis , narrowly endemic in the Caucasus region, is the only polyploid ( Brunn, 1932 ), homostylous, self-compatible species of Primula sect. Primula , a small, young clade (ca. 2.46 million years old; de Vos et al ., 2014a ) additionally comprising six diploid, heterostylous species all sharing the same base chromosome number (x=11; Richards, 2003 ). The conflicting placement of P. grandis in phylogenies inferred from few nuclear and chloroplast DNA loci ( Schmidt-Lebuhn et al ., 2012 ) and Whole Genome Sequencing (WGS) data ( Stubbs et al ., 2023 ) suggests an allotetraploid origin, but this hypothesis has never been tested via the assembly and analysis of its entire genome. Genome assemblies are available for two diploid, heterostylous relatives of P. grandis : a high-resolution, chromosome-scale assembly for Primula veris L. ( Potente et al ., 2022a ) and a fragmented draft assembly for P. vulgaris ( Cocker et al ., 2018 ). Furthermore, extensive WGS data from all species of Primula sect. Primula are available ( Stubbs et al ., 2023 , 2024 ). By integrating analyses of the here assembled, annotated genome of P. grandis with newly and previously generated WGS data in a broad comparative framework, we provide the first study of the fate of the hemizygous heterostyly supergene in a polyploid genomic background. We test the two main models for the expected number of S -loci in a homostylous, presumed allotetraploid species ( Fig. 1d ). If the species stemmed from a cross between a homostyle and a long-styled plant, two nearly homozygous alleles of the S -locus with the same disruptive mutations in CYP T are expected in the same subgenome (Model-1). If the species stemmed from a cross between two homostyles, four copies of the S -locus — two nearly homozygous alleles per subgenome with likely different disruptive CYP T mutations between subgenomes — are expected (Model-2). Importantly, homostyles are cross-compatible with long-styled but not short-styled plants, limiting the possibilities for the initial cross generating a polyploid, homostylous species ( Lewis & Jones, 1992 ). We also test the prediction that the interspecific loss of heterostyly is associated with degradation and possibly loss of CYP T but has little or no effect on the remaining S -genes. Furthermore, given the young age of the Primula sect. Primula clade and the phylogenetically proposed allopolyploid origin of P. grandis ( Schmidt-Lebuhn et al ., 2012 ; Stubbs et al ., 2023 ), we hypothesize its genome to comprise two distinct subgenomes scarcely affected by rediploidization and subgenome dominance, as predicted by theory ( Wendel, 2015 ; Feng et al ., 2024 ). We then test whether any extant species served as progenitors of P. grandis by inferring genome-wide phylogenies of Primula sect. Primula . Additionally, theory predicts that polyploid speciation should cause strong genetic bottlenecks ( Stebbins, 1950 ) leading to sharp decrease of genome-wide genetic diversity and reduced efficacy of purifying selection ( Hough et al ., 2013 ). Finally, genetic redundancy associated with polyploidization should relax selection on duplicated genes ( Ohno, 1970 ). We test the above predictions on P. grandis via demographic and population genomic analyses across Primula sect. Primula . The here-presented first genome assembly of a tetraploid, homostylous species, analyzed within a comparative genomic framework, contributes new knowledge on the genomics of shifts between ploidy levels and breeding systems and the previously unknown fate of supergenes in polyploid genomes. RESULTS Chromosome-scale assembly of P. grandis tetraploid genome The size of the P. grandis tetraploid genome estimated via flow-cytometry (898 Mb) was about twice (x 1.9) that of the closely related diploid P. veris and P. vulgaris (452 and 430 Mb, respectively; Cocker et al ., 2018 ; Potente et al ., 2022a ). To assemble a high-quality reference genome for P. grandis , long- and short-read sequences were combined with Hi-C data for scaffolding ( Figs. S1 , S2 , S3 ). The size of the assembled genome (768.24 Mb; N50 = 32.92 Mb; Fig. 2a ) fell between the sizes estimated via k -mer analysis of short-reads (697.70 Mb) and flow cytometry (∼898 Mb; Fig. S4 ). The high repetitive content (∼52%; Fig. S8 ) of the P. grandis genome might explain the bioinformatic underestimation of genome size. The BUSCO completeness score (94.4%) supported the completeness of the genome assembly ( Fig. S5 ). The final assembly produced 2134 scaffolds, of which 22 encompassed 743.54 Mb (96.78%) of the total assembly size, corresponding to the 22 chromosomes of P. grandis ( Fig. 2a, b ). The gene annotation identified 40,882 protein-coding genes distributed along the 22 chromosome-scale scaffolds ( Table S2 ). Download figure Open in new tab Fig. 2. Genome assembly and subgenome characterization of the tetraploid, homostylous Primula grandis . a) Summary statistics of the P. grandis genome assembly and gene annotation. b) Circos plot of the P. grandis chromosome-scale genome assembly showing the 22 largest scaffolds assigned to subgenome A and B, in red and blue, respectively; distributions of Transposable Elements (TE) and gene density along each chromosome are represented in yellow and green, respectively; the purple rectangle in chromosome 1B indicates the position of the S -locus. c) Collinearity analyses between the 11 chromosomes each in subgenomes A and B of P. grandis and the 11 chromosomes of P. veris : the S -locus (marked by a yellow triangle) is found exclusively in subgenome B of P. grandis and in the same chromosome (ch. 1) in both P. grandis and P. veris . d) Density distributions of divergence at synonymous sites ( Ks ) of paralogous gene copies between P. veris and both subgenomes of P. grandis . Dotted lines indicate peaks in the distribution of Ks with estimated divergence times between species in Million years ago (Mya). Crown age of Primula sect. Primula (∼2.46 million years ago; de Vos et al., 2014) is marked by a yellow triangle. Download figure Open in new tab Fig. 3. Characteristics of the S -locus supergene in a polyploid genome. a) Microsynteny analysis showing high collinearity between Primula veris and P. grandis S -loci: the grey lines between S -loci connect the exons of each of the fives S-genes ( CCM T , GLO T , CYP T , PUM T , and KFB T ); the length of the S -locus is 276kbp in P. veris and 229 kbp in P. grandis ; in both species the S -locus is flanked by two copies of the CFB gene on each side. b) Coverage analysis showing no changes across the S -locus and its up- and down-stream 200 kbp flanking regions in subgenome-B of P. grandis ; plot shows 10 kb windowed average sequencing coverage of the S -locus (y-axis) based on Whole Genome Resequencing (WGR) data from 10 P. grandi s individuals; horizontal grey dashed line indicates average sequencing depth across chromosome-1 of P. grandis subgenome-B (average = 17.59); vertical black dashed lines indicate genomic limits of S -locus. c) Selection and transcription analyses in P. grandis S -genes: Length (in basepairs, bp) per gene, estimates of nucleotide diversity (π), number of non-synonymous polymorphic sites (pN), number of synonymous polymorphic sites (pS), number of non-synonymous fixed sites (dN), number of synonymous fixed sites (dS), significance values of McDonald-Kreitman tests (MK-test pval), and Direction of Selection (DoS, with negative values indicating accumulation of slightly deleterious mutations); Expression levels in leaf, floral bud, and flower tissues of P. grandis expressed as Reads Per Kilobase per Million (RPKM); *indicates pseudogene; NA=Not Applicable. d) Structure of functional CYP T S -gene (1587 bp long, five exons with bp length in white) in P. veris and disrupted CYP T pseudogene (1068 bp recovered, exon 3 missing, insertions and deletions in exons 1, 2, 4) in P. grandis . Green and red circles indicate synonymous and non-synonymous mutations in each exon when compared to P. veris CYP T . Exon and intron sizes are not to scale. Subgenomes characteristics The k -mer-specific analysis of repetitive elements enabled the assignment of the 22 chromosome-scale scaffolds to two clearly distinct subgenomes (subgenomes-A and -B, hereafter; Fig. S6 ), each containing 11 chromosomes ( Fig. 2b ) that were highly collinear with the 11 chromosomes of P. veris ( Figs. 2c, S7, S8 ). Subgenomes-A and -B comprised 380.64 Mb and 362.90 Mb, respectively, and the 17.73 Mb size-difference between subgenomes was evenly distributed along the 11 homoeologous chromosomes ( Table S2 ). Annotation of repetitive elements revealed that subgenome-A comprised a slightly higher proportion of TEs than subgenome-B (45.63% vs. 40.95%, respectively; Fig. S9 ). Furthermore, subgenome-A had a lower number of genes (19,976 vs . 20,906, respectively; Table S2 ) and lower gene density than subgenome-B ( Fig. S10 ). Transcriptome analyses indicated minor homoeolog-expression bias (HEB) towards subgenome-B in leaves (n sub_a =245 vs n sub_b 278 gene pairs), floral buds (n sub_a 235 vs n sub_b 258 gene pairs), and flowers (n sub_a 276 vs n sub_b 316 gene pairs) ( Fig. S11 ). Estimates of genome-wide divergence at synonymous (syn) sites ( Ks ) between subgenomes-A and -B showed a peak at Ks =0.04, corresponding to a divergence time of ∼3.56 Mya (CI=3.91-3.31 Mya; Fig. 2d ). Furthermore, Ks values of P. veris vs. subgenomes-A and -B, respectively, were 0.04 and 0.02, corresponding to divergence times of ∼3.54 Mya (CI=3.88-3.28 Mya) between subgenome-A and P. veris and ∼1.94 Mya (CI=2.13-1.80 Mya) between subgenome-B and P. veris ( Fig. 2d ) . Characteristics of the S-locus in the tetraploid P. grandis To identify the P. grandis S -locus, we used BLAST to screen the P. grandis genome for the five S -genes and the four CFB genes flanking the S -locus ( CFB TL1 and CFB TL2 on the left and CFB TR1 and CFB TR2 on the right) in P. veris ( Fig. 3a ). These nine genes were found in a ∼229-kb region — characterized by a high-density of TEs — of chromosome 1 in subgenome-B ( Fig. 2b ) in the same order and orientation as in P. veris ( Fig. 3a ). Synteny analyses showed that collinearity between P. veris and P. grandis extended well beyond the S -locus in chromosome 1 ( Fig. 2c ). Coverage analysis of the P. grandis genome using WGS data indicated that the S -locus is present in both haplotypes (i.e., non-hemizygous) of chromosome 1B ( Fig. 3b ). Nucleotide diversity in P. grandis S -genes was zero in CCM T , GLO T and CYP T and very low in PUM T (1 nonsynonymous and 0 synonymous polymorphic sites) and KFB T (2 nonsynonymous and 0 synonymous polymorphic sites; Fig. 3c ), indicating low S -locus differentiation in the young, self-compatible, narrow Caucasus endemic P. grandis . Sequence comparisons between the CCM T , GLO T , PUM T , and KFB T S -genes of the homostylous P. grandis and those of the heterostylous P. veris detected no loss-of-function mutations for any of these genes in the former species. Indeed, the four genes were all transcribed, hence presumably functional, in P. grandis floral buds ( Fig. 3c ). The highest accumulation of nonsynonymous mutations (15) among the four genes above occurred in PUM T , compared to only 3 synonymous mutations ( Fig. 3c ). Furthermore, McDonald-Kreitman (MK) tests comparing S -genes between P. grandis and P. veris (which could not be performed on CCM T , GLO T and CYP T due to absence of polymorphic and/or fixed sites) did not detect significantly reduced efficacy of purifying selection on P. grandis PUM T and KFB T ( Fig. 3c ). Direction of Selection (DoS) analyses, also applicable only to PUM T and KFB T , revealed low accumulation of slightly deleterious mutations in these two genes. Finally, we found evidence of extensive degeneration in P. grandis CYP T via the accumulation of the following segmental and point mutations compared to the functional P. veris gene( Fig. 3d ): two insertions (a 1648bp insertion in exon-1 and a 3bp insertion in exon-2); two large deletions (loss of exon-3 and loss of 279 bps in exon-4); and 16 nonsynonymous mutations (four in exon-1, three in exon-2, one in exon-4, and eight in exon-5; Table S3 ). Congruently, CYP T was not expressed in leaf, floral-bud or flower transcriptomes ( Fig. 3d ), confirming CYP T pseudogenization in P. grandis . No variation was found in CYP T pseudogene of 10 P. grandis individuals. The total length of P. grandis CYP T pseudogene was ca 58 Kb, the cumulative length of its exons was 1068 bp ( Fig. 3d ). Concurrent bottlenecks in both P. grandis subgenomes The results of the stairway plots indicated that both P. grandis subgenomes had reduced effective population size, implying recent bottlenecks ( Fig. S12 ). Furthermore, model-based coalescent demographic analyses with fastsimcoal2 supported overlapping genetic bottlenecks in subgenomes-A and -B ( Fig. S13) (T BOT =25,054 [95% CI: 20,726-29,382] and T BOT =20021 [95% CI:15,830-24,211] generations ago, respectively; Fig. 4a ), implying that the two subgenomes came together via allopolyploid speciation 31,660-58,764 ybp, assuming 2 years generation time for P. grandis ( Fig. 4a ). The bottlenecks were confirmed by more positive Tajima’s D values for both P. grandis subgenomes compared to other diploid species of Primula sect. Primula sampled from the Caucasus, except for P. renifolia , suggesting a bottleneck also in this species ( Fig. 4b ). Download figure Open in new tab Fig. 4. Origin of Primula grandis and its subgenomes. a) Best-supported demographic models inferred with coalescent simulations (see Materials and Methods; Fig. S13) showing the estimated times (with 95% Confidence Intervals) of divergence between P. veris and subgenomes-A (left) and -B (right) of P. grandis (T DIV ) reported in years before present (ybp), assuming two-year generation time for P. grandis , and of the genetic bottleneck in each subgenome (T BOT ); N e indicates effective population size. b) Distribution of Tajima’s D estimates for P. grandis subgenomes-A and -B (red and blue, respectively), P. vulgaris (pink), P. veris (green), P. renifolia (yellow), P. megaseifolia (turquoise), and P. elatior (orange). Black lines within distributions denote median values of Tajima’s D; positive Tajima’s D values indicate genetic contraction, negative values indicate population expansion. c) Tanglegram of genome-wide Maximum Likelihood (ML) phylogenies inferred from collinear orthologues showing the relationships of P. grandis subgenomes-A and -B (red and blue, respectively) within Primula sect. Primula . Species codes are as follows: P. elatior ( Pela_cordi = P. elatior_ subsp. cordifolia, Pela_ela=P. elatior subsp. elatior, Pela_ela=P. elatior subsp. leucophylla, Pela_palla=P. elatior subsp. pallasi, and Pela_pseudo=P. elatior subsp. pseudoelatior ); Pintri=P. intricata; Pmey=P. meyeri; P. veris ( Pver_col=P. veris subsp. columnae, Pver_macro=P. veris subsp. macrocalyx , Pver_ver=P. veris subsp. veris ); Primula vulgaris ( Pvul_hetero=P. vulgaris subsp. heterochroma and Pvul_vul = P. vulgaris subsp. vulgaris ); Pgrandis=P. grandis, Pmega=P. megaseifolia, Pjul=P. juliae and Preni=P. renifolia . Outgroups outside Primula sect. Primula are not shown. Nodal bootstrap support (BS) values lower than 100% are reported; all other nodes received 100% BS. See Fig. S14 for complete phylogenies. Origin of the allopolyploid P. grandis Phylogenetic analyses revealed that subgenomes-A and -B from 10 individuals of P. grandis formed two strongly supported monophyletic groups ( Fig. S14) . Subgenome-A was strongly supported as sister to the remaining members of the Primula sect. Primula clade and subgenome-B was weakly supported as sister to the clade comprising Primula renifolia Volgunov, Primula elatior subsp. elatior , Primula intricata , and Primula meyeri ( Figs. 4C , S15 ), suggesting a more recent origin of P. grandis subgenome-B than subgenome-A, consistently with the divergence times estimated above ( Fig. 2d ). Population genomic consequences of polyploidization in P. grandis Primula grandis had the lowest genome-wide diversity, as estimated by S syn , and π syn , of the Primula sect. Primula species in the Caucasus, except for P. renifolia ( Fig. 5a ). Within P. grandis , both subgenomes showed similar values of nucleotide diversity (mean π syn ± sd; 0.0008 ± 0.001 and 0.0008 ± 0.001 for subgenomes-A and -B, respectively; Fig. 5a ). Furthermore, LD decay in P. grandis was slower than in P. vulgaris, P. veris , and P. megaseifolia , but faster than in P. renifolia and P. elatior from Caucasus ( Fig. S15 ). The volcano plots based on MK-tests indicate that both subgenomes of P. grandis had significantly more genes with negative values of Direction of Selection (DoS) than the genomes of diploid relatives ( Fig. 5b ). Within P. grandis , subgenome-A had eight more genes with significantly less efficient purifying selection (i.e., DoS 0) than subgenome-B. Finally, when one gene was under relaxed selection in one subgenome, its homoeologous copy in the other subgenome appeared to be constrained by selection ( Table S4 ). Download figure Open in new tab Fig. 5. Genetic diversity and selection in the tetraploid, homostylous Primula grandis . a) Summary of individuals per species of Primula sect. Primula sampled in the Caucasus and genome-wide diversity estimates including number of segregating sites (S syn ), pairwise nucleotide diversity (π syn ) at synonymous (4-fold degenerate) sites, and the ratio π of non-synonymous (non-syn; 0-fold degenerate) to synonymous sites. All values, except S syn , represent the genome-wide average over 50,000 non-overlapping windows; b) Volcano plots based on MK-tests depicting the direction of selection (DoS) in four diploid species of Primula sect. Primula and the tetraploid P. grandis [subgenome-A and subgenome-B]; negative DoS values indicate accumulation of slightly deleterious mutations, positive values indicate accumulation of slightly beneficial mutations; DoS values of zero (red line) indicate neutral mutations. Gene transcripts with significant (log 10 P = 2 in the Y-axis; P <0.01) deviation from neutrality based on MK-tests are marked by black dots; grey dots indicate non-significant deviation from neutrality in MK-tests. Primula veris was used as outgroup for the MK-test (see Material and Methods). DISCUSSION Despite the evolutionary importance of supergenes, their characteristics in polyploid genomes remain unknown. Over time, polyploid genomes are expected to undergo extensive chromosomal rearrangements and gene losses ( Li et al ., 2021 ), raising questions about supergene organization and copy number in polyploids. By focusing on the heterostyly supergene, the present study enabled the first comparison of a supergene across ploidy levels and reproductive systems. While well-characterized in diploid genomes of several heterostylous ( Cocker et al ., 2018 ; Shore et al ., 2019 ; Potente et al ., 2022a ; Gutiérrez-Valencia et al ., 2022 ; Fawcett et al ., 2023 ; Raimondeau et al ., 2024 ; Potente et al ., 2024 ) and one homostylous species ( Gutiérrez-Valencia, 2024 ), its structure in polyploid genomes was unknown. In the tetraploid, homostylous P. grandis , we found the same five S -genes (with CYP T pseudogenized) in the same order, orientation, and chromosome (chr.1) as in the diploid, heterostylous P. veris ( Fig. 3b ; Potente et al ., 2022a ) and P. vulgaris ( Li et al ., 2016 ), although the P. grandis S -locus was slightly smaller (229 Kb vs 278Kb and 260 Kb, respectively). Conversely, the distantly related, diploid, heterostylous Primula edelbergii has a larger S -locus (633 Kb), containing only four genes (with CCM T missing) in a different order and chromosome (chr.6; Potente et al ., 2024 ). These findings reveal that the organization of the S -locus in Primula is conserved across closely related species regardless of ploidy level and reproductive strategy, while diverging across larger evolutionary timescales. The number, divergence, and subgenomic location of S -locus copies offer insights about the original cross giving origin to allopolyploid, homostylous species. We discovered that the tetraploid P. grandis contains only two nearly homozygous S -locus alleles in subgenome-B ( Figs. 2 , 3 ), rather than two distinct pairs (one per subgenome) of S -locus alleles (Models 1 and 2 in Fig. 1d ). The minimal divergence and occurrence of the two S -locus alleles within the same subgenome suggest that P. grandis originated from an interspecific cross between a homostylous pollen-donor and a long-styled pollen-recipient, rather than between two homostylous parents (Models 1 and 2, respectively, in Fig. 1d ). Indeed, it is expected that the stigmas of long-styled flowers are more likely to be fertilized by heterospecific pollen from homostyles because they are less clogged by self-pollen (Model 1, Fig. 1 ; Barrett, 2002 ; Keller et al ., 2014 ). Moreover, pollen of homostyles should retain the compatibility characteristics of short-styled flowers, making it cross-compatible with long-styled stigmas. Conversely, crosses between homostyles and short-styled plants should be incompatible, as both are expected to produce pollen with the same incompatibility type ( Wedderburn & Richards, 1992 ). Indeed, experimental crosses between homostyles and long-styled plants were found to produce more seeds than crosses between homostyles of different Primula species ( Wedderburn & Richards, 1992 ). Importantly, the progeny of an allopolyploid cross between a homostyle and a long-styled plant inherit disrupted CYP T , enabling reproduction via selfing of the newly formed polyploids and species establishment. Lastly, research on Brassicaceae demonstrates that the loss of homomorphic, multi-allelic self-incompatibility in one progenitor facilitates reproduction and the establishment of new allopolyploids ( Novikova et al ., 2023 ), which aligns with our findings supporting the hypothesis that P. grandis originated from a self-compatible homostyle and a long-styled plant. Theoretical research on relaxed selection has mainly focused on the loss of phenotypic traits ( Lahti et al ., 2009 ), rather than on their controlling genes (but see Somel et al ., 2013 ; Zheng et al ., 2022 ). Heterostyly, an adaptation for outcrossing, is often lost when mates or pollinators are scarce ( Barrett, 2019 ). At the microevolutionary scale, loss of heterostyly within P. vulgaris was associated with different loss-of-function mutations in CYP T , including nonsynonymous mutations, small deletions and insertions in homostyles ( Mora-Carrera et al ., 2023 , 2024 ). At the macroevolutionary scale, the S -locus of the young homostylous P. grandis (estimated age: 31,660-58,764 years; Fig. 4a ) retains the CYP T pseudogene, but with extensive mutations, including the loss of exon-3, more than half of exon-4, and a 1648-bp deletion in exon-1 ( Fig. 3d ). Thus, evidence supports the conclusion that, as predicted from theory, relaxed selection on CYP T pseudogene allows for the accumulation of increasingly larger structural mutations in interspecific losses of heterostyly. Not surprisingly, P. grandis CYP T also accumulated the largest number (24) of point-mutations of all S -genes compared to P. veris ( Fig. 3b, c ). Contrariwise, no or very few such mutations were found in CCM T , GLO T , and KFB T ( Fig. 3c ). The only other S -gene with high numbers of point mutations was PUM T , with 15 nonsynonymous vs three synonymous mutations compared to P. veris ( Fig. 3c ). This result aligns with previously reported high ratios of divergence at nonsynonymous to synonymous sites in PUM T of P. veris and P. edelbergii ( Potente et al ., 2022a , 2024 ) suggesting relaxed selection on this gene. The low expression levels in both leaves and young floral buds of PUM T in the homostylous P. grandis ( Fig. 3c ) and in the heterostylous P. vulgaris , P. veris , and P. edelbergii ( Cocker et al ., 2018 ; Potente et al ., 2022b , 2024 ) call into question whether PUM T plays a role in controlling any heterostylous trait. Functional analyses of this gene are necessary to elucidate this question. Altogether, the evidence supports the conclusion that the macroevolutionary loss of heterostyly is associated with pseudogenization and degeneration of CYP T , as predicted, while the rest of the S -locus remains largely unaffected. As comparative genomic analyses of trait-controlling genes expand, further insights into the complex interplay among repeated trait loss, relaxed selection, pseudogenization, and the dynamics of gene loss versus rescue will continue to emerge ( Collin & Miglietta, 2008 ; Schrader et al ., 2021 ; Jones et al ., 2023 ; Moran et al ., 2023 ). Elucidating the origin and evolution of polyploids has long been a major goal of evolutionary biology and agronomy, but progress was hindered by the difficulty of sequencing polyploid genomes. The recent advent of Hi-C technology has facilitated the assembly and phasing of polyploid genomes, especially in crop plants, but also in non-model organisms ( Burton et al ., 2013 ; The International Wheat Genome Sequencing Consortium (IWGSC) et al ., 2014 ; Sun et al ., 2022 ; Peng et al ., 2022 ; Ma et al ., 2023 ). Indeed, Hi-C scaffolding enabled the high-quality assembly of the 22 chromosomes of the tetraploid P. grandis ( Figs. 2 , S2 ). The clear assignment of the 22 chromosomes to two distinct subgenomes ( Figs. 2 , S6 ), high collinearity between them ( Figs. 2C , S8 ), and recent origin (∼32,000-59,000 years ago) estimated for P. grandis ( Fig. 4a ) are consistent with the expectation of minimal genomic rearrangements in recently formed allopolyploids ( Wendel et al ., 2016 ; Mason & Wendel, 2020 ; Yuan & Song, 2023 ). Furthermore, the slightly higher number of genes ( Table S2 ), higher gene density ( Fig. S10 ), and minor expression bias of subgenome-B ( Fig. S11 ) — estimated to be younger than subgenome-A ( Fig. 2d ) — point to marginal dominance of subgenome-B over subgenome-A. Altogether, the evidence suggests that P. grandis is a recent allopolyploid with two distinct subgenomes showing low levels of rediploidization and subgenome dominance. As more high-quality polyploid and diploid genome assemblies of related species become available, they will help clarify the interactions among species age, rediploidization, and subgenome dominance ( Schiavinato et al ., 2021 ; He et al ., 2021 ; Feng et al ., 2024 ; Ma et al ., 2024 ). Key questions on polyploidy include the identification of parental origins of allopolyploid, self-compatible species and patterns of polymorphism and selection on their genomes. Our genome-wide phylogenetic analyses placed P. grandis subgenome-A as sister to the rest of Primula sect. Primula ( Fig. 4c ), consistently with its older estimated age ( Figs. 2d , 4a ), and subgenome-B as sister to a shallower clade comprising the Caucasus endemic P. renifolia and Caucasus populations of P. elatior , consistently with its younger estimated age. However, no extant diploid species were identified as possible progenitors of P. grandis ( Fig. 4c ). These findings are consistent with the incongruent relationships of P. grandis in previous phylogenetic analyses of a few nuclear and chloroplast genes ( Schmidt-Lebuhn et al ., 2012 ) and genome-wide WGS data ( Stubbs et al ., 2023 ). As expected from theory, we found that the allopolyploid speciation event that gave origin to the self-compatible P. grandis was associated with a shared, recent (∼32,000–59,000 years ago) genetic bottleneck affecting both its subgenomes ( Figs. 4a, b, S12 ). Indeed, both subgenomes of P. grandis had the lowest genome-wide diversity of all Primula sect. Primula species, except for the narrow Caucasus endemic P. renifolia ( Figs. 4 , 5 ). Also as expected, MK-test analyses indicated that both subgenomes of P. grandis have reduced efficacy of purifying selection compared to heterostylous, diploid closely related species. Furthermore, the redundancy of polyploid genomes is thought to relax selection, allowing for the accumulation of slightly deleterious and beneficial mutations more readily than in diploids ( Ohno, 1970 ; Comai, 2005 ; van de Peer et al ., 2017 ; Paape et al ., 2018 ). Conformingly, the subgenomes of P. grandis accumulated significantly more mutations of both types compared to closely related, diploid genomes ( Fig. 5b ). Genes under significantly less efficient purifying selection were found exclusively in the subgenomes of the tetraploid P. grandis , but not in the diploid genomes of Primula sect. Primula ( Fig. 5b ). Consistent with the younger age and inferred marginal dominance of subgenome-B, subgenome-A harbored both more deleterious and beneficial mutations, with only two genes under less efficient purifying selection in subgenome-B versus nine in subgenome-A ( Fig. 5b ). While there is no strong evidence of rediploidization or marked subgenome dominance, genomic redundancy has allowed slightly deleterious and beneficial mutations to accumulate. Whether redundancy will foster adaptation and long-term resilience in this homostylous, narrow endemic species remains an open question. MATERIALS AND METHODS Genome-size estimation, DNA and RNA isolation and sequencing Genome size was estimated via flow cytometry in three P. grandis individuals according to Potente et al. (2022a) . Additionally, we estimated the genome size using k -mer frequency spectra from raw long-read sequencing (see below) with GenomeScope 2.0 ( Ranallo-Benavidez et al ., 2020 ). To generate sequencing libraries, DNA was extracted from flash-frozen leaves of one individual following a modified CTAB protocol ( Potente et al ., 2022a ). Paired End (PE) 150bp reads were generated via Whole Genome Sequencing (WGS) with Illumina (∼45x coverage) at Functional Genomics Center Zurich (FGCZ, Switzerland). Additionally, long-read sequencing was performed on one PromethION flow cell at FGCZ and three MinION f Mk1B flow cells in-house, achieving a combined ∼35x coverage. Long reads were basecalled with Guppy v.6.0.1 specifying the Super accurate (SUP) model. A Hi-C library was prepared following the protocol by Grob et al. ( Grob et al ., 2014 ), then sequenced on Illumina NovaSeq 6000 (PE 150bp reads; ∼375x coverage) at FGCZ. Transcriptomes from leaves, flowers and floral buds of a single individual were obtained using the Spectrum Plant Total RNA Kit (Sigma-Aldrich). Subsequently, TruSeq Stranded mRNA libraries were prepared and sequenced on NovaSeq 6000 at FGCZ, generating ∼120 million PE 150bp reads per sample. Genome assembly and annotation Genome assembly was performed with MaSuRCa v.4.0.5 ( Zimin et al ., 2017 ); Hi-C reads were mapped to the resulting reference genome using BWA ( Li & Durbin, 2009 ) and scaffolded with YaHS v.1.2a.1 ( Zhou et al ., 2023 ); Hi-C contact map visualization and manual curation of mis-assemblies were achieved with JuiceBox ( Durand et al ., 2016 ). Primula grandis chromosome-sized scaffolds were ordered and named based on collinearity with P. veris scaffolds. A set of protein sequences for homology-based annotation was prepared by merging the OrthoDB protein data set for Viridiplantae (odb10) with a high-quality P. veris protein set that excluded monoexonic genes as performed by Potente et al. (2024) . Then, Braker3 was used to annotate the genome using the RNA-seq alignment file. We ran BUSCO v4.0.6 ( Manni et al ., 2021 ) on the coding sequences of P. grandis using the eudicot database (odb10) to assess gene-annotation completeness. Identification and annotation of repetitive elements was performed using Extensive De novo TE Annotator (EDTA) v1.9.2 ( Ou et al ., 2019 ), as in Potente et al. (2024) (SI Appendix). Subgenome characterization If P. grandis is allotetraploid, as proposed by previous phylogenetic analyses ( Schmidt-Lebuhn et al ., 2012 ; Stubbs et al ., 2023 ), it should contain two distinct subgenomes. We tested this prediction by using subgenome-specific k -mers-analyses of LTRs implemented in SubPhaser v.1.2.6 ( Jia et al ., 2022 ). To test for subgenome dominance, we checked for Homoeologous Expression Bias (HEB) towards one of the subgenomes of P. grandis as follows. First, we aligned transcriptomic data from leaves, flowers and floral buds to the reference genome using Bowtie2 v2.3.4.3 ( Langmead & Salzberg, 2012 ). Secondly, the number of aligned reads mapping to each gene was counted using htseq-count v2.0.5 ( Putri et al ., 2022 ) to estimate Reads Per Kilobase per Million (RPKM). Thirdly, HEB was estimated as the log 2 difference between RPKM of homoeologs from subgenome-A and -B, respectively, using −3 ≤ log 2 HEB ≥ 3 (i.e., 8-fold HEB bias towards either subgenome-A or -B) as significance threshold ( Smith et al ., 2019 ). Finally, we estimated the divergence times between P. grandis subgenomes and between each P. grandis subgenome and P. veris genome via the estimation of genome-wide divergence at synonymous sites ( Ks ) (see SI appendix). To infer absolute ages for genome divergence among subgenomes, we used the neutral substitution rate of 6.15 × 10 −9 substitutions per synonymous site per year previously determined for P. veris ( Potente et al ., 2022a ). S -locus identification and tests of selection on S -genes To discover whether the S -locus is found in only one or both subgenomes of P. grandis and identify its genomic location, structure and organization, we performed microsynteny analyses of P. veris S -locus against the P. grandis reference genome using MCscan ( Tang et al ., 2008 ). To determine the number of S -locus copies in the P. grandis genome, we estimated sequencing coverage analysis of the S -locus and its up- and down-stream regions using WGS data from 10 P. grandis individuals (see below). To assess whether the loss of heterostyly in P. grandis is associated with S -genes degeneration, their sequences were extracted from the reference genome using bedtools v2.29.2 ( Quinlan & Hall, 2010 ) and aligned to the coding sequences of functional P. veris S -genes using the MUSCLE alignment algorithm as implemented in MEGA X ( Kumar et al ., 2018 ). Moreover, to determine the levels of S -locus genetic diversity, we estimated nucleotide diversity (π) in all S -genes (SI Appendix) of ten P. grandis individuals (see below). Finally, to ascertain whether selection on P. grandis S -genes is relaxed, we performed McDonald-Kreitman (MK) tests by comparing the S-genes of ten P. grandis individuals with those of six P. veris individuals (see below; SI appendix). Comparative genome-wide analyses To perform comparative genomic analyses, we used a WGS data set comprising 10 newly sequenced individuals of the Caucasian endemic P. grandis and 80 previously sequenced individuals from the Caucasus of the six diploid species in Primula sect. Primula ( P. veris subsp . macrocalyx , P. vulgaris subsp . vulgaris, P. elatior subsp . pallasi , P. megaseifolia , P. renifolia ; ( Stubbs et al ., 2023 ); Table S1; SI Appendix). First, reads were trimmed with Trimmomatic v0.38 ( Bolger et al ., 2014 ). Secondly, the reads of each individual were mapped once to each subgenome of P. grandis separately using BWA-mem v7.17 ( Li & Durbin, 2009 ). This latter decision was taken due to the fact that the above species are diploid, whereas the newly assembled genome is tetraploid. Therefore all subsequent analyses were performed separately for each subgenome. Then, variant calling was performed using the functions mpileup and call included in BCFtools v1.8 ( Danecek et al ., 2021 ). Variant sites were filtered with VCFtools v0.1.14 ( Danecek et al ., 2011 ) and BCFtools. Demographic analyses - To test the expectation that polyploid speciation is associated with a genetic bottleneck, we inferred single-population demographic histories of P. grandis using Stairway Plot v2 ( Liu & Fu, 2020 ). Furthermore, to estimate the timing of the genetic bottleneck expected with P. grandis speciation, we performed model-based coalescent simulations of demographic changes with fastmsimcoal2 v2.7 ( Excoffier et al ., 2021 ) using 2D-Site Frequency Spectrum (2D-SFS; see SI Appendix). Finally, we compared the demographic history of P. grandis subgenomes-A and -B with its relatives in Primula sect. Primula by estimating genome-wide distributions of Tajima’s D in all species. Phylogenetic analyses - To determine whether any extant species in Primula sect. Primula served as progenitors of P. grandis, we first identified collinear orthologs shared between both subgenomes of P. grandis and the assembled genome of P. veris using MCscan (github.com/tanghaibao/jcvi/wiki/Mcscan-(Python-version); ( Tang et al ., 2008 )). Using the concatenated ortholog dataset, we then inferred the Maximum Likelihood (ML) phylogeny of Primula sect. Primula using IQ-TREE v.2.1.2 ( Nguyen et al ., 2015 ) and estimated statistical support for each node with 1000 ultrafast bootstraps (BS) ( Minh et al ., 2013 ; Chernomor et al ., 2016 ). Population genomic analyses and genome-wide tests of selection - To test the expectations of genome-wide reduced genetic diversity and increased Linkage Disequilibrium (LD) associated with polyploid-speciation and shift to self-compatibility, we compared the number of segregating sites (S), and nucleotide diversity (π) at both synonymous and non-synonymous sites using the python script ‘popgenWindows.py’ ( https://github.com/simonhmartin/genomics_general ) and LD decay using popLDdecay (Zhang et al., 2019) across the genomes of the tetraploid, homostylous P. grandis vs. its diploid, heterostylous relatives in Primula sect. Primula ( Fig. 5a ; see SI appendix). To test the hypothesis of genome-wide relaxed selection due to increased genetic redundancy in polyploid genomes, we compared the strength and Direction of Selection (DoS) in the genes of each P. grandis subgenome vs. its diploid relatives using the McDonald-Kreitman (MK) tests as implemented in degenotate.py ( https://github.com/harvardinformatics/degenotate ; SI appendix). DATA AVAILABILITY Raw sequencing data (long-read and short-read sequencing and Hi-C data) for the genome assembly of P. grandis will be uploaded to the NCBI SRA upon acceptance. at The 90 whole genome sequences used in this study are deposited in SRA (BioProject ID: PRJNA1066534). Code and R scripts used to run the programs and create figures will be available in ( https://github.com/EmilianoMora/primula_grandis_project ). ACKNOWLEDGEMENTS We thank the Functional Genomics Center UZH for help during library preparation. This research was supported by the Swiss National Science Foundation grant nos. 3100-061674.00/1 and 31003A_175556 to EC. REFERENCES ↵ Adams KL , Wendel JF . 2005 . Polyploidy and genome evolution in plants . Current Opinion in Plant Biology 8 : 135 – 141 . OpenUrl CrossRef PubMed Web of Science ↵ Armbruster WS , Bolstad GH , Hansen TF , Keller B , Conti E , Pélabon C . 2017 . The measure and mismeasure of reciprocity in heterostylous flowers . New Phytologist 215 : 906 – 917 . OpenUrl CrossRef PubMed ↵ Bachmann JA , Tedder A , Fracassetti M , Steige KA , Lafon-Placette C , Köhler C , Slotte T . 2021 . On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae) . Heredity 127 : 124 – 134 . OpenUrl CrossRef PubMed ↵ Baker HG . 1955 . Self-Compatibility and Establishment After ‘Long-Distance’ Dispersal . Evolution 9 : 347 – 349 . OpenUrl CrossRef Web of Science ↵ Barrett SCH . 2002 . Sexual interference of the floral kind . Heredity 88 : 154 – 159 . OpenUrl CrossRef PubMed Web of Science ↵ Barrett SCH . 2019 . ‘A most complex marriage arrangement’: recent advances on heterostyly and unresolved questions . New Phytologist 224 : 1051 – 1067 . OpenUrl CrossRef PubMed ↵ Barringer BC . 2007 . Polyploidy and self-fertilization in flowering plants . American Journal of Botany 94 : 1527 – 1533 . OpenUrl Abstract / FREE Full Text ↵ Berdan EL , Flatt T , Kozak GM , Lotterhos KE , Wielstra B . 2022 . Genomic architecture of supergenes: connecting form and function . Philosophical Transactions of the Royal Society B: Biological Sciences 377 : 20210192 . OpenUrl CrossRef PubMed ↵ Bolger AM , Lohse M , Usadel B . 2014 . Trimmomatic: a flexible trimmer for Illumina sequence data . Bioinformatics 30 : 2114 – 2120 . OpenUrl CrossRef PubMed Web of Science ↵ Brunn HG . 1932 . Cytological studies in Primula with special with special reference to the relation between the karyology and taxonomy of the genus . Symbolae Botanicae Upsalienses 1 : 3 – 239 . OpenUrl ↵ Burton JN , Adey A , Patwardhan RP , Qiu R , Kitzman JO , Shendure J . 2013 . Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions . Nature Biotechnology 31 : 1119 – 1125 . OpenUrl CrossRef PubMed ↵ Cheetham SW , Faulkner GJ , Dinger ME . 2020 . Overcoming challenges and dogmas to understand the functions of pseudogenes . Nature Reviews Genetics 21 : 191 – 201 . OpenUrl CrossRef PubMed ↵ Chernomor O , Von Haeseler A , Minh BQ. 2016 . Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices . Systematic Biology 65 : 997 – 1008 . OpenUrl CrossRef PubMed ↵ Cocker JM , Wright J , Li J , Swarbreck D , Dyer S , Caccamo M , Gilmartin PM . 2018 . Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene . Scientific Reports 8 : 17942 . OpenUrl CrossRef PubMed ↵ Collin R , Miglietta MP . 2008 . Reversing opinions on Dollo’s Law . Trends in Ecology & Evolution 23 : 602 – 609 . OpenUrl CrossRef PubMed ↵ Comai L . 2005 . The advantages and disadvantages of being polyploid . Nature Reviews Genetics 6 : 836 – 846 . OpenUrl CrossRef PubMed Web of Science ↵ Danecek P , Auton A , Abecasis G , Albers CA , Banks E , DePristo MA , Handsaker RE , Lunter G , Marth GT , Sherry ST , et al. 2011 . The variant call format and VCFtools . Bioinformatics 27 : 2156 – 2158 . OpenUrl CrossRef PubMed Web of Science ↵ Danecek P , Bonfield JK , Liddle J , Marshall J , Ohan V , Pollard MO , Whitwham A , Keane T , McCarthy SA , Davies RM , et al. 2021 . Twelve years of SAMtools and BCFtools . GigaScience 10 : giab008 . OpenUrl CrossRef PubMed ↵ Darwin C . 1877 . The different forms of flowers on plants of the same species . Chicago, USA : University of Chicago Press . ↵ Dowrick V . 1956 . Heterostyly and homostyly in Primula obconica . Heredity 10 : 219 – 236 . OpenUrl CrossRef ↵ Durand NC , Robinson JT , Shamim MS , Machol I , Mesirov JP , Lander ES , Aiden EL . 2016 . Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom . Cell Systems 3 : 99 – 101 . OpenUrl CrossRef PubMed ↵ Excoffier L , Marchi N , Marques DA , Matthey-Doret R , Gouy A , Sousa VC . 2021 . fastsimcoal2 : demographic inference under complex evolutionary scenarios (R Schwartz, Ed.) . Bioinformatics 37 : 4882 – 4885 . OpenUrl CrossRef PubMed ↵ Fawcett JA , Takeshima R , Kikuchi S , Yazaki E , Katsube-Tanaka T , Dong Y , Li M , Hunt HV , Jones MK , Lister DL , et al. 2023 . Genome sequencing reveals the genetic architecture of heterostyly and domestication history of common buckwheat . Nature Plants 9 : 1236 – 1251 . OpenUrl CrossRef PubMed ↵ Feng X , Chen Q , Wu W , Wang J , Li G , Xu S , Shao S , Liu M , Zhong C , Wu C-I , et al. 2024 . Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication . Nature Communications 15 : 1635 . OpenUrl CrossRef PubMed ↵ Flagel LE , Wendel JF . 2009 . Gene duplication and evolutionary novelty in plants . New Phytologist 183 : 557 – 564 . OpenUrl CrossRef PubMed Web of Science ↵ Grob S , Schmid MW , Grossniklaus U . 2014 . Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila . Molecular Cell 55 : 678 – 693 . OpenUrl CrossRef PubMed ↵ Guggisberg A , Baroux C , Grossniklaus U , Conti E . 2008 . Genomic Origin and Organization of the Allopolyploid Primula egaliksensis Investigated by in situ Hybridization . Annals of Botany 101 : 919 – 927 . OpenUrl CrossRef PubMed ↵ Guggisberg A , Mansion G , Conti E . 2009 . Disentangling Reticulate Evolution in an Arctic–Alpine Polyploid Complex . Systematic Biology 58 : 55 – 73 . OpenUrl CrossRef PubMed ↵ Guggisberg A , Mansion G , Kelso S , Conti E . 2006 . Evolution of biogeographic patterns, ploidy levels, and breeding systems in a diploid–polyploid species complex of Primula . New Phytologist 171 : 617 – 632 . OpenUrl CrossRef PubMed Web of Science ↵ Gutiérrez-Valencia J . 2024 . Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum . Molecular Biology and Evolution 41 . ↵ Gutiérrez-Valencia J , Fracassetti M , Berdan EL , Bunikis I , Soler L , Dainat J , Kutschera VE , Losvik A , Désamoré A , Hughes PW , et al. 2022 . Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level . Current Biology 32 : 4360 – 4371 .e6. OpenUrl CrossRef PubMed ↵ He Z , Ji R , Havlickova L , Wang L , Li Y , Lee HT , Song J , Koh C , Yang J , Zhang M , et al. 2021 . Genome structural evolution in Brassica crops . Nature Plants 7 : 757 – 765 . OpenUrl CrossRef PubMed ↵ Hough J , Williamson RJ , Wright SI . 2013 . Patterns of Selection in Plant Genomes . Annual Review of Ecology, Evolution, and Systematics 44 : 31 – 49 . OpenUrl CrossRef ↵ Husband BC , Barrett SCH . 1991 . Colonization history and population genetic structure of Eichhornia paniculata in Jamaica . Heredity 66 : 287 – 296 . OpenUrl CrossRef Web of Science ↵ Huu CN , Kappel C , Keller B , Sicard A , Takebayashi Y , Breuninger H , Nowak MD , Bäurle I , Himmelbach A , Burkart M , et al. 2016 . Presence versus absence of CYP734A50 underlies the style-length dimorphism in primroses . eLife 5 : e17956 . OpenUrl CrossRef PubMed ↵ Huu CN , Keller B , Conti E , Kappel C , Lenhard M . 2020 . Supergene evolution via stepwise duplications and neofunctionalization of a floral-organ identity gene . Proceedings of the National Academy of Sciences 117 : 23148 – 23157 . OpenUrl Abstract / FREE Full Text ↵ Igic B , Bohs L , Kohn JR . 2006 . Ancient polymorphism reveals unidirectional breeding system shifts . Proceedings of the National Academy of Sciences 103 : 1359 – 1363 . OpenUrl Abstract / FREE Full Text ↵ Jia K , Wang Z , Wang L , Li G , Zhang W , Wang X , Xu F , Jiao S , Zhou S , Liu H , et al. 2022 . SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k -mers . New Phytologist 235 : 801 – 809 . OpenUrl CrossRef PubMed ↵ Jiao Y , Wickett NJ , Ayyampalayam S , Chanderbali AS , Landherr L , Ralph PE , Tomsho LP , Hu Y , Liang H , Soltis PS , et al. 2011 . Ancestral polyploidy in seed plants and angiosperms . Nature 473 : 97 – 100 . OpenUrl CrossRef PubMed Web of Science ↵ Jones BM , Rubin BER , Dudchenko O , Kingwell CJ , Traniello IM , Wang ZY , Kapheim KM , Wyman ES , Adastra PA , Liu W , et al. 2023 . Convergent and complementary selection shaped gains and losses of eusociality in sweat bees . Nature Ecology & Evolution 7 : 557 – 569 . OpenUrl CrossRef PubMed ↵ Keller B , Thomson JD , Conti E . 2014 . Heterostyly promotes disassortative pollination and reduces sexual interference in Darwin’s primroses: evidence from experimental studies . Functional Ecology 28 : 1413 – 1425 . OpenUrl CrossRef ↵ Kumar S , Stecher G , Li M , Knyaz C , Tamura K . 2018 . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms (FU Battistuzzi, Ed.) . Molecular Biology and Evolution 35 : 1547 – 1549 . OpenUrl CrossRef PubMed ↵ Lahti DC , Johnson NA , Ajie BC , Otto SP , Hendry AP , Blumstein DT , Coss RG , Donohue K , Foster SA . 2009 . Relaxed selection in the wild . Trends in Ecology & Evolution 24 : 487 – 496 . OpenUrl CrossRef PubMed ↵ Langmead B , Salzberg SL . 2012 . Fast gapped-read alignment with Bowtie 2 . Nature Methods 9 : 357 – 359 . OpenUrl CrossRef PubMed ↵ Lewis D , Jones DA . 1992 . The genetics of heterostyly . In: Evolution and Function of Heterostyly . Springer-Verlag Berlin Heidelberg GmbH . ↵ Li J , Cocker JM , Wright J , Webster MA , McMullan M , Dyer S , Swarbreck D , Caccamo M , Oosterhout CV , Gilmartin PM . 2016 . Genetic architecture and evolution of the S locus supergene in Primula vulgaris . Nature Plants 2 : 16188 . OpenUrl CrossRef PubMed ↵ Li H , Durbin R . 2009 . Fast and accurate short read alignment with Burrows–Wheeler transform . Bioinformatics 25 : 1754 – 1760 . OpenUrl CrossRef PubMed Web of Science ↵ Li Z , McKibben MTW , Finch GS , Blischak PD , Sutherland BL , Barker MS . 2021 . Patterns and Processes of Diploidization in Land Plants . Annual Review of Plant Biology 72 : 387 – 410 . OpenUrl CrossRef PubMed ↵ Liu X , Fu Y-X . 2020 . Stairway Plot 2: demographic history inference with folded SNP frequency spectra . Genome Biology 21 : 280 . OpenUrl CrossRef PubMed ↵ Lloyd DG , Webb CJ . 1992 . The selection of heterostyly . In: Evolution and Function of Heterostyly . New York, USA : Springer-Verlag Berlin Heidelberg GmbH . ↵ Ma P-F , Liu Y-L , Guo C , Jin G , Guo Z-H , Mao L , Yang Y-Z , Niu L-Z , Wang Y-J , Clark LG , et al. 2024 . Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance . Nature Genetics 56 : 710 – 720 . OpenUrl CrossRef PubMed ↵ Ma L , Liu K-W , Li Z , Hsiao Y-Y , Qi Y , Fu T , Tang G-D , Zhang D , Sun W-H , Liu D-K , et al. 2023 . Diploid and tetraploid genomes of Acorus and the evolution of monocots . Nature Communications 14 : 3661 . OpenUrl CrossRef PubMed ↵ Manni M , Berkeley MR , Seppey M , Zdobnov EM . 2021 . BUSCO: Assessing Genomic Data Quality and Beyond . Current Protocols 1 : e323 . OpenUrl CrossRef ↵ Mason AS , Wendel JF . 2020 . Homoeologous Exchanges, Segmental Allopolyploidy, and Polyploid Genome Evolution . Frontiers in Genetics 11 : 1014 . OpenUrl CrossRef PubMed ↵ Minh BQ , Nguyen MAT , Von Haeseler A. 2013 . Ultrafast Approximation for Phylogenetic Bootstrap . Molecular Biology and Evolution 30 : 1188 – 1195 . OpenUrl CrossRef PubMed Web of Science ↵ Mora-Carrera E , Stubbs RL , Keller B , Léveillé-Bourret É , De Vos JM , Szövényi P , Conti E. 2023 . Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species . Molecular Ecology 32 : 61 – 78 . OpenUrl CrossRef ↵ Mora-Carrera E , Stubbs RL , Potente G , Yousefi N , Keller B , De Vos JM , Szövényi P , Conti E. 2024 . Genomic analyses elucidate S -locus evolution in response to intra-specific losses of distyly in Primula vulgaris . Ecology and Evolution 14 : e10940 . OpenUrl CrossRef ↵ Moran RL , Richards EJ , Ornelas-García CP , Gross JB , Donny A , Wiese J , Keene AC , Kowalko JE , Rohner N , McGaugh SE . 2023 . Selection-driven trait loss in independently evolved cavefish populations . Nature Communications 14 : 2557 . OpenUrl CrossRef PubMed ↵ Naiki A . 2012 . Heterostyly and the possibility of its breakdown by polyploidization . Plant Species Biology 27 : 3 – 29 OpenUrl CrossRef Web of Science ↵ Nguyen L-T , Schmidt HA , Von Haeseler A , Minh BQ. 2015 . IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies . Molecular Biology and Evolution 32 : 268 – 274 . OpenUrl CrossRef PubMed ↵ Nieto Feliner G , Casacuberta J , Wendel JF . 2020 . Genomics of Evolutionary Novelty in Hybrids and Polyploids . Frontiers in Genetics 11 : 792 . OpenUrl CrossRef PubMed ↵ Novikova PYu , Kolesnikova UK , Scott AD. 2023 . Ancestral self-compatibility facilitates the establishment of allopolyploids in Brassicaceae . Plant Reproduction 36 : 125 – 138 . OpenUrl CrossRef PubMed ↵ Ohno S . 1970 . Evolution by gene duplication . New York, USA : Springer-Verlag New York Inc . ↵ Otto SP , Whitton J . 2000 . Polyploid incidence and evolution . Annual Review of Genetics 34 : 401 – 437 . OpenUrl CrossRef PubMed Web of Science ↵ Ou S , Su W , Liao Y , Chougule K , Agda JRA , Hellinga AJ , Lugo CSB , Elliott TA , Ware D , Peterson T , et al. 2019 . Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline . Genome Biology 20 : 275 . OpenUrl CrossRef PubMed ↵ Paape T , Briskine RV , Halstead-Nussloch G , Lischer HEL , Shimizu-Inatsugi R , Hatakeyama M , Tanaka K , Nishiyama T , Sabirov R , Sese J , et al. 2018 . Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica . Nature Communications 9 : 3909 . OpenUrl CrossRef PubMed ↵ Paterson AH , Wendel JF , Gundlach H , Guo H , Jenkins J , Jin D , Llewellyn D , Showmaker KC , Shu S , Udall J , et al. 2012 . Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres . Nature 492 : 423 – 427 . OpenUrl CrossRef PubMed Web of Science ↵ van de Peer Y , Mizrachi E , Marchal K. 2017 . The evolutionary significance of polyploidy . Nature Reviews Genetics 18 : 411 – 424 . OpenUrl CrossRef PubMed ↵ Peng R , Xu Y , Tian S , Unver T , Liu Z , Zhou Z , Cai X , Wang K , Wei Y , Liu Y , et al. 2022 . Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons . Proceedings of the National Academy of Sciences 119 : e2208496119 . OpenUrl CrossRef PubMed ↵ Potente G , Léveillé-Bourret É , Yousefi N , Choudhury RR , Keller B , Diop SI , Duijsings D , Pirovano W , Lenhard M , Szövényi P , et al. 2022a . Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism . Molecular Biology and Evolution 39 : msac035 . OpenUrl CrossRef PubMed ↵ Potente G , Stubbs RL , Yousefi N , Pirovano W , Szövényi P , Conti E . 2022b . Comparative transcriptomics reveals commonalities and differences in the genetic underpinnings of a floral dimorphism . Scientific Reports 12 : 20771 . OpenUrl CrossRef PubMed ↵ Potente G , Yousefi N , Keller B , Mora-Carrera E , Szövényi P , Conti E. 2024 . The Primula edelbergii S -locus is an example of a jumping supergene . Molecular Ecology Resources 24 : e13988 . OpenUrl CrossRef ↵ Putri GH , Anders S , Pyl PT , Pimanda JE , Zanini F . 2022 . Analysing high-throughput sequencing data in Python with HTSeq 2.0 (V Boeva, Ed.) . Bioinformatics 38 : 2943 – 2945 . OpenUrl CrossRef PubMed ↵ Quinlan AR , Hall IM . 2010 . BEDTools: a flexible suite of utilities for comparing genomic features . Bioinformatics 26 : 841 – 842 . OpenUrl CrossRef PubMed Web of Science ↵ Raimondeau P , Ksouda S , Marande W , Fuchs A-L , Gryta H , Theron A , Puyoou A , Dupin J , Cheptou P-O , Vautrin S , et al. 2024 . A hemizygous supergene controls homomorphic and heteromorphic self-incompatibility systems in Oleaceae . Current Biology : S0960982224003695 . ↵ Ranallo-Benavidez TR , Jaron KS , Schatz MC . 2020 . GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes . Nature Communications 11 : 1432 . OpenUrl CrossRef PubMed ↵ Richards J . 2003 . Primula . Portland, USA : Timber Press . ↵ Robertson K , Goldberg EE , Igić B . 2011 . Comparative evidence for the correlated evolution of polyploidy and self-compatibility in Solanaceae: polyploidy and self-compatibility . Evolution 65 : 139 – 155 . OpenUrl CrossRef PubMed Web of Science ↵ Schiavinato M , Bodrug-Schepers A , Dohm JC , Himmelbauer H. 2021 . Subgenome evolution in allotetraploid plants . The Plant Journal 106 : 672 – 688 . OpenUrl CrossRef PubMed ↵ Schmidt-Lebuhn AN , de Vos JM , Keller B , Conti E. 2012 . Phylogenetic analysis of Primula section Primula reveals rampant non-monophyly among morphologically distinct species . Molecular Phylogenetics and Evolution 65 : 23 – 34 . OpenUrl CrossRef PubMed ↵ Schrader L , Pan H , Bollazzi M , Schiøtt M , Larabee FJ , Bi X , Deng Y , Zhang G , Boomsma JJ , Rabeling C . 2021 . Relaxed selection underlies genome erosion in socially parasitic ant species . Nature Communications 12 : 2918 . OpenUrl CrossRef PubMed ↵ Schwander T , Libbrecht R , Keller L . 2014 . Supergenes and Complex Phenotypes . Current Biology 24 : R288 – R294 . OpenUrl CrossRef PubMed ↵ Shore JS , Hamam HJ , Chafe PDJ , Labonne JDJ , Henning PM , McCubbin AG . 2019 . The long and short of the S -locus in Turnera (Passifloraceae) . New Phytologist 224 : 1316 – 1329 . OpenUrl CrossRef PubMed ↵ Simón-Porcar V , Escudero M , Santos-Gally R , Sauquet H , Schönenberger J , Johnson SD , Arroyo J . 2024 . Convergent evolutionary patterns of heterostyly across angiosperms support the pollination-precision hypothesis . Nature Communications 15 : 1237 . OpenUrl CrossRef PubMed ↵ Smith RD , Kinser TJ , Smith GDC , Puzey JR . 2019 . A likelihood ratio test for changes in homeolog expression bias . BMC Bioinformatics 20 : 149 . OpenUrl CrossRef PubMed ↵ Soltis DE , Soltis PS . 1999 . Polyploidy: recurrent formation and genome evolution . Trends in Ecology & Evolution 14 : 348 – 352 . OpenUrl CrossRef PubMed ↵ Soltis PS , Soltis DE . 2000 . The role of genetic and genomic attributes in the success of polyploids . Proceedings of the National Academy of Sciences 97 : 7051 – 7057 . OpenUrl Abstract / FREE Full Text ↵ Somel M , Wilson Sayres MA , Jordan G , Huerta-Sanchez E , Fumagalli M , Ferrer-Admetlla A , Nielsen R . 2013 . A Scan for Human-Specific Relaxation of Negative Selection Reveals Unexpected Polymorphism in Proteasome Genes . Molecular Biology and Evolution 30 : 1808 – 1815 . OpenUrl CrossRef PubMed ↵ Stebbins GL . 1950 . Variation and evolution in plants . New York, USA : Columbia University Press . ↵ Stubbs RL , Theodoridis S , Mora-Carrera E , Keller B , Potente G , Yousefi N , Jay P , Léveillé-Bourret É , Choudhury RR , Celep F , et al. 2024 . The genomes of Darwin’s primroses reveal chromosome-scale adaptive introgression and differential permeability of species boundaries . New Phytologist 241 : 911 – 925 . OpenUrl CrossRef PubMed ↵ Stubbs RL , Theodoridis S , Mora-Carrera E , Keller B , Yousefi N , Potente G , Léveillé-Bourret É , Celep F , Kochjarová J , Tedoradze G , et al. 2023 . Whole-genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot . New Phytologist 237 : 656 – 671 . OpenUrl CrossRef PubMed ↵ Sun H , Jiao W-B , Krause K , Campoy JA , Goel M , Folz-Donahue K , Kukat C , Huettel B , Schneeberger K . 2022 . Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar . Nature Genetics 54 : 342 – 348 . OpenUrl CrossRef PubMed ↵ Tang H , Wang X , Bowers JE , Ming R , Alam M , Paterson AH . 2008 . Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps . Genome Research 18 : 1944 – 1954 . OpenUrl Abstract / FREE Full Text ↵ The International Wheat Genome Sequencing Consortium (IWGSC) , Mayer KFX , Rogers J , Doležel J , Pozniak C , Eversole K , Feuillet C , Gill B , Friebe B , Lukaszewski AJ , et al. 2014 . A chromosome-based draft sequence of the hexaploid bread wheat ( Triticum aestivum ) genome . Science 345 : 1251788 . OpenUrl Abstract / FREE Full Text ↵ de Vos JM , Hughes CE , Schneeweiss GM , Moore BR , Conti E. 2014a . Heterostyly accelerates diversification via reduced extinction in primroses . Proceedings of the Royal Society B: Biological Sciences 281 : 20140075 . OpenUrl CrossRef PubMed ↵ de Vos JM , Keller B , Isham ST , Kelso S , Conti E. 2012 . Reproductive implications of herkogamy in homostylous primroses: variation during anthesis and reproductive assurance in alpine environments (T Ashman, Ed.) . Functional Ecology 26 : 854 – 865 . OpenUrl CrossRef Web of Science ↵ de Vos JM , Keller B , Zhang L-R , Nowak MD , Conti E. 2018 . Mixed Mating in Homostylous Species: Genetic and Experimental Evidence from an Alpine Plant with Variable Herkogamy, Primula halleri . International Journal of Plant Sciences 179 : 87 – 99 . OpenUrl CrossRef ↵ de Vos JM , Wüest RO , Conti E. 2014b . Small and ugly? Phylogenetic analyses of the “selfing syndrome” reveal complex evolutionary fates of monomorphic primrose flowers: evaluating the selfing syndrome in Primroses . Evolution 68 : 1042 – 1057 . OpenUrl CrossRef PubMed ↵ Wedderburn FM , Richards AJ . 1992 . Secondary homostyly in Primula L.; evidence for the model of the ‘S’ supergene . New Phytologist 121 : 649 – 655 . OpenUrl CrossRef Web of Science ↵ Wendel JF . 2015 . The wondrous cycles of polyploidy in plants . American Journal of Botany 102 : 1753 – 1756 . OpenUrl FREE Full Text ↵ Wendel JF , Cronn RC . 2003 . Polyploidy and the evolutionary history of cotton . In: Advances in Agronomy . Elsevier , 139 – 186 . ↵ Wendel JF , Jackson SA , Meyers BC , Wing RA . 2016 . Evolution of plant genome architecture . Genome Biology 17 : 37 . OpenUrl CrossRef PubMed ↵ Yuan J , Song Q . 2023 . Polyploidy and diploidization in soybean . Molecular Breeding 43 : 51 . OpenUrl CrossRef PubMed ↵ Zheng Z , Hua R , Xu G , Yang H , Shi P . 2022 . Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat . BMC Biology 20 : 44 . OpenUrl CrossRef PubMed ↵ Zhou C , McCarthy SA , Durbin R. 2023 . YaHS: yet another Hi-C scaffolding tool (C Alkan, Ed.) . Bioinformatics 39 : btac808 . OpenUrl CrossRef PubMed ↵ Zimin AV , Puiu D , Luo M-C , Zhu T , Koren S , Marçais G , Yorke JA , Dvořák J , Salzberg SL . 2017 . Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii , a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm . Genome Research 27 : 787 – 792 . OpenUrl Abstract / FREE Full Text View the discussion thread. Back to top Previous Next Posted January 22, 2025. Download PDF Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. You are going to email the following Fate of a supergene in the shift from diploidy to polyploidy Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website. Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Share Fate of a supergene in the shift from diploidy to polyploidy Emiliano Mora-Carrera , Narjes Yousefi , Giacomo Potente , Rebecca Lynn Stubbs , Barbara Keller , Étienne Léveillé-Bourret , Grob Stefan , Ferhat Celep , Giorgi Tedoradze , Elena Conti bioRxiv 2025.01.18.633704; doi: https://doi.org/10.1101/2025.01.18.633704 Share This Article: Copy Citation Tools Fate of a supergene in the shift from diploidy to polyploidy Emiliano Mora-Carrera , Narjes Yousefi , Giacomo Potente , Rebecca Lynn Stubbs , Barbara Keller , Étienne Léveillé-Bourret , Grob Stefan , Ferhat Celep , Giorgi Tedoradze , Elena Conti bioRxiv 2025.01.18.633704; doi: https://doi.org/10.1101/2025.01.18.633704 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Evolutionary Biology Subject Areas All Articles Animal Behavior and Cognition (7635) Biochemistry (17691) Bioengineering (13892) Bioinformatics (41937) Biophysics (21452) Cancer Biology (18589) Cell Biology (25504) Clinical Trials (138) Developmental Biology (13378) Ecology (19899) Epidemiology (2067) Evolutionary Biology (24320) Genetics (15609) Genomics (22506) Immunology (17736) Microbiology (40394) Molecular Biology (17181) Neuroscience (88605) Paleontology (666) Pathology (2832) Pharmacology and Toxicology (4824) Physiology (7641) Plant Biology (15156) Scientific Communication and Education (2045) Synthetic Biology (4294) Systems Biology (9825) Zoology (2271)