Polyploidy and angiosperm diversification

The Possible Earliest Allopolyploidization in Tracheophytes Revealed by Phylotranscriptomics and Morphology of Selaginellaceae

Selaginellaceae, originated in the Carboniferous and survived the Permian-Triassic mass extinction, is the largest family of lycophyte, which is sister to other tracheophytes. It stands out from tracheophytes by exhibiting extraordinary habitat diversity and lacking polyploidization. The organelle genome-based phylogenies confirmed the monophyly of Selaginella, with six or seven subgenera grouped into two superclades, but the phylogenetic positions of the enigmatic Selaginella sanguinolenta clade remained problematic. Here, we conducted a phylogenomic study on Selaginellaceae utilizing large-scale nuclear gene data from RNA-seq to elucidate the phylogeny and explore the causes of the phylogenetic incongruence of the S. sanguinolenta clade. Our phylogenetic analyses resolved three different positions of the S. sanguinolenta clade, which were supported by the sorted three nuclear gene sets, respectively. The results from the gene flow test, species network inference, and plastome-based phylogeny congruently suggested a probable hybrid origin of the S. sanguinolenta clade involving each common ancestor of the two superclades in Selaginellaceae. The hybrid hypothesis is corroborated by the evidence from rhizophore morphology and spore micromorphology. The chromosome observation and Ks distributions further suggested hybridization accompanied by polyploidization. Divergence time estimation based on independent datasets from nuclear gene sets and plastid genome data congruently inferred that allopolyploidization occurred in the Early Triassic. To our best knowledge, the allopolyploidization in the Mesozoic reported here represents the earliest record of tracheophytes. Our study revealed a unique triad of phylogenetic positions for a hybrid-originated group with comprehensive evidence and proposed a hypothesis for retaining both parental alleles through gene conversion.

Chromosome-level assembly of Lindenbergia philippensis and comparative genomic analyses shed light on genome evolution in Lamiales

Lamiales, comprising over 23,755 species across 24 families, stands as a highly diverse and prolific plant group, playing a significant role in the cultivation of horticultural, ornamental, and medicinal plant varieties. Whole-genome duplication (WGD) and its subsequent post-polyploid diploidization (PPD) process represent the most drastic type of karyotype evolution, injecting significant potential for promoting the diversity of this lineage. However, polyploidization histories, as well as genome and subgenome fractionation following WGD events in Lamiales species, are still not well investigated. In this study, we constructed a chromosome-level genome assembly of Lindenbergia philippensis (Orobanchaceae) and conducted comparative genomic analyses with 14 other Lamiales species. L. philippensis is positioned closest to the parasitic lineage within Orobanchaceae and has a conserved karyotype. Through a combination of Ks analysis and syntenic depth analysis, we reconstructed and validated polyploidization histories of Lamiales species. Our results indicated that Primulina huaijiensis underwent three rounds of diploidization events following the γ-WGT event, rather than two rounds as reported. Besides, we reconfirmed that most Lamiales species shared a common diploidization event (L-WGD). Subsequently, we constructed the Lamiales Ancestral Karyotype (LAK), comprising 11 proto-chromosomes, and elucidated its evolutionary trajectory, highlighting the highly flexible reshuffling of the Lamiales paleogenome. We identified biased fractionation of subgenomes following the L-WGD event across eight species, and highlighted the positive impacts of non-WGD genes on gene family expansion. This study provides novel genomic resources and insights into polyploidy and karyotype remodeling of Lamiales species, essential for advancing our understanding of species diversification and genome evolution.

Neopolyploidy-induced changes in giant duckweed (Spirodela polyrhiza) alter herbivore preference and performance and plant population performance

PREMISE

Polyploidy is a widespread mutational process in angiosperms that may alter population performance of not only plants but also their interacting species. Yet, knowledge of whether polyploidy affects plant-herbivore dynamics is scarce. Here, we tested whether aphid herbivores exhibit preference for diploid or neopolyploid plants, whether polyploidy impacts plant and herbivore performance, and whether these interactions depend on the plant genetic background.

METHODS

Using independently synthesized neotetraploid strains paired with their diploid progenitors of greater duckweed (Spirodela polyrhiza), we evaluated the effect of neopolyploidy on duckweed's interaction with the water-lily aphid (Rhopalosiphum nymphaeae). Using paired-choice experiments, we evaluated feeding preference of the herbivore. We then evaluated the consequences of polyploidy on aphid and plant performance by measuring population growth over multiple generations.

RESULTS

Aphids preferred neopolyploids when plants were provided at equal abundances but not at equal surface areas, suggesting the role of plant population surface area in driving this preference. Additionally, neopolyploidy increased aphid population performance, but this result was dependent on the plant's genetic lineage. Lastly, the impact of herbivory on neopolyploid vs. diploid duckweed varied greatly with genetic lineage, where neopolyploids appeared to be variably tolerant compared to diploids, sometimes mirroring the effect on herbivore performance.

CONCLUSIONS

By experimentally testing the impacts of polyploidy on trophic species interactions, we showed that polyploidization can impact the preference and performance of herbivores on their plant hosts. These results have significant implications for the establishment and persistence of plants and herbivores in the face of plant polyploidy.

The link between ancient whole-genome duplications and cold adaptations in the Caryophyllaceae

PREMISE

The Caryophyllaceae (the carnation family) have undergone multiple transitions into colder climates and convergence on cushion plant adaptation, indicating that they may provide a natural system for cold adaptation research. Previous research has suggested that putative ancient whole-genome duplications (WGDs) are correlated with niche shifts into colder climates across the Caryophyllales. Here, we explored the genomic changes potentially involved in one of these discovered shifts in the Caryophyllaceae.

METHODS

We constructed a data set combining 26 newly generated transcriptomes with 45 published transcriptomes, including 11 cushion plant species across seven genera. With this data set, we inferred a dated phylogeny for the Caryophyllaceae and mapped ancient WGDs and gene duplications onto the phylogeny. We also examined functional groups enriched for gene duplications related to the climatic shift.

RESULTS

The ASTRAL topology was mostly congruent with the current consensus of relationships within the family. We inferred 15 putative ancient WGDs in the family, including eight that have not been previously published. The oldest ancient WGD (ca. 64.4-56.7 million years ago), WGD1, was found to be associated with a shift into colder climates by previous research. Gene regions associated with ubiquitination were overrepresented in gene duplications retained after WGD1 and those convergently retained by cushion plants in Colobanthus and Eremogone, along with other functional annotations.

CONCLUSIONS

Gene family expansions induced by ancient WGDs may have contributed to the shifts to cold climatic niches in the Caryophyllaceae. Transcriptomic data are crucial resources that help unravel heterogeneity in deep-time evolutionary patterns in plants.

Evolutionary patterns of variations in chromosome counts and genome sizes show positive correlations with taxonomic diversity in tropical gingers

PREMISE

Cytogenetic traits such as an organism's chromosome number and genome size are taxonomically critical as they are instrumental in defining angiosperm diversity. Variations in these traits can be traced to evolutionary processes such as polyploidization, although geographic variations across cytogenetic traits remain underexplored. In the pantropical monocot family Zingiberaceae (~1500 species), cytogenetic traits have been well documented; however, the role of these traits in shaping taxonomic diversity and biogeographic patterns of gingers is not known.

METHODS

A time-calibrated Bayesian phylogenetic tree was constructed for 290 taxa covering three of the four subfamilies in Zingiberaceae. We tested models of chromosome number and genome size evolution within the family and whether lineage age, taxonomic diversity, and distributional range explain the variations in the cytogenetic traits. Tests were carried out at two taxonomic ranks: within Zingiberaceae and within genus Hedychium using correlations, generalized linear models and phylogenetic least square models.

RESULTS

The most frequent changes in chromosome number within Zingiberaceae were noted to be demi-polyploidization and polyploidization (~57% of the time), followed by ascending dysploidy (~27%). The subfamily Zingiberoideae showed descending dysploidy at its base, while Alpinioideae showed polyploidization at its internal nodes. Although chromosome counts and genome sizes did not corroborate with each other, suggesting that they are not equivalent; higher chromosome number variations and higher genome size variations were associated with higher taxonomic diversity and wider biogeographic distribution.

CONCLUSIONS

Within Zingiberaceae, multiple incidences of polyploidization were discovered, and cytogenetic events appear to have reduced the genome sizes and increased taxonomic diversity, distributional ranges and invasiveness.

Local adaptation, recombination, and the fate of neopolyploids

Polyploidy is widely recognized as an important speciation mechanism because it isolates tetraploids from their diploid progenitors. Polyploidy also provides new genetic material that may facilitate adaptive evolution. However, new mutations are more likely to arise after a neopolyploid already has successfully invaded a population. Thus, the role of adaptive forces in establishing a polyploid remains unclear. One solution to this apparent paradox may lie in the capacity of polyploids to suppress recombination among preexisting locally adapted alleles. The local adaptation mechanism requires that spatially heterogeneous selection acts on multiple loci and that gene flow introduces maladapted alleles to the population where the polyploid forms. The mechanism requires neither strong genetic drift nor any intrinsic benefit of genome doubling and can accommodate any mode of gene action. A unique prediction of the mechanism is that adaptive alleles should predate polyploidization, a pattern consistent with observations from a few well-studied polyploids. The mechanism is also consistent with the coexistence of both diploid and tetraploid cytotypes, fitness heterogeneity among independently derived polyploids, and the prevalence of outcrossing among older polyploids. The local adaptation mechanism also makes novel predictions about circumstances favoring polyploid invasions that can be tested using molecular genetic or comparative approaches.

Polyploidy in maize: from evolution to breeding

Polyploidy played an important role in the evolution of the three most important crops: wheat, maize and rice, each of them providing a unique model for studying allopolyploidy, segmental alloploidy or paleopolyploidy. However, its genetic and evolutionary role is still vague. The undelying mechanisms and consequences of polyploidy remain fundamental objectives in the study of eukaryotes. Maize is one of the underutilized crops at the polyploid level. This species has no stable natural polyploids, the existing ones being artificially obtained. From the experimental polyploid series of maize, only the tetraploid forms (4n = 40) are of interest. They are characterized by some valuable morphological, physiological and biochemical features, superior to the diploid forms from which they originated, but also by some drawbacks such as: reduced fertility, slower development, longer vegetation period, low productivity and adaptedness. Due to these barriers to using tetraploids in field production, maize tetraploids primarily found utility in scientific studies regarding genetic variability, inbreeding, heterosis and gene dosage effect. Since the first mention of a triploid maize plant to present, many scientists and schools, devoted their efforts to capitalize on the use of polyploidy in maize. Despite its common disadvantages as a crop, significant progress in developing tetraploid maize with good agronomic performance was achieved leading to registered tetraploid maize varieties. In this review we summarize and discuss the different aspects of polyploidy in maize, such as evolutionary context, methods of induction, morphology, fertility issue, inheritance patterns, gene expression and potential use.

Deciphering Pteronia's evolution in the Cape Floristic Region: A comprehensive study disputes polyploid deficiency and affirms diploid radiation

The Greater Cape Floristic Region (GCFR) is renowned for its exceptional biodiversity, accommodating over 11 000 plant species, notable degree of endemism, and substantial diversification within limited plant lineages, a phenomenon ascribed to historical radiation events. While both abiotic and biotic factors contribute to this diversification, comprehensive genomic alterations, recognized as pivotal in the diversification of angiosperms, are perceived as uncommon. This investigation focuses on the genus Pteronia, a prominent representative of the Asteraceae family in the GCFR. Employing NGS-based HybSeq and RADSeq methodologies, flow cytometry, karyology, and ecological modeling, we scrutinize the intricacies of its polyploid evolution. Phylogenetic reconstructions using 951 low-copy nuclear genes confirm Pteronia as a well-supported, distinct clade within the tribe Astereae. The ingroup displays a structure indicative of rapid radiation likely antedating polyploid establishment, with the two main groups demarcated by their presence or absence in the fynbos biome. Genome size analysis encompasses 1293 individuals across 347 populations, elucidating significant variation ranging from 6.1 to 34.2 pg (2C-value). Pteronia demonstrates substantially large genome sizes within Astereae and phanerophytes. Polyploidy is identified in 31% of the studied species, with four discerned ploidy levels (2x, 4x, 6x, 8x). Cytotypes exhibit marked distinctions in environmental traits, influencing their distribution across biomes and augmenting their niche differentiation. These revelations challenge the presumed scarcity of polyploidy in the Cape flora, underscoring the imperative need for detailed population studies. The intricate evolutionary history of Pteronia, characterized by recent polyploidy and genome size variation, contributes substantially to the comprehension of diversification patterns within the GCFR biodiversity hotspot.

Polyploidy and hybridization in the Mediterranean: unravelling the evolutionary history of Centaurium (Gentianaceae)

BACKGROUND AND AIMS

Polyploidy is considered one of the main mechanisms of plant evolution and speciation. In the Mediterranean Basin, polyploidy has contributed to making this region a biodiversity hotspot, along with its geological and climatic history and other ecological and biogeographical factors. The Mediterranean genus Centaurium (Gentianaceae) comprises ~25 species, of which 60 % are polyploids, including tetraploids and hexaploids. To date, the evolutionary history of centauries has been studied using Sanger sequencing phylogenies, which have been insufficient to fully understand the phylogenetic relationships in this lineage. The goal of this study is to gain a better understanding of the evolutionary history of Centaurium by exploring the mechanisms that have driven its diversification, specifically hybridization and polyploidy. We aim to identify the parentage of hybrid species, at the species or clade level, as well as assessing whether morphological traits are associated with particular ploidy levels.

METHODS

We sequenced RADseq markers from 42 samples of 28 Centaurium taxa, and performed phylogenomic analyses using maximum likelihood, summary coalescent SVDquartets and Neighbor-Net approaches. To identify hybrid taxa, we used PhyloNetworks and the fastSTRUCTURE algorithm. To infer the putative parental species of the allopolyploids, we employed genomic analyses (SNIPloid). The association between different traits and particular ploidy levels was explored with non-metric multidimensional scaling.

KEY RESULTS

Our phylogenetic analyses confirmed the long-suspected occurrence of recurrent hybridization. The allopolyploid origin of the tetraploid C. serpentinicola and the hexaploids C. mairei, C. malzacianum and C. centaurioides was also confirmed, unlike that of C. discolor. We inferred additional signatures of hybridization events within the genus and identified morphological traits differentially distributed in different ploidy levels.

CONCLUSIONS

This study highlights the important role that hybridization has played in the evolution of a Mediterranean genus such as Centaurium, leading to a polyploid complex, which facilitated its diversification and may exemplify that of other Mediterranean groups.

Influence of polyploidy on morphology and distribution of the Cypress Spurge (Euphorbia cyparissias, Euphorbiaceae)

Polyploidy can cause differences in phenotypic and physiological traits among different cytotypes of the same species. Polyploids may have larger organs or occupy different ecological niches than their diploid counterparts, therefore they are hypothesized to have larger distributions or prosper in stressful environments, such as higher elevations. The Cypress spurge (Euphorbia cyparissias L.; Euphorbiaceae) is a widespread European heteroploid species including di- (2x), tetra- (4x) and hexaploid (6x) cytotypes. We tested the hypotheses that polyploids are more widespread and more abundant at higher elevations and have larger organs than their diploid ancestors in the case of E. cyparissias. We also analysed whether genome downsizing had occurred after polyploidisation. We conducted a comprehensive geographic sampling of 617 populations of E. cyparissias throughout Europe. We estimated their relative genome size using flow cytometry and inferred ploidy level of each population. We scored 13 morphological traits of vegetative and seed characters and performed statistical analyses. The study indicates that polyploidisation facilitated colonisation of new areas in E. cyparissias, where the tetraploids are most widespread, whereas the diploids are limited to putative Pleistocene refugia, mostly in southern Europe. On the other hand, the three ploidies do not differ in their elevational distribution. Although some quantitative morphological traits exhibited an increasing trend with increasing ploidy, most traits did not differ significantly among the three ploidies, and there was no overall phenotypic differentiation among them. Given that individuals of different ploidies thrive in similar habitats across the same elevations, we suggest that ecological segregation following polyploidisation is a more important trigger for morphological differentiation than polyploidisation itself in autopolyploid plants. The study demonstrates that polyploidisation can be crucial for the colonisation of new areas and for range expansion, but it does not necessarily influence elevational distribution nor confer a different phenotype.

Utilizing a comparative approach to assess genome evolution during diploidization in Artemisia tridentata, a keystone species of western North America

PREMISE

Polyploidization is often followed by diploidization. Diploidization is generally studied using synthetic polyploid lines and/or crop plants, but rarely using extant diploids or nonmodel plants such as Artemisia tridentata. This threatened western North American keystone species has a large genome compared to congeneric Artemisia species; dominated by diploid and tetraploid cytotypes, with multiple origins of tetraploids with genome size reduction.

METHODS

The genome of an A. tridentata sample was resequenced to study genome evolution and compared to that of A. annua, a diploid congener. Three diploid genomes of A. tridentata were compared to test for multiple diploidization events.

RESULTS

The A. tridentata genome had many chromosomal rearrangements relative to that of A. annua, while large-scale synteny of A. tridentata chromosome 3 and A. annua chromosome 4 was conserved. The three A. tridentata genomes had similar sizes (4.19-4.2 Gbp), heterozygosity (2.24-2.25%), and sequence (98.73-99.15% similarity) across scaffolds, and in k-mer analyses, similar patterns of diploid heterozygous k-mers (AB = 41%, 47%, and 47%), triploid heterozygous k-mers (AAB = 18-21%), and tetraploid k-mers (AABB = 13-17%). Biallelic SNPs were evenly distributed across scaffolds for all individuals. Comparisons of transposable element (TE) content revealed differential enrichment of TE clades.

CONCLUSIONS

Our findings suggest population-level TE differentiation after a shared polyploidization-to-diploidization event(s) and exemplify the complex processes of genome evolution. This research approached provides new resources for exploration of abiotic stress response, especially the roles of TEs in response pathways.

ATAD3 Proteins: Unique Mitochondrial Proteins Essential for Life in Diverse Eukaryotic Lineages

ATPase family AAA domain-containing 3 (ATAD3) proteins are unique mitochondrial proteins that arose deep in the eukaryotic lineage but that are surprisingly absent in Fungi and Amoebozoa. These ∼600-amino acid proteins are anchored in the inner mitochondrial membrane and are essential in metazoans and Arabidopsis thaliana. ATAD3s comprise a C-terminal ATPases Associated with a variety of cellular Activities (AAA+) matrix domain and an ATAD3_N domain, which is located primarily in the inner membrane space but potentially extends to the cytosol to interact with the ER. Sequence and structural alignments indicate that ATAD3 proteins are most similar to classic chaperone unfoldases in the AAA+ family, suggesting that they operate in mitochondrial protein quality control. A. thaliana has four ATAD3 genes in two distinct clades that appear first in the seed plants, and both clades are essential for viability. The four genes are generally coordinately expressed, and transcripts are highest in growing apices and imbibed seeds. Plants with disrupted ATAD3 have reduced growth, aberrant mitochondrial morphology, diffuse nucleoids and reduced oxidative phosphorylation complex I. These and other pleiotropic phenotypes are also observed in ATAD3 mutants in metazoans. Here, we discuss the distribution of ATAD3 proteins as they have evolved in the plant kingdom, their unique structure, what we know about their function in plants and the challenges in determining their essential roles in mitochondria.

Convergent and/or parallel evolution of RNA-binding proteins in angiosperms after polyploidization

Increasing studies suggest that the biased retention of stress-related transcription factors (TFs) after whole-genome duplications (WGDs) could rewire gene transcriptional networks, facilitating plant adaptation to challenging environments. However, the role of posttranscriptional factors (e.g. RNA-binding proteins, RBPs) following WGDs has been largely ignored. Uncovering thousands of RBPs in 21 representative angiosperm species, we integrate genomic, transcriptomic, regulatomic, and paleotemperature datasets to unravel their evolutionary trajectories and roles in adapting to challenging environments. We reveal functional enrichments of RBP genes in stress responses and identify their convergent retention across diverse angiosperms from independent WGDs, coinciding with global cooling periods. Numerous RBP duplicates derived from WGDs are then identified as cold-induced. A significant overlap of 29 orthogroups between WGD-derived and cold-induced RBP genes across diverse angiosperms highlights a correlation between WGD and cold stress. Notably, we unveil an orthogroup (Glycine-rich RNA-binding Proteins 7/8, GRP7/8) and relevant TF duplicates (CCA1/LHY, RVE4/8, CBF2/4, etc.), co-retained in different angiosperms post-WGDs. Finally, we illustrate their roles in rewiring circadian and cold-regulatory networks at both transcriptional and posttranscriptional levels during global cooling. Altogether, we underline the adaptive evolution of RBPs in angiosperms after WGDs during global cooling, improving our understanding of plants surviving periods of environmental turmoil.

Allopolyploid origin and diversification of the Hawaiian endemic mints

Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai'i. The three distinct Hawaiian genera, Haplostachys, Phyllostegia, and Stenogyne, are nested inside a fourth genus, Stachys. We uncovered four independent polyploidy events within Stachys, including one allopolyploidy event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry and drift in small and fragmented populations, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms may have radiated on isolated island chains, settings that provided one of the principal natural laboratories for Darwin's thinking about the evolutionary process.

Polyploidization: A Biological Force That Enhances Stress Resistance

Organisms with three or more complete sets of chromosomes are designated as polyploids. Polyploidy serves as a crucial pathway in biological evolution and enriches species diversity, which is demonstrated to have significant advantages in coping with both biotic stressors (such as diseases and pests) and abiotic stressors (like extreme temperatures, drought, and salinity), particularly in the context of ongoing global climate deterioration, increased agrochemical use, and industrialization. Polyploid cultivars have been developed to achieve higher yields and improved product quality. Numerous studies have shown that polyploids exhibit substantial enhancements in cell size and structure, physiological and biochemical traits, gene expression, and epigenetic modifications compared to their diploid counterparts. However, some research also suggested that increased stress tolerance might not always be associated with polyploidy. Therefore, a more comprehensive and detailed investigation is essential to complete the underlying stress tolerance mechanisms of polyploids. Thus, this review summarizes the mechanism of polyploid formation, the polyploid biochemical tolerance mechanism of abiotic and biotic stressors, and molecular regulatory networks that confer polyploidy stress tolerance, which can shed light on the theoretical foundation for future research.

Angiosperm-wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits

Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types, yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and families. Thus we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny, with resolved relationships for orders and families with previously uncertain placements. Using this phylogeny as a framework, molecular dating supports a Triassic origin of the crown angiosperms, followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial Revolution. The robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types, revealing a trend of parallel carpel fusions during early diversifications in eudicots, monocots, and magnoliids. Moreover, taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits; such associations of ovary, dry and fleshy fruits define several ovary-fruit "modules" each found in multiple families. One of the frequent modules has an ovary containing multiple ovules, capsules and berries, and another with an ovary having one or two ovules, achenes (or other single-seeded dry fruits) and drupes. This new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types, such as capsule and berry, that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules (such as achenes and drupes). Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications, supporting a possible role of whole-genome duplications, in combination with climate changes and animal behaviors, in angiosperm fruit and ovary diversification.

Morphological and genetic evidence suggest gene flow among native and naturalized mint species

PREMISE

Cultivation and naturalization of plants beyond their natural range can bring previously geographically isolated taxa together, increasing the opportunity for hybridization, the outcomes of which are not predictable. Here, we explored the phenotypic and genomic effects of interspecific gene flow following the widespread cultivation of Mentha spicata (spearmint), M. longifolia, and M. suaveolens.

METHODS

We morphologically evaluated 155 herbarium specimens of three Mentha species and sequenced the genomes of a subset of 93 specimens. We analyzed the whole genomes in a population and the phylogenetic framework and associated genomic classifications in conjunction with the morphological assessments.

RESULTS

The allopolyploid M. spicata, which likely evolved in cultivation, had altered trichome characters, that is possibly a product of human selection for a more palatable plant or a byproduct of selection for essential oils. There were signs of genetic admixture between mints, including allopolyploids, indicating that the reproductive barriers between Mentha species with differences in ploidy are likely incomplete. Still, despite gene flow between species, we found that genetic variants associated with the cultivated trichome morphology continue to segregate.

CONCLUSIONS

Although hybridization, allopolyploidization, and human selection during cultivation can increase species richness (e.g., by forming hybrid taxa), we showed that unless reproductive barriers are strong, these processes can also result in mixing of genes between species and the potential loss of natural biodiversity.

Research progress on Brassicaceae plants: a bibliometrics analysis

The Brassicaceae is a worldwide family that produces ornamental flowers, edible vegetables, and oilseed plants, with high economic value in agriculture, horticulture, and landscaping. This study used the Web of Science core dataset and the CiteSpace bibliometric tool to quantitatively visualize the number of publications, authors, institutions, and countries of 3139 papers related to Brassicaceae plants from 2002 to 2022. The keywords and references were divided into two phases: Phase 1 (2002-2011) and Phase 2 (2012-2022) for quantitative and qualitative analysis. The results showed: An average annual publication volume of 149 articles, with an overall fluctuating upward trend; the research force was mainly led by Professor Ihsan A. Al-shehbaz from Missouri Botanical Garden; and the United States had the highest number of publications. In the first phase, research focused on the phylogeny of Brassicaceae plants, while the second phase delved into diverse research based on previous studies, research in areas such as polyploidy, molecular technique, physiology, and hyperaccumulator has been extended. Based on this research, we propounded some ideas for future studies on Brassicaceae plants and summarized the research gaps.

Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes

Allopolyploids represent a new frontier in species discovery among embryophytes. Within mosses, allopolyploid discovery is challenged by low morphological complexity. The rapid expansion of sequencing approaches in addition to computational developments to identifying genome merger and whole-genome duplication using variation among nuclear loci representing homeologs has allowed for increased allopolyploid discovery among mosses. Here, we test a novel approach to phasing homeologs within loci and phasing loci across subgenomes, or subgenome assignment, called Homologizer, in the family Funariaceae. We confirm the intergeneric hybrid nature of Entosthodon hungaricus, and the allopolyploid origin of Physcomitrium eurystomum and one population of Physcomitrium collenchymatum. We also reveal that hybridization gave rise to Physcomitrium immersum, as well as to yet unrecognized lineages sharing the phenotype of Physcomitrium pyriforme and Physcomitrium sphaericum. Our findings demonstrate the utility of our approach when working with polyploid genomes, and its value in identifying progenitor species using target capture data.

Differential expansion and retention patterns of LRR-RLK genes across plant evolution

To maximize overall fitness, plants must accurately respond to a host of growth, developmental, and environmental signals throughout their life. Many of these internal and external signals are perceived by the leucine-rich repeat receptor-like kinases, which play roles in regulating growth, development, and immunity. This largest family of receptor kinases in plants can be divided into subfamilies based on the conservation of the kinase domain, which demonstrates that shared evolutionary history often indicates shared molecular function. Here we investigate the evolutionary history of this family across the evolution of 112 plant species. We identify lineage-specific expansions of the malectin-domain containing subfamily LRR subfamily I primarily in the Brassicales and bryophytes. Most other plant lineages instead show a large expansion in LRR subfamily XII, which in Arabidopsis is known to contain key receptors in pathogen perception. This striking asymmetric expansion may reveal a dichotomy in the evolutionary history and adaptation strategies employed by plants. A greater understanding of the evolutionary pressures and adaptation strategies acting on members of this receptor family offers a way to improve functional predictions for orphan receptors and simplify the identification of novel stress-related receptors.

Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyse how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype and a clear indication of subgenome dominance. A male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbour three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. A genome-scale analysis suggested that subgenome dominance likely contributed to evolutionary innovation by permitting recessive subgenomes to diversify functions of novel tissue-specific duplicates. Our results provide insight into how polyploidy can give rise to novel traits in divergent and successful high-ploidy lineages.

Genome-wide identification of GTE family proteins in sugarcane (Saccharum spontaneum) reveals that SsGTEL3a confers drought tolerance

The bromodomain is a highly conserved protein domain that specifically binds to acetylated lysine residues in histones, thereby activating transcription of target genes. Although some progress in Global Transcription Factor Group E (GTE) has been achieved in numerous animals and a few plant species, no systematic analysis of GTE gene families has been reported yet in sugarcane. In our study, 37 GTE and GTE-Like (GTEL) genes were characterized in the Saccharum spontaneum. All SsGTE/SsGTEL members were heterogeneously located on all chromosomes of the sugarcane genome and divided into five groups. Transcriptome data showed that SsGTEL3a was expressed at significantly higher levels under drought stress in drought-resistant varieties than in drought-sensitive varieties. Moreover, the overexpression of SsGTEL3a significantly improved the drought tolerance in Arabidopsis through improving the scavenging ability of reactive oxygen species. Additionally, an interaction between ScFAR1 and SsGTEL3a was identified, with ScFAR1 showing a positive response to drought stress in bacterium. In summary, this systematic analysis of GTE gene family in sugarcane and functional research of SsGTEL3a broadened deeper insight into their evolutionary dynamics and functional properties and provided new candidate genes for drought-resistant molecular breeding of sugarcane.

Subgenomic Stability of Progenitor Genomes During Repeated Allotetraploid Origins of the Same Grass Brachypodium hybridum

Both homeologous exchanges and homeologous expression bias are generally found in most allopolyploid species. Whether homeologous exchanges and homeologous expression bias differ between repeated allopolyploid speciation events from the same progenitor species remains unknown. Here, we detected a third independent and recent allotetraploid origin for the model grass Brachypodium hybridum. Our homeologous exchange with replacement analyses indicated the absence of significant homeologous exchanges in any of the three types of wild allotetraploids, supporting the integrity of their progenitor subgenomes and the immediate creation of the amphidiploids. Further homeologous expression bias tests did not uncover significant subgenomic dominance in different tissues and conditions of the allotetraploids. This suggests a balanced expression of homeologs under similar or dissimilar ecological conditions in their natural habitats. We observed that the density of transposons around genes was not associated with the initial establishment of subgenome dominance; rather, this feature is inherited from the progenitor genome. We found that drought response genes were highly induced in the two subgenomes, likely contributing to the local adaptation of this species to arid habitats in the third allotetraploid event. These findings provide evidence for the consistency of subgenomic stability of parental genomes across multiple allopolyploidization events that led to the same species at different periods. Our study emphasizes the importance of selecting closely related progenitor species genomes to accurately assess homeologous exchange with replacement in allopolyploids, thereby avoiding the detection of false homeologous exchanges when using less related progenitor species genomes.

Drivers of diversification in Linum (Linaceae) by means of chromosome evolution: correlations with biogeography, breeding system and habit

BACKGROUND AND AIMS

Chromosome evolution leads to hybrid dysfunction and recombination patterns and has thus been proposed as a major driver of diversification in all branches of the tree of life, including flowering plants. In this study we used the genus Linum (flax species) to evaluate the effects of chromosomal evolution on diversification rates and on traits that are important for sexual reproduction. Linum is a useful study group because it has considerable reproductive polymorphism (heterostyly) and chromosomal variation (n = 6-36) and a complex pattern of biogeographical distribution.

METHODS

We tested several traditional hypotheses of chromosomal evolution. We analysed changes in chromosome number across the phylogenetic tree (ChromEvol model) in combination with diversification rates (ChromoSSE model), biogeographical distribution, heterostyly and habit (ChromePlus model).

KEY RESULTS

Chromosome number evolved across the Linum phylogeny from an estimated ancestral chromosome number of n = 9. While there were few apparent incidences of cladogenesis through chromosome evolution, we inferred up to five chromosomal speciation events. Chromosome evolution was not related to heterostyly but did show significant relationships with habit and geographical range. Polyploidy was negatively correlated with perennial habit, as expected from the relative commonness of perennial woodiness and absence of perennial clonality in the genus. The colonization of new areas was linked to genome rearrangements (polyploidy and dysploidy), which could be associated with speciation events during the colonization process.

CONCLUSIONS

Chromosome evolution is a key trait in some clades of the Linum phylogeny. Chromosome evolution directly impacts speciation and indirectly influences biogeographical processes and important plant traits.

The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution

Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics. While an important role for CRs in speciation has been suggested, evidence primarily stems from theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon pairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at a macroevolutionary level has been supported by associations between species diversity and rates of evolution of CRs across phylogenies, these findings are limited to a restricted range of CRs and taxa. Now that more broadly applicable and precise CR detection approaches have become available, we address the challenges in filling some of the conceptual and empirical gaps between micro- and macroevolutionary studies on the role of CRs in speciation. We synthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.

Genomic analysis of the emergent aquatic plant Sparganium stoloniferum provides insights into its clonality, local adaptation and demographic history

Clonal propagation and extensive dispersal of seeds and asexual propagules are two important features of aquatic plants that help them adapt to aquatic environments. Accurate measurements of clonality and effective clonal dispersal are essential for understanding the evolution of aquatic plants. Here, we first assembled a high-quality chromosome-level genome of a widespread emergent aquatic plant Sparganium stoloniferum to provide a reference for its population genomic study. We then performed high-depth resequencing of 173 individuals from 20 populations covering different basins across its range in China. Population genomic analyses revealed three genetic lineages reflecting the northeast (NE), southwest (SW) and northwest (NW) of its geographical distribution. The NE lineage diverged in the middle Pleistocene while the SW and NW lineages diverged until about 2400 years ago. Clonal relationship analyses identified nine populations as monoclonal population. Dispersal of vegetative propagules was identified between five populations covering three basins in the NE lineage, and dispersal distance was up to 1041 km, indicating high dispersibility in emergent aquatic plant species. We also identified lineage-specific positively selected genes that are likely to be involved in adaptations to saline wetlands and high-altitude environments. Our findings accurately measure the clonality, determine the dispersal range and frequency of vegetative propagules, and detect genetic signatures of local adaptation in a widespread emergent aquatic plant species, providing new perspectives on the evolution of aquatic plants.

Does the evolution of micromorphology accompany chromosomal changes on dysploid and polyploid levels in the Barnardia japonica complex (Hyacinthaceae)?

BACKGROUND

Chromosome number and genome size changes via dysploidy and polyploidy accompany plant diversification and speciation. Such changes often impact also morphological characters. An excellent system to address the questions of how extensive and structured chromosomal changes within one species complex affect the phenotype is the monocot species complex of Barnardia japonica. This taxon contains two well established and distinct diploid cytotypes differing in base chromosome numbers (AA: x = 8, BB: x = 9) and their allopolyploid derivatives on several ploidy levels (from 3x to 6x). This extensive and structured genomic variation, however, is not mirrored by gross morphological differentiation.

RESULTS

The current study aims to analyze the correlations between the changes of chromosome numbers and genome sizes with palynological and leaf micromorphological characters in diploids and selected allopolyploids of the B. japonica complex. The chromosome numbers varied from 2n = 16 and 18 (2n = 25 with the presence of supernumerary B chromosomes), and from 2n = 26 to 51 in polyploids on four different ploidy levels (3x, 4x, 5x, and 6x). Despite additive chromosome numbers compared to diploid parental cytotypes, all polyploid cytotypes have experienced genome downsizing. Analyses of leaf micromorphological characters did not reveal any diagnostic traits that could be specifically assigned to individual cytotypes. The variation of pollen grain sizes correlated positively with ploidy levels.

CONCLUSIONS

This study clearly demonstrates that karyotype and genome size differentiation does not have to be correlated with morphological differentiation of cytotypes.

A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights into its evolution and C4 photosynthesis

JUJUNCAO (Cenchrus fungigraminus; 2n = 4x = 28) is a Cenchrus grass with the highest biomass production among cultivated plants, and it can be used for mushroom cultivation, animal feed, and biofuel production. Here, we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated ∼2.7 million years ago (mya). Its genome consists of two subgenomes, and subgenome A shares high collinear synteny with pearl millet. We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO. Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes, which was a further indication of asymmetric DNA methylation. The three types of centromeric repeat in the JUJUNCAO genome (CEN137, CEN148, and CEN156) may have evolved independently within each subgenome, with some introgressions of CEN156 from the B to the A subgenome. We investigated the photosynthetic characteristics of JUJUNCAO, revealing its typical C4 Kranz anatomy and high photosynthetic efficiency. NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO, which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield. Taken together, our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies, as well as genetic improvement of Cenchrus grasses.

Genomics of plant speciation

Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can form. Now, the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation research. Here, we review these recent genome-enabled developments in plant speciation. We discuss complications related to identification of reproductive isolation (RI) loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation, as increasingly revealed by new sequencing technologies. Further, we review how genomics has advanced what we know of some routes to new species formation, like hybridization or whole-genome duplication, while casting doubt on others, like population bottlenecks and genetic drift. While genomics can fast-track identification of genes and mutations that confer RI, we emphasize that follow-up molecular and field experiments remain critical. Nonetheless, genomics has clarified the outsized role of ancient variants rather than new mutations, particularly early during speciation. We conclude by highlighting promising avenues of future study. These include expanding what we know so far about the role of epigenetic and structural changes during speciation, broadening the scope and taxonomic breadth of plant speciation genomics studies, and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.

Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus

Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.

Global biodiversity data suggest allopolyploid plants do not occupy larger ranges or harsher conditions compared with their progenitors

Understanding the factors determining species' geographical and environmental range is a central question in evolution and ecology, and key for developing conservation and management practices. Shortly after the discovery of polyploidy, just over 100 years ago, it was suggested that polyploids generally have greater range sizes and occur in more extreme conditions than their diploid congeners. This suggestion is now widely accepted in the literature and is attributed to polyploids having an increased capacity for genetic diversity that increases their potential for adaptation and invasiveness. However, the data supporting this idea are mixed. Here, we compare the niche of allopolyploid plants to their progenitor species to determine whether allopolyploidization is associated with increased geographic range or extreme environmental tolerance. Our analysis includes 123 allopolyploid species that exist as only one known ploidy level, with at least one known progenitor species, and at least 50 records in the Global Biodiversity Information Facility (GBIF) database. We used GBIF occurrence data and range modeling tools to quantify the geographic and environmental distribution of these allopolyploids relative to their progenitors. We find no indication that allopolyploid plants occupy more extreme conditions or larger geographic ranges than their progenitors. Data evaluated here generally indicate no significant difference in range between allopolyploids and progenitors, and where significant differences do occur, the progenitors are more likely to exist in extreme conditions. We concluded that the evidence from these data indicate allopolyploidization does not result in larger or more extreme ranges. Thus, allopolyploidization does not have a consistent effect on species distribution, and we conclude it is more likely the content of an allopolyploid's genome rather than polyploidy per se that determines the potential for invasiveness.

A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales

Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the world. However, the absence of genome data limits our understanding of the pathways involved in bract coloration and breeding. Here, we report a chromosome-level assembly of the giga-genome of Bougainvillea × buttiana 'Mrs Butt', a cultivar thought to be the origin of many other Bougainvillea cultivars. The assembled genome is ~5 Gb with a scaffold N50 of 151 756 278 bp and contains 86 572 genes which have undergone recent whole-genome duplication. We confirmed that multiple rounds of whole-genome multiplication have occurred in the evolutionary history of the Caryophyllales, reconstructed the relationship in the Caryophyllales at whole genome level, and found discordance between species and gene trees as the result of complex introgression events. We investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryophyllales species. To explore the potential formation mechanism of diverse bract colors in Bougainvillea, we analyzed the genes involved in betalain and anthocyanin biosynthesis and found extremely low expression of ANS and DFR genes in all cultivars, which may limit anthocyanin biosynthesis. Our findings indicate that the expression pattern of the betalain biosynthetic pathway did not directly correlate with bract color, and a higher expression level in the betalain biosynthetic pathway is required for colored bracts. This improved understanding of the correlation between gene expression and bract color allows plant breeding outcomes to be predicted with greater certainty.

New insights into polyploid evolution and dynamic nature of Ludwigia section Isnardia (Onagraceae)

BACKGROUND

While polyploids are common in plants, the evolutionary history and natural dynamics of most polyploid groups are still unclear. Owing to plentiful earlier systematic studies, Ludwigia sect. Isnardia (comprising 22 wetland taxa) is an ideal allopolyploid complex to investigate polyploid evolution and natural dynamics within and among taxa. With a considerable sampling, we concentrated on revisiting earlier phylogenies of Isnardia, reevaluating the earlier estimated age of the most recent common ancestor (TMRCA), exploring the correlation between infraspecific genetic diversity and ploidy levels, and inspecting interspecific gene flows among taxa.

RESULTS

Phylogenetic trees and network concurred with earlier phylogenies and hypothesized genomes by incorporating 192 atpB-rbcL and ITS sequences representing 91% of Isnardia taxa. Moreover, we detected three multi-origin taxa. Our findings on L. repens and L. sphaerocarpa were consistent with earlier studies; L. arcuata was reported as a multi-origin taxon here, and an additional evolutionary scenario of L. sphaerocarpa was uncovered, both for the first time. Furthermore, estimated Isnardia TMRCA ages based on our data (5.9 or 8.9 million years ago) are in accordance with earlier estimates, although younger than fossil dates (Middle Miocene). Surprisingly, infraspecific genetic variations of Isnardia taxa did not increase with ploidy levels as anticipated from many other polyploid groups. In addition, the exuberant, low, and asymmetrical gene flows among Isnardia taxa indicated that the reproductive barriers may be weakened owing to allopolyploidization, which has rarely been reported.

CONCLUSIONS

The present research gives new perceptions of the reticulate evolution and dynamic nature of Isnardia and points to gaps in current knowledge about allopolyploid evolution.

Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective

Allopolyploids result from hybridization between different evolutionary lineages coupled with genome doubling. Homoeologous chromosomes (chromosomes with common shared ancestry) may undergo recombination immediately after allopolyploid formation and continue over successive generations. The outcome of this meiotic pairing behavior is dynamic and complex. Homoeologous exchanges (HEs) may lead to the formation of unbalanced gametes, reduced fertility, and selective disadvantage. By contrast, HEs could act as sources of novel evolutionary substrates, shifting the relative dosage of parental gene copies, generating novel phenotypic diversity, and helping the establishment of neo-allopolyploids. However, HE patterns vary among lineages, across generations, and even within individual genomes and chromosomes. The causes and consequences of this variation are not fully understood, though interest in this evolutionary phenomenon has increased in the last decade. Recent technological advances show promise in uncovering the mechanistic basis of HEs. Here, we describe recent observations of the common patterns among allopolyploid angiosperm lineages, underlying genomic and epigenomic features, and consequences of HEs. We identify critical research gaps and discuss future directions with far-reaching implications in understanding allopolyploid evolution and applying them to the development of important phenotypic traits of polyploid crops.

Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae

An ancient hexaploidization event in the most but not all Asteraceae plants, may have been responsible for shaping the genomes of many horticultural, ornamental, and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth. However, the duplication process of this hexaploidy, as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization, are still poorly understood. We analyzed 11 genomes from 10 genera in Asteraceae, and redated the Asteraceae common hexaploidization (ACH) event ~70.7-78.6 million years ago (Mya) and the Asteroideae specific tetraploidization (AST) event ~41.6-46.2 Mya. Moreover, we identified the genomic homologies generated from the ACH, AST and speciation events, and constructed a multiple genome alignment framework for Asteraceae. Subsequently, we revealed biased fractionations between the paleopolyploidization produced subgenomes, suggesting the ACH and AST both are allopolyplodization events. Interestingly, the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae. Furthermore, we reconstructed ancestral Asteraceae karyotype (AAK) that has 9 paleochromosomes, and revealed a highly flexible reshuffling of Asteraceae paleogenome. Of specific significance, we explored the genetic diversity of Heat Shock Transcription Factors (Hsfs) associated with recursive whole-genome polyploidizations, gene duplications, and paleogenome reshuffling, and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae. Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae, and is helpful for further communication and exploration of the diversification of plant families and phenotypes.

A Study of GUS Expression in Arabidopsis as a Tool for the Evaluation of Gene Evolution, Function and the Role of Expression Derived from Gene Duplication

Gene duplication played a fundamental role in eukaryote evolution and different copies of a given gene can be present in extant species, often with expressions and functions differentiated during evolution. We assume that, when such differentiation occurs in a gene copy, this may be indicated by its maintenance in all the derived species. To verify this hypothesis, we compared the histological expression domains of the three β-glucuronidase genes (AtGUS) present in Arabidopsis thaliana with the GUS evolutionary tree in angiosperms. We found that AtGUS gene expression overlaps in the shoot apex, the floral bud and the root hairs. In the root apex, AtGUS3 expression differs completely from AtGUS1 and AtGUS2, whose transcripts are present in the root cap meristem and columella, in the staminal cell niche, in the epidermis and in the proximal cortex. Conversely, AtGUS3 transcripts are limited to the old border-like cells of calyptra and those found along the protodermal cell line. The GUS evolutionary tree reveals that the two main clusters (named GUS1 and GUS3) originate from a duplication event predating angiosperm radiation. AtGUS3 belongs to the GUS3 cluster, while AtGUS1 and AtGUS2, which originate from a duplication event that occurred in an ancestor of the Brassicaceae family, are found together in the GUS1 cluster. There is another, previously undescribed cluster, called GUS4, originating from a very ancient duplication event. While the copy of GUS4 has been lost in many species, copies of GUS3 and GUS1 have been conserved in all species examined.

Dosage balance acts as a time-dependent selective barrier to subfunctionalization

BACKGROUND

Gene duplication is an important process for genome expansion, sometimes allowing for new gene functions to develop. Duplicate genes can be retained through multiple processes, either for intermediate periods of time through processes such as dosage balance, or over extended periods of time through processes such as subfunctionalization and neofunctionalization.

RESULTS

Here, we built upon an existing subfunctionalization Markov model by incorporating dosage balance to describe the interplay between subfunctionalization and dosage balance to explore selective pressures on duplicate copies. Our model incorporates dosage balance using a biophysical framework that penalizes the fitness of genetic states with stoichiometrically imbalanced proteins. These imbalanced states cause increased concentrations of exposed hydrophobic surface areas, which cause deleterious mis-interactions. We draw comparison between our Subfunctionalization + Dosage-Balance Model (Sub + Dos) and the previous Subfunctionalization-Only (Sub-Only) Model. This comparison includes how the retention probabilities change over time, dependent upon the effective population size and the selective cost associated with spurious interaction of dosage-imbalanced partners. We show comparison between Sub-Only and Sub + Dos models for both whole-genome duplication and small-scale duplication events.

CONCLUSION

These comparisons show that following whole-genome duplication, dosage balance serves as a time-dependent selective barrier to the subfunctionalization process, by causing an overall delay but ultimately leading to a larger portion of the genome retained through subfunctionalization. This higher percentage of the genome that is ultimately retained is caused by the alternative competing process, nonfunctionalization, being selectively blocked to a greater extent. In small-scale duplication, the reverse pattern is seen, where dosage balance drives faster rates of subfunctionalization, but ultimately leads to a smaller portion of the genome retained as duplicates. This faster rate of subfunctionalization is because the dosage balance of interacting gene products is negatively affected immediately after duplication and the loss of a duplicate restores the stoichiometric balance. Our findings provide support that the subfunctionalization of genes that are susceptible to dosage balance effects, such as proteins involved in complexes, is not a purely neutral process. With stronger selection against stoichiometrically imbalanced gene partners, the rates of subfunctionalization and nonfunctionalization slow; however, this ultimately leads to a greater proportion of subfunctionalized gene pairs.

Meeting in Liguria: hybridisation between Apennine endemic Euphorbia barrelieri and western Mediterranean E. nicaeensis led to the allopolyploid origin of E. ligustica

The Mediterranean Basin is renowned for its extremely rich biota and is considered as one of the 25 Global Biodiversity Hotspots, but its diversity is not homogeneously distributed. Outstanding in the number of (endemic) species are the Ligurian Alps (Italy). At the foot of the Ligurian Alps, little above the Mediterranean Sea, a disjunct occurrence of Italian endemic Euphorbia barrelieri was reported. Using an array of integrative methods ranging from cytogenetic (chromosome number and relative genome size estimation), over phylogenetic approaches (plastid, ITS and RAD sequencing) to multivariate morphometrics we disentangled the origin of these populations that were shown to be tetraploid. We performed phylogenetic analyses of the nuclear ITS and plastid regions of a broad taxonomic sampling of Euphorbia sect. Pithyusa to identify possible species involved in the origin of the tetraploid populations and then applied various analyses of RADseq data to identify the putative parental species. Our results have shown that the Ligurian populations of E. barrelieri are of allotetraploid origin that involved E. barrelieri and western Mediterranean E. nicaeensis as parental species. We thus describe a new species, E. ligustica, and hypothesise that its adaptation to similar environments in which E. barrelieri occurs, triggered development of similar morphology, whereas its genetic composition appears to be closer to that of E. nicaeensis. Our study emphasises the importance of polyploidisation for plant diversification, highlights the value of the Ligurian Alps as a hotspot of biodiversity and endemism and underlines the importance of integrative taxonomic approaches in uncovering cryptic diversity.

Comparative chloroplast genomics of 34 species in subtribe Swertiinae (Gentianaceae) with implications for its phylogeny

BACKGROUND

Subtribe Swertiinae, a medicinally significant and highly speciose Subtribe of family Gentianaceae. Despite previous extensive studies based on both morphology and molecular data, intergeneric and infrageneric relationships within subtribe Swertiinae remain controversial.

METHODS

Here, we employed four newly generated Swertia chloroplast genomes with thirty other published genomes to elucidate their genomic characteristics.

RESULTS

The 34 chloroplast genomes were small and ranged in size from 149,036 to 154,365 bp, each comprising two inverted repeat regions (size range 25,069-26,126 bp) that separated large single-copy (80,432-84,153 bp) and small single-copy (17,887-18,47 bp) regions, and all the chloroplast genomes showed similar gene orders, contents, and structures. These chloroplast genomes contained 129-134 genes each, including 84-89 protein-coding genes, 37 tRNAs, and 8 rRNAs. The chloroplast genomes of subtribe Swertiinae appeared to have lost some genes, such as rpl33, rpl2 and ycf15 genes. Comparative analyses revealed that two mutation hotspot regions (accD-psaI and ycf1) could serve as effective molecular markers for further phylogenetic analyses and species identification in subtribe Swertiinae. Positive selection analyses showed that two genes (ccsA and psbB) had high Ka/Ks ratios, indicating that chloroplast genes may have undergone positive selection in their evolutionary history. Phylogenetic analysis showed that the 34 subtribe Swertiinae species formed a monophyletic clade, with Veratrilla, Gentianopsis and Pterygocalyx located at the base of the phylogenetic tree. Some genera of this subtribe, however, were not monophyletic, including Swertia, Gentianopsis, Lomatogonium, Halenia, Veratrilla and Gentianopsis. In addition, our molecular phylogeny was consistent with taxonomic classification of subtribe Swertiinae in the Roate group and Tubular group. The results of molecular dating showed that the divergence between subtrib Gentianinae and subtrib Swertiinae was estimated to occur in 33.68 Ma. Roate group and Tubular group in subtribe Swertiinae approximately diverged in 25.17 Ma.

CONCLUSION

Overall, our study highlighted the taxonomic utility of chloroplast genomes in subtribe Swertiinae, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of subtribe Swertiinae species.

The alternative transcription and expression characterization of Dmc1 in autotetraploid Carassius auratus

Established autotetraploids often have a highly stable meiosis with high fertility compared with neo-autotetraploids. The autotetraploid Carassius auratus (4n = 200, RRRR) (4nRR), which stemmed from whole-genome duplication of Carassius auratus red var. (2n = 100, RR) (RCC), produces diploid gametes with an adopted diploid-like chromosome pairing in meiosis and maintains the formation of autotetraploid lineages. In this study, we focused on Dmc1, a meiosis-specific recombinase during the prophase of meiosis I, and elaborated on the genetic variation, alternative transcription, expression characterization, and epigenetic modification of Dmc1 in RCC and 4nRR. Two original Dmc1 from RCC were identified in 4nRR, and two duplicated Dmc1 differences in genetic composition were observed in 4nRR. Furthermore, we only noticed that one original and one duplicated Dmc1 were expressed in RCC and 4nRR, respectively. However, both possessed identical gene expression profiles, differential expression of sexual dimorphism, and hypomethylation levels. These results indicated that the specific expression of duplicated Dmc1 may be involve in the progression of meiosis of the diploid-like chromosome pairing in autotetraploid Carassius auratus. Herein, the findings significantly increase knowledge of meiosis of autopolyploid fish and provide meaningful insights into genetic breeding in polyploidy fish.

Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants

Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, and Solanoideae) and the designation of three other subfamilies (Schizanthoideae, Schwenckioideae, and Petunioideae), with the placement of several previously unassigned genera. We placed a Solanaceae-specific whole-genome triplication (WGT1) at ∼81 million years ago (mya), before the divergence of Schizanthoideae from other Solanaceae subfamilies at ∼73 mya. In addition, we detected two gene duplication bursts (GDBs) supporting proposed WGD events and four other GDBs. An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene (sub)families revealed that 21 gene clades have retained gene duplicates. These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development. This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development, providing an improved understanding of Solanaceae evolution.

The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceae polyploidization and its distinct traits

Orychophragmus violaceus, referred to as "eryuelan" (February orchid) in China, is an early-flowering ornamental plant. The high oil content and abundance of unsaturated fatty acids in O. violaceus seeds make it a potential high-quality oilseed crop. Here, we generated a whole-genome assembly for O. violaceus using Nanopore and Hi-C sequencing technologies. The assembled genome of O. violaceus was ∼1.3 Gb in size, with 12 pairs of chromosomes. Through investigation of ancestral genome evolution, we determined that the genome of O. violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype. Comparisons between the reconstructed subgenomes of O. violaceus identified indicators of subgenome dominance, indicating that subgenomes likely originated via allotetraploidy. O. violaceus was phylogenetically close to the Brassica genus, and tetraploidy in O. violaceus occurred approximately 8.57 million years ago, close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid lineage. However, the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica, as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks. Moreover, identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O. violaceus. These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O. violaceus.

The functional significance of the stomatal size to density relationship: Interaction with atmospheric [CO2] and role in plant physiological behaviour

The limits for stomatal conductance are set by stomatal size (SS) and density (SD). An inverse relationship between SS and SD has been observed in fossil and living plants. This has led to hypotheses proposing that the ratio of SS to SD influences the diffusion pathway for CO₂ and degree of physiological stomatal control. However, conclusive evidence supportive of a functional role of the SS-SD relationship is not evident, and patterns in SS-SD may simply reflect geometric constraints in stomatal spacing over a leaf surface. We examine published and new data to investigate the potential functional significance of the relationship between SS and SD to atmospheric [CO₂] in multiple generation adaptive responses and short-term acclamatory adjustment of stomatal morphology. Consistent patterns in SS and SD were not evident in fossil and living plants adapted to high [CO₂] over many generations. However, evolutionary adaptation to [CO₂] strongly affected SS and SD responses to elevated [CO₂], with plants adapted to the 'low' [CO₂] of the past 10 million years (Myr) showing adjustment of SS-SD, while members of the same species adapted to 'high' [CO₂] showed no response. This may suggest that SS and SD responses to future [CO₂] will likely constrain the stimulatory effect of 'CO₂-fertilisation' on photosynthesis. Angiosperms generally possessed higher densities of smaller stomata that corresponded to a greater degree of physiological stomatal control consistent with selective pressures induced by declining [CO₂] over the past 90 Myr. Atmospheric [CO₂] has likely shaped stomatal size and density relationships alongside the interaction with stomatal physiological behaviour. The rate and predicted extent of future increases in [CO₂] will have profound impacts on the selective pressures shaping SS and SD. Understanding the trade-offs involved in SS-SD and the interaction with [CO₂], will be central to the development of more productive climate resilient crops.

Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication

Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order's spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.

Enrichment of intrinsically disordered residues in ohnologs facilitates abiotic stress resilience in Brassica rapa

Arabidopsis thaliana and Brassica rapa are in the same evolutionary lineage, although the latter experienced an additional whole genome triplication event. Therefore, it would be intriguing to investigate the traits that gene duplication imposes to mediate plant stress tolerance. Here, we noticed that B. rapa abiotic stress resistance (ASR) genes which code at least one stress responsive domain have a significantly higher number of paralogs than A. thaliana. Analysing the disordered content of the ASR genes in both species, we found that intrinsically disordered residues (IDR) are specifically enriched in whole genome duplication (WGD) derived paralogs. Subsequently, domain similarity analysis between WGD pairs of both species has revealed that majority of WGD pairs in B. rapa did not share domains with each other. Furthermore, domain enrichment analysis has shown that B. rapa paralogs contain 36 distinct stress responsive enriched domains, significantly higher than A. thaliana paralogs. Next, we performed MSA to investigate the domain conservation between orthologs and ohnologs pairs, we found that 80.13% of B. rapa ohnologs acquire new domains, depicting the fact that ohnologs play a significant role in stress-related behaviours. The average IDR content of the ohnologs enriching new domains after gene duplication in B. rapa (0.19), is also significantly higher than A. thaliana (0.04). Interestingly, we also found that all of these attributes i.e., exhibiting higher number of WGD paralogs and enhancement of IDR in ASR genes of B. rapa compared to A. thaliana is exclusive for ASR genes only. No such significant differences were observed in randomly selected non-ASR genes between the two species. Together these results provide strong support for the hypothesis that augmentation of IDR content followed by a whole genome duplication event imposes the stress resistance potentiality in B. rapa. This research will shed light on the mechanism of how B. rapa is able to successfully adapt to stress over the evolutionary timescale.

Apomictic Mountain Whitebeam (Sorbus austriaca, Rosaceae) Comprises Several Genetically and Morphologically Divergent Lineages

The interplay of polyploidisation, hybridization, and apomixis contributed to the exceptional diversity of Sorbus (Rosaceae), giving rise to a mosaic of genetic and morphological entities. The Sorbus austriaca species complex from the mountains of Central and South-eastern Europe represents an allopolyploid apomictic system of populations that originated following hybridisation between S. aria and S. aucuparia. However, the mode and frequency of such allopolyploidisations and the relationships among different, morphologically more or less similar populations that have often been described as different taxa remain largely unexplored. We used amplified fragment length polymorphism (AFLP) fingerprinting, plastid DNA sequencing, and analyses of nuclear microsatellites, along with multivariate morphometrics and ploidy data, to disentangle the relationships among populations within this intricate complex. Our results revealed a mosaic of genetic lineages—many of which have not been taxonomically recognised—that originated via multiple allopolyploidisations. The clonal structure within and among populations was then maintained via apomixis. Our results thus support previous findings that hybridisation, polyploidization, and apomixis are the main drivers of Sorbus diversification in Europe.

Disentangling Relationships among the Alpine Species of Luzula Sect. Luzula (Juncaceae) in the Eastern Alps

Polyploidisation, agmatoploidy and symploidy have driven the diversification of Luzula sect. Luzula. Several morphologically very similar species with different karyotypes have evolved, but their evolutionary origins and relationships are unknown. In this study, we used a combination of relative genome size and karyotype estimations as well amplified fragment length polymorphism (AFLP) fingerprinting to investigate the relationships among predominately (sub)alpine Luzula alpina, L. exspectata, L multiflora and L. sudetica in the Eastern Alps, including also some samples of L. campestris and L. taurica as outgroup. Our study revealed common co-occurrence of two or three different ploidies (di-, tetra- and hexaploids) at the same localities, and thus also common co-occurrence of different species, of which L. sudetica was morphologically, ecologically and genetically most divergent. Whereas agmatoploid L. exspectata likely originated only once from the Balkan L. taurica, and hexaploid L. multiflora once from tetraploid L. multiflora, the AFLP data suggest multiple origins of tetraploid L. multiflora, from which partly agmatoploid individuals of L. alpina likely originated recurrently by partial fragmentation of the chromosomes. In contrast to common recurrent formation of polyploids in flowering plants, populations of agmatoploids resulting by fission of complete chromosome sets appear to have single origins, whereas partial agmatoploids are formed recurrently. Whether this is a general pattern in Luzula sect. Luzula, and whether segregation of ecological niches supports the frequent co-occurrence of closely related cytotypes in mixed populations, remains the subject of ongoing research.

Morphological and environmental differentiation as prezygotic reproductive barriers between parapatric and allopatric Campanula rotundifolia agg. cytotypes

BACKGROUND AND AIMS

Reproductive isolation and local establishment are necessary for plant speciation. Polyploidy, the possession of more than two complete chromosome sets, creates a strong postzygotic reproductive barrier between diploid and tetraploid cytotypes. However, this barrier weakens between polyploids (e.g. tetraploids and hexaploids). Reproductive isolation may be enhanced by cytotype morphological and environmental differentiation. Moreover, morphological adaptations to local conditions contribute to plant establishment. However, the relative contributions of ploidy level and the environment to morphology have generally been neglected. Thus, the extent of morphological variation driven by ploidy level and the environment was modelled for diploid, tetraploid and hexaploid cytotypes of Campanula rotundifolia agg. Cytotype distribution was updated, and morphological and environmental differentiation was tested in the presence and absence of natural contact zones.

METHODS

Cytotype distribution was assessed from 231 localities in Central Europe, including 48 localities with known chromosome counts, using flow cytometry. Differentiation in environmental niche and morphology was tested for cytotype pairs using discriminant analyses. A structural equation model was used to explore the synergies between cytotype, environment and morphology.

KEY RESULTS

Tremendous discrepancies were revealed between the reported and detected cytotype distribution. Neither mixed-ploidy populations nor interploidy hybrids were detected in the contact zones. Diploids had the broadest environmental niche, while hexaploids had the smallest and specialized niche. Hexaploids and spatially isolated cytotype pairs differed morphologically, including allopatric tetraploids. While leaf and shoot morphology were influenced by environmental conditions and polyploidy, flower morphology depended exclusively on the cytotype.

CONCLUSIONS

Reproductive isolation mechanisms vary between cytotypes. While diploids and polyploids are isolated postzygotically, the environmental niche shift is essential between higher polyploids. The impact of polyploidy and the environment on plant morphology implies the adaptive potential of polyploids, while the exclusive relationship between flower morphology and cytotype highlights the role of polyploidy in reproductive isolation.

Navigating the CoGe Online Software Suite for Polyploidy Research

The CoGe software suite at genomevolution.org hosts a number of tools that facilitate genomic research on plant and animal whole-genome multiplication-polyploidy. SynMap permits analysis and visualization of two-way syntenic dotplot alignments of genomes, includes many options and data/graphics download possibilities, and even permits three-genome synteny maps and interactive views. FractBias is a tool that operates within SynMap that permits calculation and graphic display of genome fragments (such as chromosomes) of one species mapped to another, displaying both blockwise homology depths and the extent of syntenic gene (syntelog) loss following polyploidy events. SynMap macrosynteny results can segue into the microsynteny tool GEvo, which provides genome-browser-like views of homologous genome blocks. CoGe FeatView allows call-up of given gene features already stored in the CoGe resource, and CoGeBlast permits searches for additional features that can be analyzed or downloaded further. Links from these tools can be fed into SynFind, which can find syntenic blocks surrounding a feature across multiple specified genomes while also simultaneously providing overall genome-wide syntenic depth calculations that can be interpreted to reflect polyploidy levels. Here, we describe basic use of these tools on the CoGe software suite.