Biology subjects

Edger, P. P.

Publications and source records attributed to Edger, P. P..

At least 19 recordsLinked to original sources

bioRxiv2026

Chromosome-scale genome assembly of the North American invasive Asteraceae, Tanacetum vulgare (common tansy)

Common tansy (Tanacetum vulgare), a significant agricultural invasive species, threatens forage productivity, livestock carrying capacity, and plant biodiversity across North American agroecosystems. Despite being a close relative to the ornamental Asteraceae Chrysanthemum, T. vulgare genomic studies are severely lacking, but remain critical to the development of novel weed management tools and the investigation of plant invasion evolution. In this study, we performed the assembly and annotation of the diploid genome (2n=2x=18) of an invasive North American T. vulgare genotype using long-read PacBio HiFi and Iso-Seq sequencing technology. The assembled haplotype genome comprised 9 pseudomolecules with a total size of ~4.8 Gb and a scaffold N50 of 546 Mb. In addition, both the plastid and mitochondrial genome sequences were assembled. BUSCO analysis revealed a high overall genome completeness with 69,343 predicted protein-coding genes (AED<0.6: 98%). A high-quality North American invasive reference T. vulgare genome, complementing a recent one assembled for a native European accession, is critical for the investigation of plant invasion biology, genome evolution, and the future development of novel genetic biocontrol weed management technologies.

genomics↗

bioRxiv2026

Landrace and bred accessions of allotetraploid sour cherry (Prunus cerasus L.) reveal variation in subgenome dosage and subgenome expression bias

Subgenome dominance is a phenomenon observed in many allopolyploids where one parental genome exhibits stronger influence over phenotype than the other parental genomes. This may present as preferential retention of one subgenome through fractionation, replacement via homoeologous exchange, or as subgenome expression bias, where one subgenome is expressed at a higher abundance compared to other subgenomes. Sour cherry (Prunus cerasus) is an allotetraploid fruit tree species resulting from an interspecific cross between extant relatives of ground cherry (P. fruticosa) and sweet cherry (P. avium). Prior comparative genomic analyses suggest that the sour cherry cultivar Montmorency contains three subgenomes. Subgenomes A and A, each present in one copy, are derived from a P. fruticosa-like ancestor, and B, present in two copies, is derived from a P. avium-like ancestor. In this study we investigated the subgenome dynamics of the three subgenomes of sour cherry in four diverse landraces and two cultivars, including Montmorency. We found evidence of 26 homoeologous exchange events and five whole-homoeolog replacements relative to Montmorency in three of the six accessions. We also detected subgenome expression bias favoring the A and A subgenomes over the B subgenome, the magnitude of which differs between accessions and changes over the course of fruit development. Lastly, we show differences in dosage variation and expression bias of four previously-described genes in Montmorency associated with fruit softening, a key trait in this crop. These findings on subgenome dominance offer valuable insights into how this phenomenon may influence traits important for sour cherry breeding.

genetics↗

bioRxiv2025

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome

O_LIEukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. However, harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and utilize genetic diversity. C_LIO_LIHere, we explore seven complete genomes of the emerging biofuel crop pennycress (Thlaspi arvense) drawn from across the speciess current genetic diversity to catalogue variation in genome structure and content. C_LIO_LIAcross this new pangenome resource, we find contrasting evolutionary modes in different genomic regions. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. In contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions, even in fast-evolving immune genes where microsynteny breaks down across species but the macrosynteny of gene cluster positioning is maintained. C_LIO_LIOur findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows rearrangement and presence-absence variation on a local scale. This diversity is invisible to classical reference-based approaches and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop. C_LI

genomics↗

bioRxiv2025

Chromosome-scale genome assembly for Yellow Wood sorrel, Oxalis stricta

Yellow wood sorrel (Oxalis stricta L.), also known as sourgrass, juicy fruit, or sheep weed, is a member of the Oxalidaceae family. Yellow wood sorrel is commonly considered a weed and while native to North America, it is distributed across Europe, Asia, and Africa. To date, only two other genomes from the Oxalidaceae family have been published, star fruit (Averrhoa carambola L.) and Oxalis articulata Savingy. Here, we present a chromosome-scale assembly for O. stricta, revealing its allotetraploid nature and synteny within its two subgenomes as well as synteny with A. carambola and O. articulata. Using Oxford Nanopore Technologies long-read sequences coupled with chromatin capture sequencing, we generated a 436 Mb chromosome-scale assembly of O. stricta with a scaffold N50 length of 36.2 Mb that is anchored to 12 chromosomes across the two subgenomes. Assessment of the final genome assembly using the Long Terminal Repeat Assembly Index yielded a score of 13.12 and assessment of Benchmarking Universal Single Copy Orthologs revealed 99.3% complete orthologs; both metrics are suggestive of a high-quality reference genome. Total repetitive sequence content in the O. stricta genome was 39.7% with retroelements being the largest class of transposable elements. Annotation of protein-coding genes yielded 61,550 high confidence genes encoding 115,089 gene models. Synteny between the two O. stricta subgenomes was present in 91 syntenic blocks containing 40,705 genes, of which, 76.6% were present in 1:1 syntenic relationships between the two subgenomes. The availability of an annotated chromosome-scale high quality genome assembly for O. stricta will provide a launching point to understand the high fecundity of this weed and provide further foundation for comparative genomics within the Oxalidaceae.

genomics↗

bioRxiv2024

Late Quaternary climatic impact on the woodland strawberry genome: a perennial herb's tale

Exploring a species paleohistory is crucial for understanding its responsiveness to climatic events, identifying drivers of adaptation, and developing effective biodiversity conservation strategies in the face of ongoing climate change. We analyzed 200 genomes of the perennial herb woodland strawberry (Fragaria vesca L.) from across Europe and investigated the population structure and demographic history of the species during past geoclimatic events. We found a clear division of populations into western and eastern genetic clusters, indicative of distinct glacial refugia and adaptations to variation in temperature seasonality. The eastern core populations were several times larger (defined as effective population size, NE) than populations in other regions, showed no evidence of inbreeding, and were resilient to several glacial maxima. However, we observed decreasing NE and higher inbreeding in populations toward range edges, particularly in the north, where these individuals went through bottlenecks during glaciations. Population divergence suggested that western and eastern Europe were colonized from separate refugia in multiple waves during the Holocene, while the largest current populations from the northern Mediterranean to southern regions of the Nordic countries formed a connected population chain with gene flow between eastern core populations and western Europe, primarily occurring through Central Europe. Similar patterns of colonization and hybridization may have occurred during past interglacial periods, contributing to the present-day population structure of woodland strawberry. We suggest that the unprecedented resolution of the species climatic history across six glacial-interglacial cycles presented here holds the promise of transforming the general understanding of species paleohistory through geoclimatically tracing ancestral haplotypes.

plant biology↗

bioRxiv2024

Allopolyploidy expanded gene content but not pangenomic variation in the hexaploid oilseed Camelina sativa

Ancient whole-genome duplications (WGDs) are believed to facilitate novelty and adaptation by providing the raw fuel for new genes. However, it is unclear how recent WGDs may contribute to evolvability within recent polyploids. Hybridization accompanying some WGDs may combine divergent gene content among diploid species. Some theory and evidence suggest that polyploids have a greater accumulation and tolerance of gene presence-absence and genomic structural variation, but it is unclear to what extent either is true. To test how recent polyploidy may influence pangenomic variation, we sequenced, assembled, and annotated twelve complete, chromosome-scale genomes of Camelina sativa, an allohexaploid biofuel crop with three distinct subgenomes. Using pangenomic comparative analyses, we characterized gene presence-absence and genomic structural variation both within and between the subgenomes. We found over 75% of ortholog gene clusters are core in Camelina sativa and <10% of sequence space was affected by genomic structural rearrangements. In contrast, 19% of gene clusters were unique to one subgenome, and the majority of these were Camelina-specific (no ortholog in Arabidopsis). We identified an inversion that may contribute to vernalization requirements in winter-type Camelina, and an enrichment of Camelina-specific genes with enzymatic processes related to seed oil quality and Camelinas unique glucosinolate profile. Genes related to these traits exhibited little presence-absence variation. Our results reveal minimal pangenomic variation in this species, and instead show how hybridization accompanied by WGD may benefit polyploids by merging diverged gene content of different species.

genomics↗

bioRxiv2024

Chromosome-scale Salvia hispanica L. (Chia) genome assembly reveals rampant Salvia interspecies introgression

Salvia hispanica L. (Chia), a member of the Lamiaceae, is an economically important crop in Mesoamerica, with health benefits associated with its seed fatty acid composition. Chia varieties are distinguished based on seed color including mixed white and black (Chia pinta) and black (Chia negra). To facilitate research on Chia and expand on comparative analyses within the Lamiaceae, we generated a chromosome-scale assembly of a Chia pinta accession and performed comparative genome analyses with a previously published Chia negra genome assembly. The Chia pinta and negra genome sequences were highly similar as shown by a limited number of single nucleotide polymorphisms and extensive shared orthologous gene membership. There is an enrichment of terpene synthases in the Chia pinta genome relative to the Chia negra genome. We sequenced and analyzed the genomes of 20 Chia accessions with differing seed color and geographic origin revealing population structure within S. hispanica and interspecific introgressions of Salvia species. As the genus Salvia is polyphyletic, its evolutionary history remains unclear. Using large-scale synteny analysis within the Lamiaceae and orthologous group membership, we resolved the phylogeny of Salvia species. This study and its collective resources further our understanding of genomic diversity in this food crop and the extent of inter-species hybridizations in Salvia. PLAIN LANGUAGE SUMMARYChia pinta is an economically important crop due to the high fatty acid present in the seeds. There are multiple types of Chia based on the seeds color including mixed which and black (Chia pinta), black (Chia negra), and white (Chia blanca). We generated a genome assembly of Chia pinta and compared it to existing genome assemblies. While the assemblies are highly similar there are key differences in terpene synthase composition between Chia pinta and Chia negra. We also sequenced 20 other Chia accessions with different seed color and geographic origin to determine a population structure within Chia. We generated genomic resources to further our understanding of this food crop. ABBREVIATIONSBGC Biosynthetic gene cluster BUSCO Benchmarking Universal Single Copy Orthologs GO Gene ontology SNP Single nucleotide polymorphism TIR Terminal inverted repeat TPS Terpene synthase WGS Whole genome shotgun

genomics↗

bioRxiv2023

Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

genomics↗

bioRxiv2022

The last missing piece of the Triangle of U: the evolution of the tetraploid Brassica carinata genome

Ethiopian mustard (Brassica carinata) is an ancient crop with significant potential for expanded cultivation as a biodiesel feedstock. The remarkable stress resilience of B. carinata and desirable seed fatty acid profile addresses the ongoing food vs. fuel debate as the crop is productive on marginal lands otherwise not suitable for even closely related species. B. carinata is one of six key Brassica spp. that share three major genomes: three diploid species (AA, BB, CC) that spontaneously hybridized in a pairwise manner, forming three allotetraploid species (AABB, AACC, and BBCC). Each of these genomes has been researched extensively, except for that of B. carinata. In the present study, we report a high-quality, 1.31 Gbp genome with 156.9-fold sequencing coverage for B. carinata var. Gomenzer, completing and confirming the classic Triangle of U, a theory of the evolutionary relationships among these six species that arose almost a century ago. Our assembly provides insights into the genomic features that give rise to B. carinatas superior agronomic traits for developing more climate-resilient Brassica crops with excellent oil production. Notably, we identified an expansion of transcription factor networks and agronomically-important gene families. Completing the Triangle of U comparative genomics platform allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in domestication and agronomical improvement.

genetics↗

bioRxiv2021

A genome in flux: homoeologous exchanges, subgenome dominance, and gene dosage balance constraints in resynthesized allopolyploid Brassica napus

The Gene Balance Hypothesis (GBH) proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions of networks, pathways, and protein complexes to maintain balanced stoichiometry of interacting proteins, because perturbations to stoichiometric balance can result in reduced fitness. This selection has been called dosage balance selection. Dosage balance selection is also hypothesized to constrain expression responses to dosage changes, making dosage-sensitive genes (those encoding members of interacting proteins) experience more similar expression changes. In allopolyploids, where whole-genome duplication involves hybridization of diverged lineages, organisms often experience homoeologous exchanges (HEs) that recombine, duplicate, and delete homoeologous regions of the genome and alter the expression of homoeologous gene pairs. Although the GBH makes predictions about the expression response to HEs, they have not been empirically tested. We used genomic and transcriptomic data from six resynthesized, isogenic Brassica napus lines over ten generations to identify HEs, analyzed expression responses, and tested for patterns of genomic imbalance. Groups of dosage-sensitive genes had less variable expression responses to HEs than dosage-insensitive genes, a sign that their relative dosage is constrained. This difference was absent for homoeologous pairs whose expression was biased toward the BnA subgenome. Finally, the expression response to HEs was more variable than the response to WGD, suggesting HEs create genomic imbalance. These findings expand our knowledge of the impact of dosage balance selection on genome evolution and potentially connect patterns in polyploid genomes over time; from homoeolog expression bias to duplicate gene retention.

evolutionary biology↗

bioRxiv2021

Blueprint for Phasing and Assembling the Genomes of Heterozygous Polyploids: Application to the Octoploid Genome of Strawberry

The challenge of allelic diversity for assembling haplotypes is exemplified in polyploid genomes containing homoeologous chromosomes of identical ancestry, and significant homologous variation within their ancestral subgenomes. Cultivated strawberry (Fragaria x ananassa) and its wild progenitors are outbred octoploids (2n = 8x = 56) in which up to eight homologous and homoeologous alleles are preserved. This introduces significant risk of haplotype collapse, switching, and chimeric fusions during assembly. Using third generation HiFi sequences from PacBio, we assembled the genome of the day-neutral octoploid F. x ananassa hybrid Royal Royce from the University of California. Our goal was to produce subgenome-and haplotype-resolved assemblies of all 56 chromosomes, accurately reconstructing the parental haploid chromosome complements. Previous work has demonstrated that partitioning sequences by parental phase supports direct assembly of haplotypes in heterozygous diploid species. We leveraged the accuracy of HiFi sequence data with pedigree-informed sequencing to partition long read sequences by phase, and reduce the downstream risk of subgenomic chimeras during assembly. We were able to utilize an octoploid strawberry recombination breakpoint map containing 3.6 M variants to identify and break chimeric junctions, and perform scaffolding of the phase-1 and phase-2 octoploid assemblies. The N50 contiguity of the phase-1 and phase-2 assemblies prior to scaffolding and gap-filling was 11 Mb. The final haploid assembly represented seven of 28 chromosomes in a single contiguous sequence, and averaged fewer than three gaps per pseudomolecule. Additionally, we re-annotated the octoploid genome to produce a custom F. x ananassa repeat library and improved set of gene models based on IsoSeq transcript data and an expansive RNA-seq expression atlas. Here we present FaRR1, a gold-standard reference genome of F. x ananassa cultivar Royal Royce to assist future genomic research and molecular breeding of allo-octoploid strawberry.

genomics↗

bioRxiv2021

Convergent evolution of polyploid genomes from across the eukaryotic tree of life

By modeling the homoeologous gene losses that occurred in fifty genomes deriving from ten distinct polyploidy events, we show that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes or yeasts. The models suggest these events were nearly all allopolyploidies, with two distinct progenitors contributing to the modern species. We show that many of the events show a relative rate of duplicate gene loss prior to the first post-polyploidy speciation that is significantly higher than in later phases of their evolution. The relatively low selective constraint seen for the single-copy genes these losses produced lead us to suggest that most of the purely selectively neutral duplicate gene losses occur in the immediate post-polyploid period. We also find ongoing and extensive reciprocal gene losses (RGL; alternative losses of duplicated ancestral genes) between these genomes. With the exception of a handful of closely related taxa, all of these polyploid organisms are separated from each other by tens to thousands of reciprocal gene losses. As a result, it is very unlikely that viable diploid hybrid species could form between these taxa, since matings between such hybrids would tend to produce offspring lacking essential genes. It is therefore possible that the relatively high frequency of recurrent polyploidies in some lineages may be due to the ability of new polyploidies to bypass RGL barriers.

evolutionary biology↗

bioRxiv2021

The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae)

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for designing new approaches in crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species are able to revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions.

evolutionary biology↗

bioRxiv2021

Machine learning approaches to identify core and dispensable genes in pangenomes

A gene in a given taxonomic group is either present in every individual (core), or absent in at least a single individual (dispensable). Previous pangenomic studies have identified certain functional differences between core and dispensable genes. However, identifying if a gene belongs to the core or dispensable portion of the genome requires the construction of a pangenome, which involves sequencing the genomes of many individuals. Here we aim to leverage the previously characterized core and dispensable gene content for two grass species (Brachypodium distachyon and Oryza sativa) to construct a machine learning model capable of accurately classifying genes as core or dispensable using only a single annotated reference genome. Such a model may mitigate the need for pangenome construction, an expensive hurdle especially in orphan crops which often lack the adequate genomic resources.

bioinformatics↗

bioRxiv2020

Genetic and Genomic Resources to Study Natural Variation in Brassica rapa

ABSTRACTThe globally important crop Brassica rapa, a close relative of Arabidopsis, is an excellent system for modeling our current knowledge of plant growth on a morphologically diverse crop. The long history of B. rapa domestication across Asia and Europe provides a unique collection of locally adapted varieties that span large climatic regions with various abiotic and biotic stress tolerance traits. This diverse gene pool provides a rich source of targets with the potential for manipulation towards the enhancement of productivity of crops both within and outside the Brassicaceae. To expand the genetic resources available to study natural variation in B. rapa, we constructed an Advanced Intercross Recombinant Inbred (AI-RIL) population using B. rapa subsp. trilocularis (Yellow Sarson) R500 and the B. rapa subsp. parachinensis (Cai Xin) variety L58. Our current understanding of genomic structure variation across crops suggests that a single reference genome is insufficient for capturing the genetic diversity within a species. To complement this AI-RIL population and current and future B. rapa genomic resources, we generated a de novo genome assembly of the B. rapa subsp. trilocularis (Yellow Sarson) variety R500, the maternal parent of the AI-RIL population. The genetic map for the R500 x L58 population generated using this de novo genome was used to map QTL for seed coat color and revealed the improved mapping resolution afforded by this new assembly.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2020

Surprising amount of stasis in repetitive genome content across the Brassicales

Genome size of plants has long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana - chosen as the model plant system for this reason - as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we find no correlation between genome size and TE content, and more surprisingly we identify no significant changes to TE landscape following WGD.

evolutionary biology↗

bioRxiv2019

Chromosome Evolution of Octoploid Strawberry

The allo-octoploid cultivated strawberry (Fragaria x ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we show that octoploid Fragaria species harbor millions of subgenome-specific DNA variants. Their diversity was sufficient to distinguish duplicated (homoeologous and paralogous) DNA sequences and develop 50K and 850K SNP genotyping arrays populated with co-dominant, disomic SNP markers distributed throughout the octoploid genome. Whole-genome shotgun genotyping of an interspecific segregating population yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks spanning 3,394 cM in F. chiloensis subsp. lucida, and 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning 2,017 cM in F. x ananassa. These studies provide a dense genomic framework of subgenome-specific DNA markers for seamlessly cross-referencing genetic and physical mapping information, and unifying existing chromosome nomenclatures. Through comparative genetic mapping, we show that the genomes of geographically diverse wild octoploids are effectively diploidized and completely collinear. The preservation of genome structure among allo-octoploid taxa is a critical factor in the unique history of garden strawberry, where unimpeded gene flow supported both its origin and domestication through repeated cycles of interspecific hybridization.

genomics↗

bioRxiv2019

Replaying the evolutionary tape to investigate subgenome dominance in allopolyploidBrassica napus

Interspecific hybridization and allopolyploidization merges evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is "dominant" over the other subgenome, having a greater number of reatined duplicate genes and being more highly expressed. Which subgenome becomes dominantly expressed in allopolyploids remains poorly understood. Here we "replayed the evolutionary tape" with six isogenic resynthesized Brassica napus (rapeseed) allopolyploid lines and investigated subgenome dominance patterns over the first ten generations. We found that the same subgenome was consistently more dominantly expressed in all lines and generations. Furthermore, DNA methylation differences between subgenomes mirrored the observed gene expression bias towards the Brassica oleracea derived C subgenome in all lines and generations. These differences in gene expression and methylation were also found when comparing the progenitor genomes, suggesting subgenome dominance is related to inherited parental genome differences rather than a byproduct of allopolyploidization. Gene network analyses indicated an enrichment for network interactions and several biological functions for C subgenome biased pairs, but no enrichment was observed for A subgenome biased pairs. These findings demonstrate that "replaying the evolutionary tape" in allopolyploids results in repeatable and predictable subgenome expression dominance patterns based on preexisting genetic differences among the parental species. These findings have major implications regarding the genotypic and phenotypic diversity observed following plant hybridization in both ecological and agricultural contexts.

evolutionary biology↗