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 6 allopolyploid lineages that represent 4 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 noncytonuclear 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.     

CYTONUCLEAR INTERACTIONS CAN FAVOR THE EVOLUTION OF GENOMIC IMPRINTING

Interactions between cytoplasmic (generally organelle) and nuclear genomes may be relatively common and could potentially have major fitness consequences. As in the case of within-genome epistasis, this cytonuclear epistasis can favor the evolutionary coadaptation of high-fitness combinations of nuclear and cytoplasmic alleles. Because cytoplasmic factors are generally uniparentally inherited, the cytoplasmic genome is inherited along with only one of the nuclear haplotypes, and therefore, coadaptation is expected to evolve through the interaction of these coinherited (usually maternally inherited) genomes. Here I show that, as a result of this coinheritance of the two genomes, cytonuclear epistasis can favor the evolution of genomic imprinting such that, when the cytoplasmic factor is maternally inherited, selection favors maternal expression of the nuclear locus and when the factor is paternally inherited selection favors paternal expression. Genomic imprinting evolves in this model because it leads to a pattern of gene expression in the nuclear haplotype that is coadapted with (i.e., adaptively coordinated with) gene expression in the coinherited cytoplasmic genome.     

Intergenomic epistasis for fitness: within-population interactions between cytoplasmic and nuclear genes in Drosophila melanogaster

The symbiotic relationship between the mitochondrial and nuclear genomes coordinates metabolic energy production and is fundamental to life among eukaryotes. Consequently, there is potential for strong selection to shape interactions between these two genomes. Substantial research attention has focused on the possibility that within-population sequence polymorphism in mitochondrial DNA (mtDNA) is maintained by mitonuclear fitness interactions. Early theory predicted that selection will often eliminate mitochondrial polymorphisms. However, recent models demonstrate that intergenomic interactions can promote the maintenance of polymorphism, especially if the nuclear genes involved are linked to the X chromosome. Most empirical studies to date that have assessed cytonuclear fitness interactions have studied variation across populations and it is still unclear how general and strong such interactions are within populations. We experimentally tested for cytonuclear interactions within a laboratory population of Drosophila melanogaster using 25 randomly sampled cytoplasmic genomes, expressed in three different haploid nuclear genetic backgrounds, while eliminating confounding effects of intracellular bacteria (e.g., Wolbachia). We found sizable cytonuclear fitness interactions within this population and present limited evidence suggesting that these effects were sex specific. Moreover, the relative fitness of cytonuclear genotypes was environment specific. Sequencing of mtDNA (2752 bp) revealed polymorphism within the population, suggesting that the observed cytoplasmic genetic effects may be mitochondrial in origin.     

The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments

Subgenome dominance after whole-genome duplication (WGD) has been observed in many plant species. However, the degree to which the chromatin environment affects this bias has not been explored. Here, we compared the dominant subgenome (maize1) and the recessive subgenome (maize2) with respect to patterns of sequence substitutions, genes expression, transposable element accumulation, small interfering RNAs, DNA methylation, histone modifications, and accessible chromatin regions (ACRs). Our data show that the degree of bias between subgenomes for all the measured variables does not vary significantly when both of the WGD genes are located in pericentromeric regions. Our data further indicate that the location of maize1 genes in chromosomal arms is pivotal for maize1 to maintain its dominance, but location has a less effect on maize2 homoeologs. In addition to homoeologous genes, we compared ACRs, which often harbor cis-regulatory elements, between the two subgenomes and demonstrate that maize1 ACRs have a higher level of chromatin accessibility, a lower level of sequence substitution, and are enriched in chromosomal arms. Furthermore, we find that a loss of maize1 ACRs near their nearby genes is associated with a reduction in purifying selection and expression of maize1 genes relative to their maize2 homoeologs. Taken together, our data suggest that chromatin environment and cis-regulatory elements are important determinants shaping the divergence and evolution of duplicated genes.     

Does one subgenome become dominant in the formation and evolution of a polyploid?

BackgroundPolyploids are common in flowering plants and they tend to have more expanded ranges of distributions than their diploid progenitors. Possible mechanisms underlying polyploid success have been intensively investigated. Previous studies showed that polyploidy generates novel changes and that subgenomes in allopolyploid species often differ in gene number, gene expression levels and levels of epigenetic alteration. It is widely believed that such differences are the results of conflicts among the subgenomes. These differences have been treated by some as subgenome dominance, and it is claimed that the magnitude of subgenome dominance increases in polyploid evolution.ScopeIn addition to changes which occurred during evolution, differences between subgenomes of a polyploid species may also be affected by differences between the diploid donors and changes which occurred during polyploidization. The variable genome components in many plant species are extensive, which would result in exaggerated differences between a subgenome and its progenitor when a single genotype or a small number of genotypes are used to represent a polyploid or its donors. When artificially resynthesized polyploids are used as surrogates for newly formed genotypes which have not been exposed to evolutionary selection, differences between diploid genotypes available today and those involved in the formation of the natural polyploid genotypes must also be considered.ConclusionsContrary to the now widely held views that subgenome biases in polyploids are the results of conflicts among the subgenomes and that one of the parental subgenomes generally retains more genes which are more highly expressed, available results show that subgenome biases mainly reflect legacy from the progenitors and that they can be detected before the completion of polyploidization events. Further, there is no convincing evidence that the magnitudes of subgenome biases have significantly changed during evolution for any of the allopolyploid species assessed.     

Divergent homoeolog evolution of the anthocyanin regulatory gene R in Oryza allopolyploids

Polyploidization is an important evolutionary force in plant speciation and diversification. Retention and elimination of homoeologs derived by polyploidization are prevalent, whereas the evolutionary details of some duplicated genes in closely related natural polyploids are largely unknown. In the present study, we used an important regulatory gene (R) that encodes a bHLH protein in the anthocyanin metabolism pathway to demonstrate divergent evolutionary fates of homoeologs among four related Oryza allotetraploids. The BBCC genome species O. punctata Kotschy ex Steud. maintained both of its homoeologs, whereas three CCDD genome species (O. alta Swallen, O. grandiglumis (Döll) Prod., and O. latifolia Desv.) lost their C subgenome homoeologous copies. In addition, the evolutionary rates of the homoeologs in the polyploids were equivalent to their corresponding homologs in diploids. We also found a slightly higher level of nucleotide diversity inR for the C subgenome homoeolog than for the B subgenome counterpart in O. punctata. After comparing the two types of polyploids, we conclude that inconsistent evolutionary patterns of R in these polyploids are probably associated with different evolutionary time, asymmetrical subgenome evolutionary dynamics, and unique demographical characteristics of these species.     

Nuclear–cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number

The plant genome is partitioned across three distinct subcellular compartments: the nucleus, mitochondria, and plastids. Successful coordination of gene expression among these organellar genomes and the nuclear genome is critical for plant function and fitness. Whole genome duplication (WGD) events in the nucleus have played a major role in the diversification of land plants and are expected to perturb the relative copy number (stoichiometry) of nuclear, mitochondrial, and plastid genomes. Thus, elucidating the mechanisms whereby plant cells respond to the cytonuclear stoichiometric imbalance that follows WGDs represents an important yet underexplored question in understanding the evolutionary consequences of genome doubling. We used droplet digital PCR to investigate the relationship between nuclear and organellar genome copy numbers in allopolyploids and their diploid progenitors in both wheat and Arabidopsis. Polyploids exhibit elevated organellar genome copy numbers per cell, largely preserving the cytonuclear stoichiometry observed in diploids despite the change in nuclear genome copy number. To investigate the timescale over which cytonuclear stoichiometry may respond to WGD, we also estimated the organellar genome copy number in Arabidopsis synthetic autopolyploids and in a haploid-induced diploid line. We observed corresponding changes in organellar genome copy number in these laboratory-generated lines, indicating that at least some of the cellular response to cytonuclear stoichiometric imbalance is immediate following WGD. We conclude that increases in organellar genome copy numbers represent a common response to polyploidization, suggesting that maintenance of cytonuclear stoichiometry is an important component in establishing polyploid lineages.     

Subgenome evolution in allotetraploid plants

Polyploidization is a well-known speciation and adaptation mechanism. Traces of former polyploidization events were discovered within many genomes, and especially in plants. Allopolyploidization by interspecific hybridization between two species is common. Among hybrid plants, many are domesticated species of agricultural interest and many of their genomes and of their presumptive parents have been sequenced. Hybrid genomes remain challenging to analyse because of the presence of multiple subgenomes. The genomes of hybrids often undergo rearrangement and degradation over time. Based on 10 hybrid plant genomes from six different genera, with hybridization dating from 10,000 to 5 million years ago, we assessed subgenome degradation, subgenomic intermixing and biased subgenome fractionation. The restructuring of hybrid genomes does not proceed proportionally with the age of the hybrid. The oldest hybrids in our data set display completely different fates: whereas the subgenomes of the tobacco plant Nicotiana benthamiana are in an advanced stage of degradation, the subgenomes of quinoa (Chenopodium quinoa) are exceptionally well conserved by structure and sequence. We observed statistically significant biased subgenome fractionation in seven out of 10 hybrids, which had different ages and subgenomic intermixing levels. Hence, we conclude that no correlation exists between biased fractionation and subgenome intermixing. Lastly, domestication may encourage or hinder subgenome intermixing, depending on the evolutionary context. In summary, comparative analysis of hybrid genomes and their presumptive parents allowed us to determine commonalities and differences between their evolutionary fates. In order to facilitate the future analysis of further hybrid genomes, we automated the analysis steps within manticore , which is publicly available at https://github.com/MatteoSchiavinato/manticore.git .     

THE EFFECT OF NUCLEAR AND CYTOPLASMIC GENES ON FITNESS AND LOCAL ADAPTATION IN AN ANNUAL LEGUME,CHAMAECRISTA FASCICULATA

The role of nuclear genes in local adaptation has been well documented. However, the role of maternally inherited cytoplasmic genes to the evolution of natural populations has been relatively unstudied. To evaluate the contribution of cytoplasmic and nuclear genomes and their interactions to local adaptation we created second-generation backcross hybrids between a Maryland and an Illinois population of the annual legume Chamaecrista fasciculata. Backcross progeny were planted in the sites native to each population for two years and we quantified germination, survivorship, fruit production, vegetative biomass, and cumulative fitness. We found limited evidence for the contribution of either cytoplasmic or nuclear genes to local adaptation. In Maryland plants had greater survivorship, biomass, fruit production, and cumulative fitness if their nuclear genome was composed predominately of native Maryland genes; cytoplasmic genes did not affect fitness. In Illinois local cytoplasm marginally enhanced fitness, whereas Maryland nuclear genes outperformed local nuclear genes. Interactions between cytoplasmic and nuclear genes influenced seed weight, vegetative biomass, and fitness and therefore may affect evolution of these characters. Genetic effects were stronger acting through seed size than directly on characters. However, seed size differences between the two populations were largely genetic and therefore selection on fitness components is likely to result in evolutionary change. The contribution of nuclear and cytoplasmic genes to fitness components varied across sites and years, suggesting that experiments should be replicated and conducted under natural conditions to understand the influence of these genomes and their interactions to population differentiation.     

Cytonuclear genetic signatures of hybridization phenomena: Rationale,utility, and empirical examples from fishes and other aquatic animals

By definition, organisms of hybrid ancestry carry amalgamations of divergent genomes. Thus, exaggerated effects of genomic interactions might be anticipated in hybrid populations, thereby magnifying the impact of natural selection and making this and other evolutionary forces easier to document. Mating biases and other gender-based asymmetries also frequently characterize hybrid populations. Thus, maternally inherited cytoplasmic polymorphisms assayed jointly with those at biparentally inherited nuclear loci provide powerful genetic markers to dissect ethological, ecological, and evolutionary processes in hybrid settings. Population-level topics that can be addressed using cytonuclear markers include the frequency of hybridization and introgression in nature, behavioral and ecological factors (such as mating preferences and hybrid fitnesses) influencing the genetic architectures of hybrid zones, the degree of consistency in genetic outcomes across multiple hybrid contact regions, and environmental impacts (including the introduction of alien species) on hybridization processes. Several empirical studies on fish populations in hybrid settings illustrate the application of cytonuclear appraisals in such contexts.     

Coevolution in Hybrid Genomes: Nuclear-Encoded Rubisco Small Subunits and Their Plastid-Targeting Translocons Accompanying Sequential Allopolyploidy Events in Triticum

The Triticum/Aegilops complex includes hybrid species resulting from homoploid hybrid speciation and allopolyploid speciation. Sequential allotetra- and allohexaploidy events presumably result in two challenges for the hybrids, which involve 1) cytonuclear stoichiometric disruptions caused by combining two diverged nuclear genomes with the maternal inheritance of the cytoplasmic organellar donor; and 2) incompatibility of chimeric protein complexes with diverged subunits from nuclear and cytoplasmic genomes. Here, we describe coevolution of nuclear rbcS genes encoding the small subunits of Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) and nuclear genes encoding plastid translocons, which mediate recognition and translocation of nuclear-encoded proteins into plastids, in allopolyploid wheat species. We demonstrate that intergenomic paternal-to-maternal gene conversion specifically occurred in the genic region of the homoeologous rbcS3 gene from the D-genome progenitor of wheat (abbreviated as rbcS3D) such that it encodes a maternal-like or B-subgenome-like SSU3D transit peptide in allohexaploid wheat but not in allotetraploid wheat. Divergent and limited interaction between SSU3D and the D-subgenomic TOC90D translocon subunit is implicated to underpin SSU3D targeting into the chloroplast of hexaploid wheat. This implicates early selection favoring individuals harboring optimal maternal-like organellar SSU3D targeting in hexaploid wheat. These data represent a novel dimension of cytonuclear evolution mediated by organellar targeting and transportation of nuclear proteins.     

Homoeolog Expression Is Modulated Differently by Different Subgenomes in <Emphasis Type="Italic">Brassica napus</Emphasis> Hybrids and Allotetraploids

Synthetic and natural allotetraploid Brassica napus (2n?=?38, AACC) have been widely used as a model to study the genetic changes associated with allopolyploidization; however, there has been little research on the homoeolog expression patterns and the roles of cis and trans regulation. Herein, homoeolog expression patterns were assessed by using RNA-seq for two interspecific hybrids (A_nC_o with the extracted A subgenome from natural B. napus, and A_rC_o with the A subgenome from extant B. rapa), synthetic and natural allopolyploids (C_oC_oA_rA_r and A_nA_nC_nC_n), and the diploid parents. The ranges of homoeolog expression bias decreased after hybridization, whereas the extents of homoeolog expression bias and non-conserved expression, especially transgressive expression, increased over evolutionary time. Despite sharing the same C subgenome parent, these two hybrids showed different homolog expression patterns in many respects. In A_nC_o, the trans-regulatory factors from C_o subgenome tended to cause downregulation of A_n subgenome homoeologs, but trans-regulatory factors from the A_n subgenome acted as both activators and repressors, and such asymmetric effects of trans-regulatory factors might explain why the homoeolog expression was biased toward the C subgenome after genome merger. No significant asymmetric effects of trans-regulatory factors were found in A_rC_o, which was consistent with the overall balanced expression of homoeologs. These results suggested that A subgenomes with different regulatory systems might act differently in modulating homoeolog expression after merger with the C subgenome, resulting in either balanced or unbalanced homoeolog expression biases.     

Nonneutral evolution of organelle genes in Silene vulgaris

Knowledge of mitochondrial gene evolution in angiosperms has taken a dramatic shift within the past decade, from universal slow rates of nucleotide change to a growing realization of high variation in rates among lineages. Additionally, evidence of paternal inheritance of plant mitochondria and recombination among mitochondrial genomes within heteroplasmic individuals has led to speculation about the potential for independent evolution of organellar genes. We report intraspecific mitochondrial and chloroplast sequence variation in a cosmopolitan sample of 42 Silene vulgaris individuals. There was remarkably high variation in two mitochondrial genes (atp1, atp9) and additional variation within a third gene (cob). Tests for patterns of nonneutral evolution were significant for atp1 and atp9, indicative of the maintenance of balanced polymorphisms. Two chloroplast genes (matK, ndhF) possessed less, but still high, variation and no divergence from neutral expectations. Phylogenetic patterns of organelle genes in both the chloroplast and mitochondria were incongruent, indicating the potential for independent evolutionary trajectories. Evidence indicated reassociation among cytoplasmic genomes and recombination between mitochondrial genes and within atp1, implying transient heteroplasmy in ancestral lineages. Although the mechanisms for long-term maintenance of mitochondrial polymorphism are currently unknown, frequency-dependent selection on linked cytoplasmic male sterility genes is a potential candidate.     

Ecological selection maintains cytonuclear incompatibilities in hybridizing sunflowers

Despite the recent renaissance in studies of ecological speciation, the connection between ecological selection and the evolution of reproductive isolation remains tenuous. We tested whether habitat adaptation of cytoplasmic genomes contributes to the maintenance of reproductive barriers in hybridizing sunflower species, Helianthus annuus and Helianthus petiolaris. We transplanted genotypes of the parental species, reciprocal F1 hybrids and all eight possible backcross combinations of nuclear and cytoplasmic genomes into the contrasting xeric and mesic habitats of the parental species. Analysis of survivorship across two growing seasons revealed that the parental species' cytoplasms were strongly locally adapted and that cytonuclear interactions (CNIs) significantly affected the fitness and architecture of hybrid plants. A significant fraction of the CNIs have transgenerational effects, perhaps due to divergence in imprinting patterns. Our results suggest a common means by which ecological selection may contribute to speciation and have significant implications for the persistence of hybridizing species.