Literatura académica sobre el tema "Cytonuclear interactions"

AbstractThe function and evolution of eukaryotic cells depend upon direct molecular interactions between gene products encoded in nuclear and cytoplasmic genomes. Understanding how these cytonuclear interactions drive molecular evolution and generate genetic incompatibilities between isolated populations and species is of central importance to eukaryotic biology. Plants are an outstanding system to investigate such effects because of their two different genomic compartments present in the cytoplasm (mitochondria and plastids) and the extensive resources detailing subcellular targeting of nuclear-encoded proteins. However, the field lacks a consistent classification scheme for mitochondrial- and plastid-targeted proteins based on their molecular interactions with cytoplasmic genomes and gene products, which hinders efforts to standardize and compare results across studies. Here, we take advantage of detailed knowledge about the model angiosperm Arabidopsis thaliana to provide a curated database of plant cytonuclear interactions at the molecular level. CyMIRA (Cytonuclear Molecular Interactions Reference for Arabidopsis) is available at http://cymira.colostate.edu/ and https://github.com/dbsloan/cymira and will serve as a resource to aid researchers in partitioning evolutionary genomic data into functional gene classes based on organelle targeting and direct molecular interaction with cytoplasmic genomes and gene products. It includes 11 categories (and 27 subcategories) of different cytonuclear complexes and types of molecular interactions, and it reports residue-level information for cytonuclear contact sites. We hope that this framework will make it easier to standardize, interpret, and compare studies testing the functional and evolutionary consequences of cytonuclear interactions.

Although the contribution of cytonuclear interactions to plant fitness variation is relatively well documented at the interspecific level, the prevalence of cytonuclear interactions at the intraspecific level remains poorly investigated. In this study, we set up a field experiment to explore the range of effects that cytonuclear interactions have on fitness-related traits in Arabidopsis thaliana. To do so, we created a unique series of 56 cytolines resulting from cytoplasmic substitutions among eight natural accessions reflecting within-species genetic diversity. An assessment of these cytolines and their parental lines scored for 28 adaptive whole-organism phenotypes showed that a large proportion of phenotypic traits (23 of 28) were affected by cytonuclear interactions. The effects of these interactions varied from slight but frequent across cytolines to strong in some specific parental pairs. Two parental pairs accounted for half of the significant pairwise interactions. In one parental pair, Ct-1/Sha, we observed symmetrical phenotypic responses between the two nuclear backgrounds when combined with specific cytoplasms, suggesting nuclear differentiation at loci involved in cytonuclear epistasis. In contrast, asymmetrical phenotypic responses were observed in another parental pair, Cvi-0/Sha. In the Cvi-0 nuclear background, fecundity and phenology-related traits were strongly affected by the Sha cytoplasm, leading to a modified reproductive strategy without penalizing total seed production. These results indicate that natural variation in cytoplasmic and nuclear genomes interact to shape integrative traits that contribute to adaptation, thereby suggesting that cytonuclear interactions can play a major role in the evolutionary dynamics of A. thaliana.

Abstract We extend our investigation of cytonuclear selection by determining when differential selection between the sexes will generate allele frequency changes or cytonuclear disequilibria in populations with constant viability selection and an adult census. We demonstrate analytically that there can be a cytonuclear hitchhiking effect upon a selectively neutral marker in either sex provided the other marker is selected in that sex and there is allelic disequilibrium between the loci in females. Cytonuclear disequilibria are generated de novo in both sexes when both loci affect fitness in females and there is a nonmultiplicative fitness interaction between them. Similar fitness interactions in males generate male disequilibria only. Through numerical analyses, we investigate the potential magnitude of such disequilibria, their qualitative dynamics, the expected frequency of detectable disequilibria under particular patterns or strengths of selection, and the possible disequilibrium sign patterns resulting from selection. These adult/viability results subsume those for populations with a gamete census and either constant fertility or viability selection. Although previous work suggests that the disequilibria generated by cytonuclear selection may be difficult to detect experimentally, this study shows that cytonuclear disequilibria at life stages with sex differences can be useful markers of the presence and strength of selection.

AbstractTheoretical and empirical studies have shown that selection cannot maintain a joint nuclear-cytoplasmic polymorphism within a population except under restrictive conditions of frequency-dependent or sex-specific selection. These conclusions are based on fitness interactions between a diploid autosomal locus and a haploid cytoplasmic locus. We develop a model of joint transmission of X chromosomes and cytoplasms and through simulation show that nuclear-cytoplasmic polymorphisms can be maintained by selection on X-cytoplasm interactions. We test aspects of the model with a “diallel” experiment analyzing fitness interactions between pairwise combinations of X chromosomes and cytoplasms from wild strains of Drosophila melanogaster. Contrary to earlier autosomal studies, significant fitness interactions between X chromosomes and cytoplasms are detected among strains from within populations. The experiment further demonstrates significant sex-by-genotype interactions for mtDNA haplotype, cytoplasms, and X chromosomes. These interactions are sexually antagonistic—i.e., the “good” cytoplasms in females are “bad” in males—analogous to crossing reaction norms. The presence or absence of Wolbachia did not alter the significance of the fitness effects involving X chromosomes and cytoplasms but tended to reduce the significance of mtDNA fitness effects. The negative fitness correlations between the sexes demonstrated in our empirical study are consistent with the conditions that maintain cytoplasmic polymorphism in simulations. Our results suggest that fitness interactions with the sex chromosomes may account for some proportion of cytoplasmic variation in natural populations. Sexually antagonistic selection or reciprocally matched fitness effects of nuclear-cytoplasmic genotypes may be important components of cytonuclear fitness variation and have implications for mitochondrial disease phenotypes that differ between the sexes.

Abstract Organellar genomes are considered to be strictly uniparentally-inherited. Uniparental inheritance allows for cytonuclear coevolution and the development of highly coordinated cytonuclear interactions. Yet, instances of biparental inheritance have been documented across eukaryotes. Biparental inheritance in otherwise uniparentally-inherited organelles is termed leakage (maternal or paternal) and allows for the presence of multiple variants of the same organellar genome within an individual, called heteroplasmy. It is unclear what, if any, evolutionary consequences are placed on nuclear and/or organellar genomes due to heteroplasmy. One way of accessing cytonuclear interactions and potential coevolution is through calculating cytonuclear linkage disequilibrium (cnLD), or the non-random association of alleles between nuclear and organellar genomes. Patterns of cnLD can indicate positive or negative cytonuclear selection, coevolution between the nuclear and organellar genomes, non-traditional organellar inheritance, or instances of ancestral heteroplasmy. In plants, cytonuclear interactions have been shown to play a role in cytoplasmic male sterility which occurs in gynodioecious species and is associated with leakage. We used the gynodioecious species, Daucus carota L. spp. carota, or wild carrot, to investigate cnLD. We genotyped a total of 265 individuals from two regions of the USA at 15 nuclear microsatellites, the mitochondrial genes cox1 and atp9, and an intergenic region between trnS and trnG (StoG) in the plastid genome to calculate nuclear–nuclear LD (nucLD), cnLD, and organellar LD (i.e., within the mtDNA and between mtDNA and ptDNA) within the two regions. We were further able to identify cox1 and StoG heteroplasmy and calculate some of the same LD measures within heteroplasmic and homoplasmic (non-heteroplasmic) datasets. We used a Z-transformation test to demonstrate that heteroplasmic individuals display significantly higher levels of cnLD within both regions. In spite of this, within and between organellar LD is low to moderate. Given these patterns of LD in two regions of the USA in which gene flow has been shown to occur between crop and wild carrot, we suggest that heteroplasmy is an evolutionary mechanism which permits the maintenance of cnLD while also acting to disrupt organellar LD.

Abstract Phylogenomic analyses are recovering previously hidden histories of hybridization, revealing the genomic consequences of these events on the architecture of extant genomes. We applied phylogenomic techniques and several complementary statistical tests to show that introgressive hybridization appears to have occurred between close relatives of Arabidopsis, resulting in cytonuclear discordance and impacting our understanding of species relationships in the group. The composition of introgressed and retained genes indicates that selection against incompatible cytonuclear and nuclear–nuclear interactions likely acted during introgression, whereas linkage also contributed to genome composition through the retention of ancient haplotype blocks. We also applied divergence-based tests to determine the species branching order and distinguish donor from recipient lineages. Surprisingly, these analyses suggest that cytonuclear discordance arose via extensive nuclear, rather than cytoplasmic, introgression. If true, this would mean that most of the nuclear genome was displaced during introgression whereas only a small proportion of native alleles were retained.

Via l'émergence de barrières à la reproduction qui isolent les populations les unes des autres, la spéciation est le processus qui conduit à la formation de nouvelles espèces. Par ailleurs, les génomes organellaires peuvent être impliqués dans ce processus, par le biais d'incompatibilités cytonucléaires. Leur mode de transmission peut également influencer l'évolution de l'isolement reproducteur (IR) entre populations. Dans ce travail de thèse, j'ai travaillé sur l'influence des génomes organellaires sur l'évolution de l'isolement reproducteur entre quatres lignées de Silene nutans et ai tenté de reconstruire le scénario évo-démographique qui a façonné leur évolution. Dans un premier temps, via l'utilisation de données génomiques et transcriptomiques, nous avons tenté d'identifier des candidats d'incompatibilités chloro-nucléaires impliquées dans l'IR entre ces lignées. Nous avons ensuite approfondi l'analyse d'un complexe candidat: le ribosome chloroplastique. Par ailleurs, l'IR semble être incomplet entre ces lignées puisque certains hybrides ont survécu. Nous avons donc testé une transmission paternelle du génome chloroplastique chez cette espèce, qui pourrait avoir sauvé certains de ces hybrides. Nous avons génotypé les hybrides survivants pour six SNP chloroplastiques et déterminé s'ils avaient hérité du génome chloroplastique paternel ou maternel. En permettant la transmission d'un génome chloroplastique moins incompatible, la fuite paternelle semble bien avoir sauvé certains de ces hybrides. Les génomes mitochondriaux pourraient également être impliqués dans l'IR, par le biais d'incompatibilités mito-nucléaires. Du fait de leur co-transmission, les génomes organellaires sont supposés être en déséquilibre de liaison étroit, présentant ainsi des schémas évolutifs similaires. Nous les avons comparés en utilisant les données génomiques des deux génomes organellaires, pour des individus des quatre lignées. Ces schémas évolutifs se sont révélés particulièrement contrastés, les gènes mitochondriaux présentant du polymorphisme partagé à l'inverse des gènes chloroplastiques contenant des substitutions fixées différemment entre lignées. Des événements de type recombinaison ont également été identifiés dans les gènes mitochondriaux. Enfin, nous avons reconstruit l'histoire évo-démographique des quatre lignées de S. nutans, en utilisant les données RNAseq et des méthodes ABC. Un scénario de spéciation allopatrique a été identifiée entre les quatre lignées, avec des temps de séparation cohérent avec les maximums glaciaires
Speciation is the process by which the emergence of reproductive barriers isolate populations from one another and ultimately lead to the formation of new species. How these reproductive barriers emerge is a core question when thinking of speciation. Organellar genomes might be involved in the speciation process, through cytonuclear incompatibilities. Their mode of transmission might also influence the pace of reproductive isolation evolution. In my PhD, I worked on how organellar genomes influence the evolution of reproductive isolation between isolated lineages of S. nutans and which evo-demographic scenario shaped their evolution. Using plastid genomic and nuclear transcriptomic data we tried, in the first chapter, to identify candidates for plastid-nuclear incompatibilities involved in RI between lineages of S. nutans. We further dug into one plastid candidate complexe, the plastid ribosome. Because RI seems to be incomplete between lineages of S. nutans as some inter-lineage hybrids survived, we tested for paternal leakage of the plastid genome. We genotyped the surviving hybrids for plastid SNPs and analyzed whether they inherited the paternal or maternal plastid genomes. By allowing the transmission of the less incompatible plastid genome, paternal leakage rescued some of the inter-lineage hybrids. The mitochondrial genome could also be involved in the RI, through mito-nuclear incompatibilities. Because of their co-transmission, organellar genomes are supposed to be in tight linkage-disequilibrium, so exhibiting similar evolutionary patterns. Using genomic data for both organellar genomes for individuals of the four lineages we compared their evolutionary patterns. They were different with mitochondrial genes exhibiting many shared polymorphisms while plastid genomes many fixed substitutions between lineages. Recombination-like events were also identified in the mitochondrial genes. Lastly, we reconstructed the evo-demographic histories of the four lineages of S. nutans, using RNAseq data and ABC methods. Allopatric speciation was identified between the four lineages, with split times consistent with the glacial maxima