Nonadditive gene expression in polyploids

Intraspecific diploidization of a halophyte root fungus drives heterosis

How organisms respond to environmental stress is a key topic in evolutionary biology. This study focused on the genomic evolution of Laburnicola rhizohalophila, a dark-septate endophytic fungus from roots of a halophyte. Chromosome-level assemblies were generated from five representative isolates from structured subpopulations. The data revealed significant genomic plasticity resulting from chromosomal polymorphisms created by fusion and fission events, known as dysploidy. Analyses of genomic features, phylogenomics, and macrosynteny have provided clear evidence for the origin of intraspecific diploid-like hybrids. Notably, one diploid phenotype stood out as an outlier and exhibited a conditional fitness advantage when exposed to a range of abiotic stresses compared with its parents. By comparing the gene expression patterns in each hybrid parent triad under the four growth conditions, the mechanisms underlying growth vigor were corroborated through an analysis of transgressively upregulated genes enriched in membrane glycerolipid biosynthesis and transmembrane transporter activity. In vitro assays suggested increased membrane integrity and lipid accumulation, as well as decreased malondialdehyde production under optimal salt conditions (0.3 M NaCl) in the hybrid. These attributes have been implicated in salinity tolerance. This study supports the notion that hybridization-induced genome doubling leads to the emergence of phenotypic innovations in an extremophilic endophyte.

hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).

Evolutionary insights into the organization of chromatin structure and landscape of transcriptional regulation in plants

Development of complex traits necessitates the functioning and coordination of intricate regulatory networks involving multiple genes. Understanding 3D chromatin structure can facilitate insight into the regulation of gene expression by regulatory elements. This potential, of visualizing the role of chromatin organization in the evolution and function of regulatory elements, remains largely unexplored. Here, we describe new perspectives that arise from the dual considerations of sequence variation of regulatory elements and chromatin structure, with a special focus on whole-genome doubling or polyploidy. We underscore the significance of hierarchical chromatin organization in gene regulation during evolution. In addition, we describe strategies for exploring chromatin organization in future investigations of regulatory evolution in plants, enabling insights into the evolutionary influence of regulatory elements on gene expression and, hence, phenotypes.

Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton

Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings of duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern gene regulatory control. Here, we characterized genome-wide nucleosome organization and chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n = 4X = 52), relative to its two diploid parents (AA or DD genome) and their synthetic diploid hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average nucleosome spacing in diploids, and this intergenomic difference diminished in the allopolyploid but not hybrid. Allopolyploidization also exhibited increased accessibility at promoters genome-wide and synchronized cis-regulatory motifs between subgenomes. A prominent cis-acting control was inferred for chromatin dynamics and demonstrated by transposable element removal from promoters. Linking accessibility to gene expression patterns, we found distinct regulatory effects for hybridization and later allopolyploid stages, including nuanced establishment of homoeolog expression bias and expression level dominance. Histone gene expression and nucleosome organization are coordinated through chromatin accessibility. Our study demonstrates the capability to track high-resolution chromatin structure dynamics and reveals their role in the evolution of cis-regulatory landscapes and duplicate gene expression in polyploids, illuminating regulatory ties to subgenomic asymmetry and dominance.

Cytonuclear interplay in auto- and allopolyploids: a multifaceted perspective from the Festuca-Lolium complex

Restoring cytonuclear stoichiometry is necessary after whole-genome duplication (WGD) and interspecific/intergeneric hybridization in plants. We investigated this phenomenon in auto- and allopolyploids of the Festuca-Lolium complex providing insights into the mechanisms governing cytonuclear interactions in early polyploid and hybrid generations. Our study examined the main processes potentially involved in restoring the cytonuclear balance after WGD comparing diploids and new and well-established autopolyploids. We uncovered that both the number of chloroplasts and the number of chloroplast genome copies were significantly higher in the newly established autopolyploids and grew further in more established autopolyploids. The increase in the copy number of the chloroplast genome exceeded the rise in the number of chloroplasts and fully compensated for the doubling of the nuclear genome. In addition, changes in nuclear and organelle gene expression were insignificant. Allopolyploid Festuca × Lolium hybrids displayed potential structural conflicts in parental protein variants within the cytonuclear complexes. While biased maternal allele expression has been observed in numerous hybrids, our results suggest that its role in cytonuclear stabilization in the Festuca × Lolium hybrids is limited. This study provides insights into the restoration of the cytonuclear stoichiometry, yet it emphasizes the need for future research to explore post-transcriptional regulation and its impact on cytonuclear gene expression stoichiometry. Our findings may enhance the understanding of polyploid plant evolution, with broader implications for the study of cytonuclear interactions in diverse biological contexts.

Friends without benefits: Extensive cytotype sympatry and polyploid persistence in an African geophyte

PREMISE

Polyploidy is a major factor in plant adaptation and speciation. Multiple mechanisms contribute to autopolyploid frequency within populations, but uncertainties remain regarding mechanisms that facilitate polyploid establishment and persistence. Here we aimed to document and predict cytotype distributions of Oxalis obliquifolia Steud. ex A. Rich. across Gauteng, South Africa, and test for evidence of possible mechanisms, including morphological, phenological, and reproductive traits, that may potentially facilitate polyploid persistence.

METHODS

Over 320 O. obliquifolia plants from 25 sites were cytotyped using flow cytometry, and DNA ploidy was confirmed using meiotic chromosome squashes. Cytotypes were mapped and correlations with abiotic variables assessed using ordinations. To assess morphological and phenological associations with cytotype, we grew multiple cytotypes in a common garden, measured phenotypic traits and compared them using linear models and discriminant analyses. Intercytotype reproductive isolation was assessed using crossing experiments, and AMOVAs based on ITS DNA sequences tested for cytogeographic structure.

RESULTS

Six cytotypes were identified, and most sites had multiple cytotypes. Abiotic variables were not predictive of cytotype distribution. A clear gigas effect was present. Differences in flower size and phenology suggested pollinator interactions could play a role in polyploid persistence. Intercytotype crosses produced seed at low frequency. DNA data suggested diploids and polyploids were largely reproductively isolated in situ, and polyploidization events were not frequent enough to explain high cytotype sympatry.

CONCLUSIONS

Diploids and polyploids are behaving as separate species, despite little observable niche differentiation and non-zero potential intercytotype seed set. Tests on biotic interactions and intercytotype F1 fitness may provide insights into diploid and polyploid coexistence.

Investigation of regulatory divergence between homoeologs in the recently formed allopolyploids, Tragopogon mirus and T. miscellus (Asteraceae)

Polyploidy is an important evolutionary process throughout eukaryotes, particularly in flowering plants. Duplicated gene pairs (homoeologs) in allopolyploids provide additional genetic resources for changes in molecular, biochemical, and physiological mechanisms that result in evolutionary novelty. Therefore, understanding how divergent genomes and their regulatory networks reconcile is vital for unraveling the role of polyploidy in plant evolution. Here, we compared the leaf transcriptomes of recently formed natural allotetraploids (Tragopogon mirus and T. miscellus) and their diploid parents (T. porrifolius X T. dubius and T. pratensis X T. dubius, respectively). Analysis of 35 400 expressed loci showed a significantly higher level of transcriptomic additivity compared to old polyploids; only 22% were non-additively expressed in the polyploids, with 5.9% exhibiting transgressive expression (lower or higher expression in the polyploids than in the diploid parents). Among approximately 7400 common orthologous regions (COREs), most loci in both allopolyploids exhibited expression patterns that were vertically inherited from their diploid parents. However, 18% and 20.3% of the loci showed novel expression bias patterns in T. mirus and T. miscellus, respectively. The expression changes of 1500 COREs were explained by cis-regulatory divergence (the condition in which the two parental subgenomes do not interact) between the diploid parents, whereas only about 423 and 461 of the gene expression changes represent trans-effects (the two parental subgenomes interact) in T. mirus and T. miscellus, respectively. The low degree of both non-additivity and trans-effects on gene expression may present the ongoing evolutionary processes of the newly formed Tragopogon polyploids (~80-90 years).

Subgenome evolutionary dynamics in allotetraploid ferns: insights from the gene expression patterns in the allotetraploid species Phegopteris decursivepinnata (Thelypteridacea, Polypodiales)

Allopolyploidization often leads to disruptive conflicts among more than two sets of subgenomes, leading to genomic modifications and changes in gene expression. Although the evolutionary trajectories of subgenomes in allopolyploids have been studied intensely in angiosperms, the dynamics of subgenome evolution remain poorly understood in ferns, despite the prevalence of allopolyploidization. In this study, we have focused on an allotetraploid fern-Phegopteris decursivepinnata-and its diploid parental species, P. koreana (K) and P. taiwaniana (T). Using RNA-seq analyses, we have compared the gene expression profiles for 9,540 genes among parental species, synthetic F1 hybrids, and natural allotetraploids. The changes in gene expression patterns were traced from the F1 hybrids to the natural allopolyploids. This study has revealed that the expression patterns observed in most genes in the F1 hybrids are largely conserved in the allopolyploids; however, there were substantial differences in certain genes between these groups. In the allopolyploids compared with the F1 hybrids, the number of genes showing a transgressive pattern in total expression levels was increased. There was a slight reduction in T-dominance and a slight increase in K-dominance, in terms of expression level dominance. Interestingly, there is no obvious bias toward the T- or K-subgenomes in the number and expression levels overall, showing the absence of subgenome dominance. These findings demonstrated the impacts of the substantial transcriptome change after hybridization and the moderate modification during allopolyploid establishment on gene expression in ferns and provided important insights into subgenome evolution in polyploid ferns.

Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression

Hybridization coupled to polyploidy, or allopolyploidy, has dramatically shaped the evolution of flowering plants, teleost fishes, and other lineages. Studies of recently formed allopolyploid plants have shown that the two subgenomes that merged to form that new allopolyploid do not generally express their genes equally. Instead, one of the two subgenomes expresses its paralogs more highly on average. Meanwhile, older allopolyploidy events tend to show biases in duplicate losses, with one of the two subgenomes retaining more genes than the other. Since reduced expression is a pathway to duplicate loss, understanding the origins of expression biases may help explain the origins of biased losses. Because we expect gene expression levels to experience stabilizing selection, our conceptual frameworks for how allopolyploid organisms form tend to assume that the new allopolyploid will show balanced expression between its subgenomes. It is then necessary to invoke phenomena such as differences in the suppression of repetitive elements to explain the observed expression imbalances. Here we show that, even for phenotypically identical diploid progenitors, the inherent kinetics of gene expression give rise to biases between the expression levels of the progenitor genes in the hybrid. Some of these biases are expected to be gene-specific and not give rise to global differences in progenitor gene expression. However, particularly in the case of allopolyploids formed from progenitors with different genome sizes, global expression biases favoring one subgenome are expected immediately on formation. Hence, expression biases are arguably the expectation upon allopolyploid formation rather than a phenomenon needing explanation. In the future, a deeper understanding of the kinetics of allopolyploidy may allow us to better understand both biases in duplicate losses and hybrid vigor.

Nonadditive and allele-specific expression of ghrelin in hybrid tilapia

Background

Interspecies hybridization is an important breeding method to generate fishes with heterosis in aquaculture. Using this method, hybrid Nile tilapia (Oreochromis niloticus, ♀) × blue tilapia (Oreochromis aureus, ♂) has been produced and widely farmed due to its growth and appetite superiorities. However, the genetic mechanism of these advanced traits is still not well understood. Ghrelin is a crucial gene that regulates growth and appetite in fishes. In the present study, we focused on the expression characteristics and its regulation of ghrelin in the hybrid.

Results

The tissue distribution analysis showed that ghrelin was predominantly expressed in the stomach in the hybrid. Ghrelin was more highly expressed in the stomach in the hybrid and Nile tilapia, compared to blue tilapia, showing a nonadditive pattern. Two single-nucleotide polymorphism (SNP) sites were identified including T/C and C/G from the second exon in the ghrelin gene from Nile tilapia and blue tilapia. By pyrosequencing based on the SNP sites, the allele-specific expression (ASE) of ghrelin in the hybrid was assayed. The result indicated that ghrelin in the hybrid showed higher maternal allelic transcript ratios. Fasting significantly increased ghrelin overall expression at 4, 8, 12, 24, and 48 h. In addition, higher maternal allelic transcript ratios were not changed in the fasting hybrids at 48 h. The cis and trans effects were determined by evaluating the overall expression and ASE values in the hybrid. The expression of ghrelin was mediated by compensating cis and trans effects in hybrid.

Conclusion

In summary, the present lines of evidence showed the nonadditive expression of ghrelin in the hybrid tilapia and its regulation by subgenomes, offering new insight into gene expression characteristics in hybrids.

Transcriptome Shock in Developing Embryos of a Brassica napus and Brassica rapa Hybrid

Interspecific crosses that fuse the genomes of two different species may result in overall gene expression changes in the hybrid progeny, called 'transcriptome shock'. To better understand the expression pattern after genome merging during the early stages of allopolyploid formation, we performed RNA sequencing analysis on developing embryos of Brassica rapa, B. napus, and their synthesized allotriploid hybrids. Here, we show that the transcriptome shock occurs in the developing seeds of the hybrids. Of the homoeologous gene pairs, 17.1% exhibit expression bias, with an overall expression bias toward B. rapa. The expression level dominance also biases toward B. rapa, mainly induced by the expression change in homoeologous genes from B. napus. Functional enrichment analysis revealed significant differences in differentially expressed genes (DEGs) related to photosynthesis, hormone synthesis, and other pathways. Further study showed that significant changes in the expression levels of the key transcription factors (TFs) could regulate the overall interaction network in the developing embryo, which might be an essential cause of phenotype change. In conclusion, the present results have revealed the global changes in gene expression patterns in developing seeds of the hybrid between B. rapa and B. napus, and provided novel insights into the occurrence of transcriptome shock for harnessing heterosis.

Genome shock in a synthetic allotetraploid wheat invokes subgenome-partitioned gene regulation, meiotic instability, and karyotype variation

It is becoming increasingly evident that interspecific hybridization at the homoploid level or coupled with whole-genome duplication (i.e. allopolyploidization) has played a major role in biological evolution. However, the direct impacts of hybridization and allopolyploidization on genome structure and function, phenotype, and fitness remains to be fully understood. Synthetic hybrids and allopolyploids are trackable experimental systems that can be used to address this issue. In this study, we resynthesized a pair of reciprocal F1 hybrids and corresponding reciprocal allotetraploids using the two diploid progenitor species of bread wheat (Triticum aestivum, BBAADD), namely T. urartu (AA) and Aegilops tauschii (DD). By comparing phenotypes related to growth, development, and fitness, and by analysing genome expression in both hybrids and allotetraploids in relation to the parents, we found that the types and trends of karyotype variation in the immediately formed allotetraploids were correlated with both instability of meiosis and chromosome- and subgenome-biased expression. We determined clear advantages of allotetraploids over diploid F1 hybrids in several morphological traits including fitness that mirrored the tissue- and developmental stage-dependent subgenome-partitioning of the allotetraploids. The allotetraploids were meiotically unstable primarily due to homoeologous pairing that varied dramatically among the chromosomes. Nonetheless, the manifestation of organismal karyotype variation and the occurrence of meiotic irregularity were not concordant, suggesting a role of functional constraints probably imposed by subgenome- and chromosome-biased gene expression. Our results provide new insights into the direct impacts and consequences of hybridization and allopolyploidization that are relevant to evolution and likely to be informative for future crop improvement approaches using synthetic polyploids.

Developmental Instability and Gene Dysregulation in an Extracted Tetraploid from Hexaploid Wheat

The BBAA subgenomes of hexaploid common wheat can be 'extracted' to constitute a viable and self-reproducing novel tetraploid wheat, termed extracted tetraploid wheat (ETW). Prior studies have shown ETW manifesting phenotypic abnormalities and alteration in gene expression and epigenetic modifications. No population level investigation has been conducted, leaving the issue unclear regarding whether developmental stability, an essential property evolved in all natural organisms, might have been undermined in ETW. Here, we measured variations in five morphological traits and somatic chromosomal stability in populations of ETW and of its hexaploid donor, a resynthesized hexaploid and a natural tetraploid wheat. We observed phenotypic defects in ETW. Meanwhile, we documented much greater within-population variations in ETW than in the other wheat genotypes, most probably due to disrupted developmental stability in ETW. Also, somatic structural chromosome variations were detected only in ETW. Comparative transcriptome analyses indicated that the disrupted developmental stability of ETW is likely linked to massive dysregulation of genome-wide gene expression rather than to genetic mutations. Population network analysis of gene expression implicated intrinsic connectivity among the variable traits, while gene set enrichment analysis provided possible links between dysregulated gene expression and interlaced trait variation.

Effects of Allopolyploidization and Homoeologous Chromosomal Segment Exchange on Homoeolog Expression in a Synthetic Allotetraploid Wheat under Variable Environmental Conditions

Allopolyploidy through the combination of divergent genomes into a common nucleus at doubled dosage is known as a potent genetic and evolutionary force. As a macromutation, a striking feature of allopolyploidy in comparison with other mutational processes is that 'genome shock' can be evoked, thereby generating rapid and saltational biological consequences. A major manifestation of genome shock is genome-wide gene expression rewiring, which previously remained to be fully elucidated. Here, using a large set of RNAseq-based transcriptomic data of a synthetic allotetraploid wheat (genome AADD) and its parental species, we performed in-depth analyses of changes in the genome-wide gene expression under diverse environmental conditions at the subgenome (homoeolog) level and investigated the additional effects of homoeologous chromosomal segment exchanges (abbreviated HEs). We show that allopolyploidy caused large-scale changes in gene expression that were variable across the conditions and exacerbated by both stresses and HEs. Moreover, although both subgenomes (A and D) showed clear commonality in the changes, they responded differentially under variable conditions. The subgenome- and condition-dependent differentially expressed genes were enriched for different gene ontology terms implicating different biological functions. Our results provide new insights into the direct impacts of allopolyploidy on condition-dependent changes in subgenome expression and the additional effects of HEs in nascent allopolyploidy.

Allelic expression of AhNSP2-B07 due to parent of origin affects peanut nodulation

Legumes are well-known for establishing a symbiotic relationship with rhizobia in root nodules to fix nitrogen from the atmosphere. The nodulation signaling pathway 2 (NSP2) gene plays a critical role in the symbiotic signaling pathway. In cultivated peanut, an allotetraploid (2n = 4x = 40, AABB) legume crop, natural polymorphisms in a pair of NSP2 homoeologs (N_a and N_b) located on chromosomes A08 and B07, respectively, can cause loss of nodulation. Interestingly, some heterozygous (N_Bn_b) progeny produced nodules, while some others do not, suggesting non-Mendelian inheritance in the segregating population at the N_b locus. In this study, we investigated the non-Mendelian inheritance at the N_B locus. Selfing populations were developed to validate the genotypical and phenotypical segregating ratios. Allelic expression was detected in roots, ovaries, and pollens of heterozygous plants. Bisulfite PCR and sequencing of the N_b gene in gametic tissue were performed to detect the DNA methylation variations of this gene in different gametic tissues. The results showed that only one allele at the Nb locus expressed in peanut roots during symbiosis. In the heterozygous (N_bn_b) plants, if dominant allele expressed, the plants produced nodules, if recessive allele expressed, then no nodules were produced. qRT-PCR experiments revealed that the expression of N_b gene in the ovary was extremely low, about seven times lower than that in pollen, regardless of genotypes or phenotypes of the plants at this locus. The results indicated that N_b gene expression in peanut depends on the parent of origin and is imprinted in female gametes. However, no significant differences of DNA methylation level were detected between these two gametic tissues by bisulfite PCR and sequencing. The results suggested that the remarkable low expression of N_b in female gametes may not be caused by DNA methylation. This study provided a unique genetic basis of a key gene involved in peanut symbiosis, which could facilitate understanding the regulation of gene expression in symbiosis in polyploid legumes.

Transgenerational Paternal Inheritance of TaCKX GFMs Expression Patterns Indicate a Way to Select Wheat Lines with Better Parameters for Yield-Related Traits

Members of the TaCKX gene family (GFMs) encode the cytokinin oxygenase/dehydrogenase enzyme (CKX), which irreversibly degrades cytokinins in the organs of wheat plants; therefore, these genes perform a key role in the regulation of yield-related traits. The purpose of the investigation was to determine how expression patterns of these genes, together with the transcription factor-encoding gene TaNAC2-5A, and yield-related traits are inherited to apply this knowledge to speed up breeding processes. The traits were tested in 7 days after pollination (DAP) spikes and seedling roots of maternal and paternal parents and their F₂ progeny. The expression levels of most of them and the yield were inherited in F₂ from the paternal parent. Some pairs or groups of genes cooperated, and some showed opposite functions. Models of up- or down-regulation of TaCKX GFMs and TaNAC2-5A in low-yielding maternal plants crossed with higher-yielding paternal plants and their high-yielding F₂ progeny reproduced gene expression and yield of the paternal parent. The correlation coefficients between TaCKX GFMs, TaNAC2-5A, and yield-related traits in high-yielding F₂ progeny indicated which of these genes were specifically correlated with individual yield-related traits. The most common was expressed in 7 DAP spikes TaCKX2.1, which positively correlated with grain number, grain yield, spike number, and spike length, and seedling root mass. The expression levels of TaCKX1 or TaNAC2-5A in the seedling roots were negatively correlated with these traits. In contrast, the thousand grain weight (TGW) was negatively regulated by TaCKX2.2.2, TaCKX2.1, and TaCKX10 in 7 DAP spikes but positively correlated with TaCKX10 and TaNAC2-5A in seedling roots. Transmission of TaCKX GFMs and TaNAC2-5A expression patterns and yield-related traits from parents to the F₂ generation indicate their paternal imprinting. These newly shown data of nonmendelian epigenetic inheritance shed new light on crossing strategies to obtain a high-yielding F₂ generation.

Sequence capture: Obsolete or irreplaceable? A thorough validation across phylogenetic distances and its applicability to hybrids and allopolyploids

As whole-genome sequencing has become pervasive, some have suggested that reduced genomic representation approaches, for example, sequence capture, are becoming obsolete. In the present study, we argue that these techniques still provide excellent tools in terms of price and quality of data as well as in their ability to provide markers with specific features, as required, for example, in phylogenomics. A potential drawback of the wide-scale application of reduced representation approaches could be their drop in efficiency with increasing phylogenetic distance from the reference species. While some studies have focused on the degree and performance of reduced representation techniques in such situations, to our knowledge, none of them evaluated their applicability to inter-specific hybrids and polyploids. This highlights a significant gap in current knowledge since there is increasing evidence for the frequent occurrence of natural hybrids and polyploids, as well as for the major importance of both phenomena in evolution. The main aim of the present study was to carry out a thorough validation of SEQcap applicability to (1) a set of non-model taxa with a wide range of phylogenetic relatedness and (2) inter-specific hybrids of various ploidies and genomic compositions. Considering the latter point, we especially focused on mechanisms causing allelic bias and consequent allelic dropout, as these could have confounding effects with respect to the evolutionary genomic dynamics of hybrids, especially in asexuals, which virtually reproduce as a frozen F1 generation.

Subgenome-dominant expression and alternative splicing in response to Sclerotinia infection in polyploid Brassica napus and progenitors

Polyploidy has played an extensive role in the evolution of flowering plants. Allopolyploids, with subgenomes containing duplicated gene pairs called homeologs, can show rapid transcriptome changes including novel alternative splicing (AS) patterns. The extent to which abiotic stress modulates AS of homeologs is a nascent topic in polyploidy research. We subjected both resynthesized and natural lines of polyploid Brassica napus, along with the progenitors Brassica rapa and Brassica oleracea, to infection with the fungal pathogen Sclerotinia sclerotiorum. RNA-sequencing analyses revealed widespread divergence between polyploid subgenomes in both gene expression and AS patterns. Resynthesized B. napus displayed significantly more A and C subgenome biased homeologs under pathogen infection than during uninfected growth. Differential AS (DAS) in response to infection was highest in natural B. napus (12 709 DAS events) and lower in resynthesized B. napus (8863 DAS events). Natural B. napus had more upregulated events and fewer downregulated events. There was a global expression bias towards the B. oleracea-derived (C) subgenome in both resynthesized and natural B. napus, enhanced by widespread non-parental downregulation of the B. rapa-derived (A) homeolog. In the resynthesized B. napus, this resulted in a disproportionate C subgenome contribution to the pathogen defense response, characterized by biases in both transcript expression levels and the proportion of induced genes. Our results elucidate the complex ways in which Sclerotinia infection affects expression and AS of homeologous genes in resynthesized and natural B. napus.

New cup out of old coffee: contribution of parental gene expression legacy to phenotypic novelty in coffee beans of the allopolyploid Coffea arabica L

BACKGROUND AND AIMS

Allopolyploidization is a widespread phenomenon known to generate novel phenotypes by merging evolutionarily distinct parental genomes and regulatory networks in a single nucleus. The objective of this study was to investigate the transcriptional regulation associated with phenotypic novelty in coffee beans of the allotetraploid Coffea arabica.

METHODS

A genome-wide comparative transcriptomic analysis was performed in C. arabica and its two diploid progenitors, C. canephora and C. eugenioides. Gene expression patterns and homeologue expression were studied on seeds at five different maturation stages. The involvement of homeologue expression bias (HEB) in specific traits was addressed both by functional enrichment analyses and by the study of gene expression in the caffeine and chlorogenic acid biosynthesis pathways.

KEY RESULTS

Expression-level dominance in C. arabica seed was observed for most of the genes differentially expressed between the species. Approximately a third of the genes analysed showed HEB. This proportion increased during seed maturation but the biases remained equally distributed between the sub-genomes. The relative expression levels of homeologues remained relatively constant during maturation and were correlated with those estimated in leaves of C. arabica and interspecific hybrids between C. canephora and C. eugenioides. Functional enrichment analyses performed on genes exhibiting HEB enabled the identification of processes potentially associated with physiological traits. The expression profiles of the genes involved in caffeine biosynthesis mirror the differences observed in the caffeine content of mature seeds of C. arabica and its parental species.

CONCLUSIONS

Neither of the two sub-genomes is globally preferentially expressed in C. arabica seeds, and homeologues appear to be co-regulated by shared trans-regulatory mechanisms. The observed HEBs are thought to be a legacy of gene expression differences inherited from diploid progenitor species. Pre-existing functional divergences between parental species appear to play an important role in controlling the phenotype of C. arabica seeds.

Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrid

Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.

Molecular evidence for adaptive evolution of drought tolerance in wild cereals

The considerable drought tolerance of wild cereal crop progenitors has diminished during domestication in the pursuit of higher productivity. Regaining this trait in cereal crops is essential for global food security but requires novel genetic insight. Here, we assessed the molecular evidence for natural variation of drought tolerance in wild barley (Hordeum spontaneum), wild emmer wheat (Triticum dicoccoides), and Brachypodium species collected from dry and moist habitats at Evolution Canyon, Israel (ECI). We report that prevailing moist vs dry conditions have differentially shaped the stomatal and photosynthetic traits of these wild cereals in their respective habitats. We present the genomic and transcriptomic evidence accounting for differences, including co-expression gene modules, correlated with physiological traits, and selective sweeps, driven by the xeric site conditions on the African Slope (AS) at ECI. Co-expression gene module 'circadian rhythm' was linked to significant drought-induced delay in flowering time in Brachypodium stacei genotypes. African Slope-specific differentially expressed genes are important in barley drought tolerance, verified by silencing Disease-Related Nonspecific Lipid Transfer 1 (DRN1), Nonphotochemical Quenching 4 (NPQ4), and Brassinosteroid-Responsive Ring-H1 (BRH1). Our results provide new genetic information for the breeding of resilient wheat and barley in a changing global climate with increasingly frequent drought events.

Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly

Natural isolates of the potato and tomato pathogen Phytophthora infestans exhibit substantial variation in virulence, chemical sensitivity, ploidy, and other traits. A chromosome-scale assembly was developed to expand genomic resources for this oomyceteous microbe, and used to explore the basis of variation. Using PacBio and Illumina data, a long-range linking library, and an optical map, an assembly was created and coalesced into 15 pseudochromosomes spanning 219 Mb using SNP-based genetic linkage data. De novo gene prediction combined with transcript evidence identified 19,981 protein-coding genes, plus about eight thousand tRNA genes. The chromosomes were comprised of a mosaic of gene-rich and gene-sparse regions plus very long centromeres. Genes exhibited a biased distribution across chromosomes, especially members of families encoding RXLR and CRN effectors which clustered on certain chromosomes. Strikingly, half of F1 progeny of diploid parents were polyploid or aneuploid. Substantial expression level polymorphisms between strains were identified, much of which could be attributed to differences in chromosome dosage, transposable element insertions, and adjacency to repetitive DNA. QTL analysis identified a locus on the right arm of chromosome 3 governing sensitivity to the crop protection chemical metalaxyl. Strains heterozygous for resistance often experienced megabase-sized deletions of that part of the chromosome when cultured on metalaxyl, increasing resistance due to loss of the sensitive allele. This study sheds light on diverse phenomena affecting variation in P. infestans and relatives, helps explain the prevalence of polyploidy in natural populations, and provides a new foundation for biologic and genetic investigations.

Comparative transcriptome and proteome reveal synergistic functions of differentially expressed genes and proteins implicated in an over-dominant silkworm heterosis of increased silk yield

We previously observed an over-dominant silkworm heterosis of increased yield in a cross of Bombyx mori nuclear polyhydrosis virus-resistant strain NB with a susceptible strain 306. In the present study, we found that heterosis also exists in crosses of NB with other susceptible strains, indicating it is a more general phenomenon. We performed comparative transcriptome and proteome and identified 1624 differentially expressed genes (DEGs) and 298 differentially expressed proteins (DEPs) in silk glands between parents and F1 hybrids, of which 24 DEGs/DEPs showed consistent expression at mRNA and protein levels revealed by Venn joint analysis. Their expressions are completely non-additive, mainly transgressive and under low-parent, suggesting recombination of parental genomes may be the major genetic mechanism for the heterosis. GO and KEGG analyses revealed that they may function in generally similar but distinctive aspects of metabolisms and processes with signal transduction and translation being most affected. Notably, they may not only up-regulate biosynthesis and transport of silk proteins but also down-regulate other unrelated processes, synergistically and globally remodelling the silk gland to increase yield and cause the heterosis. Our findings contribute insights into the understanding of silkworm heterosis and silk gland development and provide targets for transgenic manipulation to further increase the silk yield.

Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution?

The prevalence of polyploidy in wild and crop species has stimulated debate over its evolutionary advantages and disadvantages. Previous studies have focused on changes occurring at the polyploidization events, including genome-wide changes termed "genome shock," as well as ancient polyploidy. Recent bioinformatics advances and empirical studies of Arabidopsis and wheat relatives are filling a research gap: the functional evolutionary study of polyploid species using RNA-seq, DNA polymorphism, and epigenomics. Polyploid species can become generalists in natura through environmental robustness by inheriting and merging parental stress responses. Their evolvability is enhanced by mutational robustness working on inherited standing variation. The identification of key genes responsible for gradual adaptive evolution will encourage synthetic biological approaches to transfer polyploid advantages to other species.

Genome-wide characterization of ovate family protein gene family associated with number of seeds per silique in Brassica napus

Ovate family proteins (OFPs) were firstly identified in tomato as proteins controlling the pear shape of the fruit. Subsequent studies have successively proved that OFPs are a class of negative regulators of plant development, and are involved in the regulation of complex traits in different plants. However, there has been no report about the functions of OFPs in rapeseed growth to date. Here, we identified the OFPs in rapeseed at the genomic level. As a result, a total of 67 members were obtained. We then analyzed the evolution from Arabidopsis thaliana to Brassica napus, illustrated their phylogenetic and syntenic relationships, and compared the gene structure and conserved domains between different copies. We also analyzed their expression patterns in rapeseed, and found significant differences in the expression of different members and in different tissues. Additionally, we performed a GWAS for the number of seeds per silique (NSPS) in a rapeseed population consisting of 204 natural accessions, and identified a new gene BnOFP13_2 significantly associated with NSPS, which was identified as a novel function of OFPs. Haplotype analysis revealed that the accessions with haplotype 3 had a higher NSPS than other accessions, suggesting that BnOFP13_2 is associated with NSPS. Transcript profiling during the five stages of silique development demonstrated that BnOFP13_2 negatively regulates NSPS. These findings provide evidence for functional diversity of OFP gene family and important implications for oilseed rape breeding.

Variation in cytonuclear expression accommodation among allopolyploid plants

Cytonuclear coevolution is a common feature among plants, which coordinates gene expression and protein products between the nucleus and organelles. Consequently, lineage-specific differences may result in incompatibilities between the nucleus and cytoplasm in hybrid taxa. Allopolyploidy is also a common phenomenon in plant evolution. The hybrid nature of allopolyploids may result in cytonuclear incompatibilities, but the massive nuclear redundancy created during polyploidy affords additional avenues for resolving cytonuclear conflict (i.e., cytonuclear accommodation). Here we evaluate expression changes in organelle-targeted nuclear genes for six allopolyploid lineages that represent four genera (i.e., Arabidopsis, Arachis, Chenopodium, and Gossypium) and encompass a range in polyploid ages. Because incompatibilities between the nucleus and cytoplasm could potentially result in biases toward the maternal homoeolog and/or maternal expression level, we evaluate patterns of homoeolog usage, expression bias, and expression-level dominance in cytonuclear genes relative to the background of non-cytonuclear expression changes and to the diploid parents. Although we find subsets of cytonuclear genes in most lineages that match our expectations of maternal preference, these observations are not consistent among either allopolyploids or categories of organelle-targeted genes. Our results indicate that cytonuclear expression evolution may be subtle and variable among genera and genes, likely reflecting a diversity of mechanisms to resolve nuclear-cytoplasmic incompatibilities in allopolyploid species.

Parental legacy versus regulatory innovation in salt stress responsiveness of allopolyploid cotton (Gossypium) species

Polyploidy provides an opportunity for evolutionary innovation and species diversification, especially under stressful conditions. In allopolyploids, the conditional dynamics of homoeologous gene expression can be either inherited from ancestral states pre-existing in the parental diploids or novel upon polyploidization, the latter potentially permitting a wider range of phenotypic responses to stresses. To gain insight into regulatory mechanisms underlying the diversity of salt resistance in Gossypium species, we compared global transcriptomic responses to modest salinity stress in two allotetraploid (AD-genome) cotton species, Gossypium hirsutum and G. mustelinum, relative to their model diploid progenitors (A-genome and D-genome). Multivariate and pairwise analyses of salt-responsive changes revealed a profound alteration of gene expression for about one third of the transcriptome. Transcriptional responses and associated functional implications of salt acclimation varied across species, as did species-specific coexpression modules among species and ploidy levels. Salt responsiveness in both allopolyploids was strongly biased toward the D-genome progenitor. A much lower level of transgressive downregulation was observed in the more salt-tolerant G. mustelinum than in the less tolerant G. hirsutum. By disentangling inherited effects from evolved responses, we show that expression biases that are not conditional upon salt stress approximately equally reflect parental legacy and regulatory novelty upon allopolyploidization, whereas stress-responsive biases are predominantly novel, or evolved, in allopolyploids. Overall, our work suggests that allopolyploid cottons acquired a wide range of stress response flexibility relative to their diploid ancestors, most likely mediated by complex suites of duplicated genes and regulatory factors.

Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis

Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism.

Admixture of divergent genomes facilitates hybridization across species in the family Brassicaceae

Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species are rare in nature due to reproductive barriers but how such hurdles can be overcome is largely unknown. Here we report the hybrid genome structure of xBrassicoraphanus, a synthetic allotetraploid of Brassica rapa and Raphanus sativus. We performed cytogenetic analysis and de novo genome assembly to examine chromosome behaviors and genome integrity in the hybrid. Transcriptome analysis was conducted to investigate expression of duplicated genes in conjunction with epigenome analysis to address whether genome admixture entails epigenetic reconfiguration. Allotetraploid xBrassicoraphanus retains both parental chromosomes without genome rearrangement. Meiotic synapsis formation and chromosome exchange are avoided between nonhomologous progenitor chromosomes. Reconfiguration of transcription network occurs, and less divergent cis-elements of duplicated genes are associated with convergent expression. Genome-wide DNA methylation asymmetry between progenitors is largely maintained but, notably, B. rapa-originated transposable elements are transcriptionally silenced in xBrassicoraphanus through gain of DNA methylation. Our results demonstrate that hybrid genome stabilization and transcription compatibility necessitate epigenome landscape adjustment and rewiring of cis-trans interactions. Overall, this study suggests that a certain extent of genome divergence facilitates hybridization across species, which may explain the great diversification and expansion of angiosperms during evolution.

A prototype of the mammalian sulfotransferase 1 (SULT1) family in Xenopus laevis: Characterization of a biased usage of SULT1 genes located in the S-subgenome

BLAST searches previously carried out against Xenopus genome databases, using the cloned X. laevis cytosolic sulfotransferase 1 (SULT1) cDNA sequence, revealed the presence of more than a dozen members of this gene family. Among them, 11 genes composed of five sets, four pairs and a triplet, were homeologous genes in the X. laevis allotetraploid genome consisting of S- and L-subgenomes (≥83% identity within a set). Phylogenetic and synteny analyses of tetrapod SULT1 genes demonstrated that X. laevis possessed six subfamilies, four of which were related to mammalian SULT1 gene subfamilies, while two were ectothermic vertebrate-specific and amphibian-specific SULT1 gene subfamilies. Five sets of homeologous SULT1 genes were located as a gene cluster, and showed S-subgenome-biased gene expression patterns. Acetylation levels of histone H3 at lysine 9 and H4 were also higher in the homeologous SULT1 genes on the S-subgenome than those on the L-subgenome, however, methylation levels of histone H3 at lysine 9 and DNA methylation levels showed no correlation with their transcript levels. In conclusion, histone modifications such as acetylation may be a key factor that controls the S-subgenome-biased expression of the homeologous SULT1 genes.

Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli

Patchouli (Pogostemon cablin (Blanco) Benth.), a member of the Lamiaceae family, is an important aromatic plant that has been widely used in medicine and perfumery. Here, we report a 1.94 Gb chromosome-scale assembly of the patchouli genome (contig N50 = 7.97 Mb). The gene annotation reveals that tandem duplication of sesquiterpene biosynthetic genes may be a major contributor to the biosynthesis of patchouli bioactivity components. We further phase the genome into two distinct subgenomes (A and B), and identify a chromosome substitution event that have occurred between them. Further investigations show that a burst of universal LTR-RTs in the A subgenome lead to the divergence between two subgenomes. However, no significant subgenome dominance is detected. Finally, we track the evolutionary scenario of patchouli including whole genome tetraploidization, subgenome divergency, hybridization, and chromosome substitution, which are the key forces to determine the complexity of patchouli genome. Our work sheds light on the evolutionary history of patchouli and offers unprecedented genomic resources for fundamental patchouli research and elite germplasm development.

The ploidy level of patchouli, an aromatic plant in the Lamiaceae family, remain unclear. Here, the authors assemble a chromosome-level and haplotype-resolved genome for patchouli and reveal that it is tetraploid hybrid as well as compensated aneuploidy.

Expression complementation of gene presence/absence polymorphisms in hybrids contributes importantly to heterosis in sunflower

INTRODUCTION

Numerous crops have transitioned to hybrid seed production to increase yields and yield stability through heterosis. However, the molecular mechanisms underlying heterosis and its stability across environments are not yet fully understood.

OBJECTIVES

This study aimed to (1) elucidate the genetic and molecular mechanisms underlying heterosis in sunflower, and (2) determine how heterosis is maintained under different environments.

METHODS

Genome-wide association (GWA) analyses were employed to assess the effects of presence/absence variants (PAVs) and stop codons on 16 traits phenotyped in the sunflower association mapping population at three locations. To link the GWA results to transcriptomic variation, we sequenced the transcriptomes of two sunflower cultivars and their F₁ hybrid (INEDI) under both control and drought conditions and analyzed patterns of gene expression and alternative splicing.

RESULTS

Thousands of PAVs were found to affect phenotypic variation using a relaxed significance threshold, and at most such loci the "absence" allele reduced values of heterotic traits, but not those of non-heterotic traits. This pattern was strengthened for PAVs that showed expression complementation in INEDI. Stop codons were much rarer than PAVs and less likely to reduce heterotic trait values. Hybrid expression patterns were enriched for the GO category, sensitivity to stimulus, but all genotypes responded to drought similarily - by up-regulating water stress response pathways and down-regulating metabolic pathways. Changes in alternative splicing were strongly negatively correlated with expression variation, implying that alternative splicing in this system largely acts to reinforce expression responses.

CONCLUSION

Our results imply that complementation of expression of PAVs in hybrids is a major contributor to heterosis in sunflower, consistent with the dominance model of heterosis. This mechanism can account for yield stability across different environments. Moreover, given the much larger numbers of PAVs in plant vs. animal genomes, it also offers an explanation for the stronger heterotic responses seen in the former.

Transcriptome shock in interspecific F1 allotriploid hybrids between Brassica species

Interspecific hybridization drives the evolution of angiosperms and can be used to introduce novel alleles for important traits or to activate heterosis in crop breeding. Hybridization brings together gene expression networks from two different species, potentially causing global alterations of gene expression in the F1 plants which is called 'transcriptome shock'. Here, we explored such a transcriptome shock in allotriploid Brassica hybrids. We generated interspecific F1 allotriploid hybrids between the allotetraploid species Brassica napus and three accessions of the diploid species Brassica rapa. RNA-seq of the F1 hybrids and the parental plants revealed that 26.34-30.89% of genes were differentially expressed between the parents. We also analyzed expression level dominance and homoeolog expression bias between the parents and the F1 hybrids. The expression-level dominance biases of the Ar, An, and Cn subgenomes was genotype and stage dependent, whereas significant homoeolog expression bias was observed among three subgenomes from different parents. Furthermore, more genes were involved in trans regulation than in cis regulation in allotriploid F1 hybrids. Our findings provide new insights into the transcriptomic responses of cross-species hybrids and hybrids showing heterosis, as well as a new method for promoting the breeding of desirable traits in polyploid Brassica species.

Salinity Tolerance in a Synthetic Allotetraploid Wheat (SlSlAA) Is Similar to Its Higher Tolerant Parent Aegilops longissima (SlSl) and Linked to Flavonoids Metabolism

Allotetraploidization between A and S (closely related to B) genome species led to the speciation of allotetraploid wheat (genome BBAA). However, the immediate metabolic outcomes and adaptive changes caused by the allotetraploidization event are poorly understood. Here, we investigated how allotetraploidization affected salinity tolerance using a synthetic allotetraploid wheat line (genome S^lS^lAA, labeled as 4x), its Aegilops longissima (genome S^lS^l, labeled as S^lS^l) and Triticum urartu (AA genome, labeled as AA) parents. We found that the degree of salinity tolerance of 4x was similar to its S^lS^l parent, and both were substantially more tolerant to salinity stress than AA. This suggests that the S^lS^l subgenome exerts a dominant effect for this trait in 4x. Compared with S^lS^l and 4x, the salinity-stressed AA plants did not accumulate a higher concentration of Na⁺ in leaves, but showed severe membrane peroxidation and accumulated a higher concentration of ROS (H₂O₂ and O₂ ^⋅⁣-) and a lesser concentration of flavonoids, indicating that ROS metabolism plays a key role in saline sensitivity. Exogenous flavonoid application to roots of AA plants significantly relieved salinity-caused injury. Our results suggest that the higher accumulation of flavonoids in S^lS^l may contribute to ROS scavenging and salinity tolerance, and these physiological properties were stably inherited by the nascent allotetraploid S^lS^lAA.

Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition

Polyploidy and life-strategy transitions between annuality and perenniality often occur in flowering plants. However, the evolutionary propensities of polyploids and the genetic bases of such transitions remain elusive. We assembled chromosome-level genomes of representative perennial species across the genus Glycine including five diploids and a young allopolyploid, and constructed a Glycine super-pangenome framework by integrating 26 annual soybean genomes. These perennial diploids exhibit greater genome stability and possess fewer centromere repeats than the annuals. Biased subgenomic fractionation occurred in the allopolyploid, primarily by accumulation of small deletions in gene clusters through illegitimate recombination, which was associated with pre-existing local subgenomic differentiation. Two genes annotated to modulate vegetative-reproductive phase transition and lateral shoot outgrowth were postulated as candidates underlying the perenniality-annuality transition. Our study provides insights into polyploid genome evolution and lays a foundation for unleashing genetic potential from the perennial gene pool for soybean improvement.

Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner

BACKGROUND

Cultivated peanut (Arachis hypogaea, AABB genome), an allotetraploid from a cross between A. duranensis (AA genome) and A. ipaensis (BB genome), is an important oil and protein crop with released genome and RNA-seq sequence datasets. These datasets provide the molecular foundation for studying gene expression and evolutionary patterns. However, there are no reports on the proteomic data of A. hypogaea cv. Tifrunner, which limits understanding of its gene function and protein level evolution.

RESULTS

This study sequenced the A. hypogaea cv. Tifrunner leaf and root proteome using the tandem mass tag technology. A total of 4803 abundant proteins were identified. The 364 differentially abundant proteins were estimated by comparing protein abundances between leaf and root proteomes. The differentially abundant proteins enriched the photosystem process. The number of biased abundant homeologs between the two sub-genomes A (87 homeologs in leaf and root) and B (69 and 68 homeologs in leaf and root, respectively) was not significantly different. However, homeologous proteins with biased abundances in different sub-genomes enriched different biological processes. In the leaf, homeologs biased to sub-genome A enriched biosynthetic and metabolic process, while homeologs biased to sub-genome B enriched iron ion homeostasis process. In the root, homeologs with biased abundance in sub-genome A enriched inorganic biosynthesis and metabolism process, while homeologs with biased abundance in sub-genome B enriched organic biosynthesis and metabolism process. Purifying selection mainly acted on paralogs and homeologs. The selective pressure values were negatively correlated with paralogous protein abundance. About 77.42% (24/31) homeologous and 80% (48/60) paralogous protein pairs had asymmetric abundance, and several protein pairs had conserved abundances in the leaf and root tissues.

CONCLUSIONS

This study sequenced the proteome of A. hypogaea cv. Tifrunner using the leaf and root tissues. Differentially abundant proteins were identified, and revealed functions. Paralog abundance divergence and homeolog bias abundance was elucidated. These results indicate that divergent abundance caused retention of homologs in A. hypogaea cv. Tifrunner.

Spatial and Temporal Transcriptomic Heredity and Asymmetry in an Artificially Constructed Allotetraploid Wheat (AADD)

Polyploidy, or whole-genome duplication (WGD), often induces dramatic changes in gene expression due to "transcriptome shock. " However, questions remain about how allopolyploidy (the merging of multiple nuclear genomes in the same nucleus) affects gene expression within and across multiple tissues and developmental stages during the initial foundation of allopolyploid plants. Here, we systematically investigated the immediate effect of allopolyploidy on gene expression variation in an artificial allopolyploidy system consisting of a constructed allotetraploid wheat (AADD genome, accession AT2) and its diploid progenitors Triticum urartu and Aegilops tauschii. We performed comprehensive RNA sequencing of 81 samples from different genotypes, tissues, and developmental stages. First, we found that intrinsic interspecific differences between the diploid parents played a major role in establishing the expression architecture of the allopolyploid. Nonetheless, allopolyploidy per se also induced dramatic and asymmetric patterns of differential gene expression between the subgenomes, and genes from the D subgenome exhibited a more drastic response. Second, analysis of homoeolog expression bias (HEB) revealed that the D subgenome exhibited significant expression bias and that de novo-generated HEB was attributed mainly to asymmetrical differential gene expression. Homoeolog-specific expression (HSE) analyses showed that the cis-only regulatory pattern was predominant in AT2, reflecting significant divergence between the parents. Co-expression network analysis revealed that homoeolog expression connectivity (HEC) was significantly correlated with sequence divergence in cis elements between subgenomes. Interestingly, allopolyploidy-induced reconstruction of network modules was also associated with different HSE patterns. Finally, a transcriptome atlas of spike development demonstrated that the phenotypic similarity of AT2 to T. urartu may be attributed to the combination of relatively stable expression of A-subgenome genes and drastic downregulation of their D-subgenome homoeologs. These findings provide a broad, multidimensional characterization of allopolyploidy-induced transcriptomic responses and suggest that allopolyploidy can have immediate and complex regulatory effects on the expression of nuclear genes.

Impact of polyploidy on plant tolerance to abiotic and biotic stresses

Polyploidy, defined as the coexistence of three or more complete sets of chromosomes in an organism's cells, is considered as a pivotal moving force in the evolutionary history of vascular plants and has played a major role in the domestication of several crops. In the last decades, improved cultivars of economically important species have been developed artificially by inducing autopolyploidy with chemical agents. Studies on diverse species have shown that the anatomical and physiological changes generated by either natural or artificial polyploidization can increase tolerance to abiotic and biotic stresses as well as disease resistance, which may positively impact on plant growth and net production. The aim of this work is to review the current literature regarding the link between plant ploidy level and tolerance to abiotic and biotic stressors, with an emphasis on the physiological and molecular mechanisms responsible for these effects, as well as their impact on the growth and development of both natural and artificially generated polyploids, during exposure to adverse environmental conditions. We focused on the analysis of those types of stressors in which more progress has been made in the knowledge of the putative morpho-physiological and/or molecular mechanisms involved, revealing both the factors in common, as well as those that need to be addressed in future research.

Genome Fractionation and Loss of Heterozygosity in Hybrids and Polyploids: Mechanisms, Consequences for Selection, and Link to Gene Function

Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. The subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that opens up unexpected evolutionary pathways. To elucidate this problem, we compared published cytogenetic and RNAseq data with exome sequences of asexual diploid and polyploid hybrids between three fish species; Cobitis elongatoides, C. taenia, and C. tanaitica. Clonal genomes remained generally static at chromosome-scale levels but their heterozygosity gradually deteriorated at the level of individual genes owing to allelic deletions and conversions. Interestingly, the impact of both processes varies among animals and genomic regions depending on ploidy level and the properties of affected genes. Namely, polyploids were more tolerant to deletions than diploid asexuals where conversions prevailed, and genomic restructuring events accumulated preferentially in genes characterized by high transcription levels and GC-content, strong purifying selection and specific functions like interacting with intracellular membranes. Although hybrids were phenotypically more similar to C. taenia, we found that they preferentially retained C. elongatoides alleles. This demonstrates that favored subgenome is not necessarily the transcriptionally dominant one. This study demonstrated that subgenomes in asexual hybrids and polyploids evolve under a complex interplay of selection and several molecular mechanisms whose efficiency depends on the organism's ploidy level, as well as functional properties and parental ancestry of the genomic region.

Deciphering ploidal levels of Lippia alba by using proteomics

Lippia alba (Mill.) N.E. Brown (Verbenaceae), popularly known as "lemon balm" or "bushy matgrass", is widely used in folk medicine due to its anti-inflammatory, antispasmodic, analgesic, and digestive properties. It was described as an autopolyploid complex with five cytotypes (2n = 30, 38, 45, 60 and 90). To enhance our understanding of the biological variation of the species, we investigated, comparatively, the proteomic profile of all ploidal levels (diploid, aneuploid, triploid, tetraploid, and hexaploid). Leaf proteins were extracted with subsequent separation by two-dimensional electrophoresis, spot analysis, and protein identification by mass spectrometry. By comparing the proteomic profile of diploid accession to the profile of the other ploidal levels we identified differential expression between the analysed spots. We identified 34 proteins with differential expression between the ploidal levels in comparison with the diploid. The identified proteins seem to play relevant roles in the primary metabolism of L. alba suggesting that a specific set of proteins was selected during the polyploidization process, being the triploid the most different one. Given that protein composition can substantially affect the desired therapeutic effect, we posit that further combination of proteomic and metabolomic studies may help to unravel genetic variations and phenotypic profiles in L. alba.

Localization of RNA Pol II CTD (S5) and Transcriptome Analysis of Testis in Diploid and Tetraploid Hybrids of Red Crucian Carp (♀) × Common Carp (♂)

Polyploidy occurs naturally in fish; however, the appearance of these species is an occasional and gradual process, which makes it difficult to trace the changes in phenotypes, genotypes, and regulation of gene expression. The allotetraploid hybrids (4nAT) of red crucian carp (RCC; ♀) × common carp (CC; ♂) generated from interspecies crossing are a good model to investigate the initial changes after allopolyploidization. In the present study, we focused on the changes in the active sites of the testicular transcriptome of the allotetraploid by localization of RNA Pol II CTD YSPTSPS (phospho S5) using immunofluorescence and RNA-seq data via bioinformatic analysis. The results showed that there was no significant difference in signal counts of the RNA Pol II CTD (S5) between the different types of fish at the same stages, including RCC, CC, 2nF₁, and 4nAT, which means that the number of transcriptionally active sites on germ cell chromosomes was not affected by the increase in chromosome number. Similarly, RNA-seq analysis indicated that in the levels of chromosomes and 10-kb regions in the genome, there were no significant changes in the highly active sites in RCC, 2nF₁, and 4nAT. These findings suggest that at the beginning of tetraploid origin, the active transcriptome site of 4nAT in the testis was conserved in the regions of the genome compared to that in RCC and 2nF₁. In conclusion, 4nAT shared a similar gene expression model in the regions of the genome with RCC and 2nF₁ with significantly different expression levels.

The Genomic Processes of Biological Invasions: From Invasive Species to Cancer Metastases and Back Again

The concept of invasion is useful across a broad range of contexts, spanning from the fine scale landscape of cancer tumors up to the broader landscape of ecosystems. Invasion biology provides extraordinary opportunities for studying the mechanistic basis of contemporary evolution at the molecular level. Although the field of invasion genetics was established in ecology and evolution more than 50 years ago, there is still a limited understanding of how genomic level processes translate into invasive phenotypes across different taxa in response to complex environmental conditions. This is largely because the study of most invasive species is limited by information about complex genome level processes. We lack good reference genomes for most species. Rigorous studies to examine genomic processes are generally too costly. On the contrary, cancer studies are fortified with extensive resources for studying genome level dynamics and the interactions among genetic and non-genetic mechanisms. Extensive analysis of primary tumors and metastatic samples have revealed the importance of several genomic mechanisms including higher mutation rates, specific types of mutations, aneuploidy or whole genome doubling and non-genetic effects. Metastatic sites can be directly compared to primary tumor cell counterparts. At the same time, clonal dynamics shape the genomics and evolution of metastatic cancers. Clonal diversity varies by cancer type, and the tumors’ donor and recipient tissues. Still, the cancer research community has been unable to identify any common events that provide a universal predictor of “metastatic potential” which parallels findings in evolutionary ecology. Instead, invasion in cancer studies depends strongly on context, including order of events and clonal composition. The detailed studies of the behavior of a variety of human cancers promises to inform our understanding of genome level dynamics in the diversity of invasive species and provide novel insights for management.

Homeolog expression quantification methods for allopolyploids

Genome duplication with hybridization, or allopolyploidization, occurs in animals, fungi and plants, and is especially common in crop plants. There is an increasing interest in the study of allopolyploids because of advances in polyploid genome assembly; however, the high level of sequence similarity in duplicated gene copies (homeologs) poses many challenges. Here we compared standard RNA-seq expression quantification approaches used currently for diploid species against subgenome-classification approaches which maps reads to each subgenome separately. We examined mapping error using our previous and new RNA-seq data in which a subgenome is experimentally added (synthetic allotetraploid Arabidopsis kamchatica) or reduced (allohexaploid wheat Triticum aestivum versus extracted allotetraploid) as ground truth. The error rates in the two species were very similar. The standard approaches showed higher error rates (>10% using pseudo-alignment with Kallisto) while subgenome-classification approaches showed much lower error rates (<1% using EAGLE-RC, <2% using HomeoRoq). Although downstream analysis may partly mitigate mapping errors, the difference in methods was substantial in hexaploid wheat, where Kallisto appeared to have systematic differences relative to other methods. Only approximately half of the differentially expressed homeologs detected using Kallisto overlapped with those by any other method in wheat. In general, disagreement in low-expression genes was responsible for most of the discordance between methods, which is consistent with known biases in Kallisto. We also observed that there exist uncertainties in genome sequences and annotation which can affect each method differently. Overall, subgenome-classification approaches tend to perform better than standard approaches with EAGLE-RC having the highest precision.

Endosperm-based incompatibilities in hybrid monkeyflowers

Endosperm is an angiosperm innovation central to their reproduction whose development, and thus seed viability, is controlled by genomic imprinting, where expression from certain genes is parent-specific. Unsuccessful imprinting has been linked to failed inter-specific and inter-ploidy hybridization. Despite their importance in plant speciation, the underlying mechanisms behind these endosperm-based barriers remain poorly understood. Here, we describe one such barrier between diploid Mimulus guttatus and tetraploid Mimulus luteus. The two parents differ in endosperm DNA methylation, expression dynamics, and imprinted genes. Hybrid seeds suffer from underdeveloped endosperm, reducing viability, or arrested endosperm and seed abortion when M. guttatus or M. luteus is seed parent, respectively, and transgressive methylation and expression patterns emerge. The two inherited M. luteus subgenomes, genetically distinct but epigenetically similar, are expressionally dominant over the M. guttatus genome in hybrid embryos and especially their endosperm, where paternal imprints are perturbed. In aborted seeds, de novo methylation is inhibited, potentially owing to incompatible paternal instructions of imbalanced dosage from M. guttatus imprints. We suggest that diverged epigenetic/regulatory landscapes between parental genomes induce epigenetic repatterning and global shifts in expression, which, in endosperm, may uniquely facilitate incompatible interactions between divergent imprinting schemes, potentially driving rapid barriers.

Reciprocal allopolyploid grasses (Festuca × Lolium) display stable patterns of genome dominance

Allopolyploidization entailing the merger of two distinct genomes in a single hybrid organism, is an important process in plant evolution and a valuable tool in breeding programs. Newly established hybrids often experience massive genomic perturbations, including karyotype reshuffling and gene expression modifications. These phenomena may be asymmetric with respect to the two progenitors, with one of the parental genomes being "dominant." Such "genome dominance" can manifest in several ways, including biased homoeolog gene expression and expression level dominance. Here we employed a k-mer-based approach to study gene expression in reciprocal Festuca pratensis Huds. × Lolium multiflorum Lam. allopolyploid grasses. Our study revealed significantly more genes where expression mimicked that of the Lolium parent compared with the Festuca parent. This genome dominance was heritable to successive generation and its direction was only slightly modified by environmental conditions and plant age. Our results suggest that Lolium genome dominance was at least partially caused by its more efficient trans-acting gene expression regulatory factors. Unraveling the mechanisms responsible for propagation of parent-specific traits in hybrid crops contributes to our understanding of allopolyploid genome evolution and opens a way to targeted breeding strategies.

Interspecific hybridization as a driver of fungal evolution and adaptation

Cross-species gene transfer is often associated with bacteria, which have evolved several mechanisms that facilitate horizontal DNA exchange. However, the increased availability of whole-genome sequences has revealed that fungal species also exchange DNA, leading to intertwined lineages, blurred species boundaries or even novel species. In contrast to prokaryotes, fungal DNA exchange originates from interspecific hybridization, where two genomes are merged into a single, often highly unstable, polyploid genome that evolves rapidly into stabler derivatives. The resulting hybrids can display novel combinations of genetic and phenotypic variation that enhance fitness and allow colonization of new niches. Interspecific hybridization led to the emergence of important pathogens of humans and plants (for example, various Candida and 'powdery mildew' species, respectively) and industrially important yeasts, such as Saccharomyces hybrids that are important in the production of cold-fermented lagers or cold-cellared Belgian ales. In this Review, we discuss the genetic processes and evolutionary implications of fungal interspecific hybridization and highlight some of the best-studied examples. In addition, we explain how hybrids can be used to study molecular mechanisms underlying evolution, adaptation and speciation, and serve as a route towards development of new variants for industrial applications.

Trajectories of Homoeolog-Specific Expression in Allotetraploid Tragopogon castellanus Populations of Independent Origins

Polyploidization can have a significant ecological and evolutionary impact by providing substantially more genetic material that may result in novel phenotypes upon which selection may act. While the effects of polyploidization are broadly reviewed across the plant tree of life, the reproducibility of these effects within naturally occurring, independently formed polyploids is poorly characterized. The flowering plant genus Tragopogon (Asteraceae) offers a rare glimpse into the intricacies of repeated allopolyploid formation with both nascent (< 90 years old) and more ancient (mesopolyploids) formations. Neo- and mesopolyploids in Tragopogon have formed repeatedly and have extant diploid progenitors that facilitate the comparison of genome evolution after polyploidization across a broad span of evolutionary time. Here, we examine four independently formed lineages of the mesopolyploid Tragopogon castellanus for homoeolog expression changes and fractionation after polyploidization. We show that expression changes are remarkably similar among these independently formed polyploid populations with large convergence among expressed loci, moderate convergence among loci lost, and stochastic silencing. We further compare and contrast these results for T. castellanus with two nascent Tragopogon allopolyploids. While homoeolog expression bias was balanced in both nascent polyploids and T. castellanus, the degree of additive expression was significantly different, with the mesopolyploid populations demonstrating more non-additive expression. We suggest that gene dosage and expression noise minimization may play a prominent role in regulating gene expression patterns immediately after allopolyploidization as well as deeper into time, and these patterns are conserved across independent polyploid lineages.

Epigenetics and the success of invasive plants

Biological invasions impose ecological and economic problems on a global scale, but also provide extraordinary opportunities for studying contemporary evolution. It is critical to understand the evolutionary processes that underly invasion success in order to successfully manage existing invaders, and to prevent future invasions. As successful invasive species sometimes are suspected to rapidly adjust to their new environments in spite of very low genetic diversity, we are obliged to re-evaluate genomic-level processes that translate into phenotypic diversity. In this paper, we review work that supports the idea that trait variation, within and among invasive populations, can be created through epigenetic or other non-genetic processes, particularly in clonal invaders where somatic changes can persist indefinitely. We consider several processes that have been implicated as adaptive in invasion success, focusing on various forms of 'genomic shock' resulting from exposure to environmental stress, hybridization and whole-genome duplication (polyploidy), and leading to various patterns of gene expression re-programming and epigenetic changes that contribute to phenotypic variation or even novelty. These mechanisms can contribute to transgressive phenotypes, including hybrid vigour and novel traits, and may thus help to understand the huge successes of some plant invaders, especially those that are genetically impoverished. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

The members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here, we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring before the arrival of the third. We also, for the 90,000 individual genes in our study, make parental subgenome assignments, inferring, with measured uncertainty, from which of the progenitor genomes of the allohexaploidy each gene derives. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.

Whole-Genome Sequence of Synthesized Allopolyploids in Cucumis Reveals Insights into the Genome Evolution of Allopolyploidization

The importance of allopolyploidy in plant evolution has been widely recognized. The genetic changes triggered by allopolyploidy, however, are not yet fully understood due to inconsistent phenomena reported across diverse species. The construction of synthetic polyploids offers a controlled approach to systematically reveal genomic changes that occur during the process of polyploidy. This study reports the first fully sequenced synthetic allopolyploid constructed from a cross between Cucumis sativus and C. hystrix, with high-quality assembly. The two subgenomes are confidently partitioned and the C. sativus-originated subgenome predominates over the C. hystrix-originated subgenome, retaining more sequences and showing higher homeologous gene expression. Most of the genomic changes emerge immediately after interspecific hybridization. Analysis of a series of genome sequences from several generations (S0, S4-S13) of C. ×hytivus confirms that genomic changes occurred in the very first generations, subsequently slowing down as the process of diploidization is initiated. The duplicated genome of the allopolyploid with double genes from both parents broadens the genetic base of C. ×hytivus, resulting in enhanced phenotypic plasticity. This study provides novel insights into plant polyploid genome evolution and demonstrates a promising strategy for the development of a wide array of novel plant species and varieties through artificial polyploidization.